Advanced Concepts in Genetics: Quiz 1 – Flashcards
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|3D chromosome organization|
|The chromatin domain can be discontinuously established and maintained. Nuclear pore proteins tether heterochromatin to the nuclear envelope, forming a peri-nuclear domain rich in silencing factors. In one model for how heterochromatin can reversibly activate nearby genes (causing epigenetic changes during PEV and TPE), genes are drawn into the silencing heterochromatin domain are turned off, and genes outside the domain are turned on. There may be long-range 3D interactions and spill-over based on TPE.|
|A proto-silencer of mating type loci in S. cerevisiae. An element found in the subtelomere. Relays and enhances spreading of silencing away from telomeres.|
|A modification of histone N-termini. Lysine (K) and arginine (R) residues are acetylated. Acetylation of H3K16 means that the DNA is transcribed. Deacetylation of H4K16 means that the DNA must not be transcribed. Acetylation can predispose adjacent nucleosomes to be acetylated.|
An idea used by Darwin to explain heritable variation. Put forth by Lamarck. Gemmules respond in adaptive ways to an individual's external environment and experience. Altered gemmules are passed on to offspring, allowing for inheritance of acquired characteristics. Today it is considered incorrect, disproved by experiments of Joshua and Esther Lederberger as well as Luria Delbruck.
|A dormant origin of replication in HMRa and HML?. Binds to SIR1 via ORC. A proto-silencer of the mating type loci. An element found in the subtelomere. Relays and enhances spreading of silencing away from telomeres. A proto-silencer when isolated, but a silencer when in clusters.|
|Occurs in response to certain environmental conditions. Must exist to help organisms survive in specific environments, thus speeding up adaptation and evolution. Otherwise, there must be another mechanism for heritable adaptation. Can occur in bacteria on selective media.|
|An engineered reporter gene. Synthesizes a precursor of adenine. Processes a byproduct which otherwise reacts with oxygen and gradually turns red. It confers a white colour to the colony; if the colony is white, ADE2 is active. If the colony is red, ADE2 is inactive. Can be used to screen for genetic screening for suppressor mutants of H4K16Q, which results in loss of silencing. When ADE2 is next to the telomere, colonies contain red and white segments, due to TPE; you can count how many conversion events occurred.|
|A modification of histone N-termini.|
|Forms of the same gene that contain different mutations. Determines how the genetic trait is displayed as a phenotype. During mitosis, alleles are segregated into gametes, and are independently inherited through the process of meiosis. Alleles residing on the same chromosome segregate as a linked group.|
|Animal clones exhibit differences in growth and development, even though their DNA is identical.|
|A cis-element which dampens the effect of a strong silencer. Can cause PEV.|
A histone chaperone which disassembles the nucleosome right before passage of the replication fork. Bound to the helicase MCM. It breaks the interaction between H3/H4 dimers.
|As it differentiates, the nucleus has dark areas of heterochromatin, in massive blocks. In chickens, blood cells have nuclei.|
|Displays codominance. There are alleles A, B, and O. A and B are codominant, and O is recessive.|
|A worm. Has 100 Mb of DNA, 18,400 genes, 6 chromosomes, and 180 genes/Mb.|
Chromatin assembly factor
A histone chaperone. Studied in Cheloufi et al (2015). Travels right behind the replication fork, associating with the replicative clamp PCNA. Old histones are ferried to it by ASF1 and FACT, and it re-assembles them into nucleosomes. If mutated, reduces frequency of conversions at the telomere. A model for how heterochromatin can reversibly activate nearby genes (causing epigenetic changes during PEV and TPE): new histones are also delivered to CAF1, and assembled in the nucleosomes. If the replication fork stalls, the supply of old histones is disrupted; it is possible that CAF1 and other chaperones continue to assemble nucleosomes from new histones only, losing epigenetic marks. It is suppressed in homozygous and heterozygous MEFs that carry certain alleles. Its suppression enhances reprogramming for different cell conversion systems, by multiple magnitudes, in a variety of cell types, depending on dose and duration. Suppression causes changes in histone modifications, resulting in a more open chromatin structure at enhancer elements during early reprogramming. HPS cells were reprogrammed in the presence of the suppression of CAF1 components and similar enhanced reprogramming results were obtained. Acts as a gatekeeper across different cell types, even when using transcription factors other than OKSM to induce cell lineage transformation.
Molecular biology shows that genetic information is faithfully transmitted, from DNA, to RNA, to protein. It can go backwards, with RNA-mediated repression of genes.
DNA - RNA > protein
|Silent chromatin. Contains different histone variants from heterochromatin or euchromatin. Acts as a proto-silencer. Builds a weak heterochromatin block.|
|Cheloufi et al (2015)|
The histone chaperone CAF1 safeguards somatic cell identity
Ectopic expression of 4 OKSM transcription factors is enough to reprogram cells into iPSCs. Researchers sought to elucidate mechanisms in place to safeguard somatic cell identity. Changes in histone modifications are accompanied by a decrease in somatic heterochromatin domains, increased binding of Sox2 to pluripotency-specific targets, and activation of associated genes. Discoveries pave the way for further studies to establish enhanced strategies for the modulation of cellular plasticity in regenerative and research settings.
|Cheloufi et al (2015) experimental details|
|Screened RNAi for chromatin barriers to reprogramming. Used two parallel strategies for screening chromatin-focused shRNA libraries in transgenic mouse embryonic fibroblast cells harbouring a doxycycline-inducible OKSM casette necessary for reprogramming. Screens for retroviruses containing 1075 shRNAs targeting 243 genes were transduced into individual MEFs. A pool of retroviruses containing 5049 shRNAs targeting 615 known and predicted chromatin regulators were transduced into MEFs. Silencing of chromatin mRNAs complementary to the shRNAs occurred. OKSM expression was induced via the addition of doxycycline, the generation of iPSC cells occurred, and relative reprogramming efficiency ratios were calculated. Chaf1a and Chaf1b (components of CAF1) emerged as major hits: repressors of iPSC formation. Additional hits included a novel repressor Ube2i, a SUMO conjugating enzyme, and H3K9 methyltransferase Setdb1. Used chimeras to determine effects of transient suppression during reprogramming. shRNAs and OKSM were both expressed in reprogrammable MEFs for 7 days. Oct4-GFP+ cells were purified using FACs, followed by dox withdrawal, to select for transgene-independent iPSCs. iPSCs were injected into mouse blastocysts, producing agouti chimeras that were bred with albino females, producing agouti germline offspring. Indicates suppression during reprogramming does not affect iPSCs' ability to differentiate in vivo. Performed ChIP seq analysis to study the epigenetics of Sox2 antibodies then cross-linkage was reversed and DNA sequenced. Chaf1a knockdown cells showed Sox2 binding sites enriched for ES-cell specific Sox2 targets, which contributes to reprogramming efficiency.|
|Provides for the complexity and huge size of genomes in eukaryotes, and is involved in gene regulation and expression. It is central to epigenetics. Structure can be heritable. Affected by non-coding RNA. DNA packaged with proteins. Found in the nucleus. The higher order of 30 nm chromatin fibre consists of nucleosomes on a jointed chain of DNA; "beads on a string". Consists of DNA wrapped around nucleosomes, with H1 in linked regions. Has simple, repetitive structure with spacing of sites accessible to nuclease digestion. Not uniform. There can be common signatures for cancer and other diseases. Includes euchromatin and heterochromatin; many of their functional differences are due to biochemical modifications of histones and DNA.|
|In a given tissue, the same loci are always heterochromatic or euchromatic; this means that chromatin structure must be heritable. Dividing cells have a mechanism to re-build chromatin structures after every cell division. There is plenty of circumstantial evidence showing that one established, it is heritable. Heritability warrants tissue-specific gene expression and irreversible cell differentiation. Once the set of necessary active genes for the tissue is established, all other genes are silenced for the duration of the life of the organism.|
|The boundary between centromeric heterochromatin and euchromatin. A cis element which restricts the spreading of heterochromatin. Variegated silencing of the gene is caused by "oozing" of heterochromatin proteins over a hypothetical heterochromatin-euchromatin boundary by mechanisms similar to SIR-dependent spreading in yeast. Does not change the amount of silencers. When the gene for synthesis of red eye pigment, White is in this location, it causes PEV in Drosophila. There is position effect, causing genes in this location to be expressed only in some facets of the eye; expression is metastable. In one model for how heterochromatin can reversibly activate nearby genes (causing epigenetic changes during PEV and TPE), the spreading of heterochromatin is halted by a hypothetical chromatin boundary. For this model, if gene A is inactivated more frequently than gene B, gene A will always be off when gene B is off. If gene A is on where gene B is off, there must be 3D chromosome organization.|
|Chromo domain (CD)|
|A domain of HP1. Recognizes H3K9Me modification. A reader.|
|Chromo shado domain (CSD)|
|A domain of HP1. Recruits enzymes including HDAC, H3 methyltransferase, and DNA methyltransferase.|
|A Mendelian theory. Heritability is driven by alleles arranged in chromosomes.|
|A linear macromolecule of DNA and proteins. DNA contains arranged genes. Proteins have a structural role. Alleles residing on the same chromosome segregate as a linked group. Its 3D structure can affect gene expression.|
|A rare event in which genes are repositioned. Normally, meiotic recombination exchanges the material between chromatids, but does not change the position of the genes relative to each other.|
|DNA elements which reside on the same DNA strand as the gene on which they act. Regulatory cis elements are identified by cloning them next to a reporter gene, and measuring the activity of the reporter. Includes silencers, proto-sileners, anti-silencers, and chromatin boundaries. Includes E and I.|
|When two alleles can be expressed simultaneously. Includes blood types.|
|There is an F2 phenotype ratio of 9:3:3:1.|
|Sequences which are the same in many species. Have significant function, associated with something extremely important. Histones are conserved.|
|Regions of heterochromatin that exhibit heterochromatic packaging in all cells, all the time. Includes mating type loci in S. cerevisiae, one of the X-chromosome in female mammal cells, multiple repetitive elements, telomeres, and repetitive sequences.|
|Histones H2A, H2B, H3, and H4. Two each of the four form the 8-subunit octameric structure of the nucleosome. Have alignment similarity, with highly conserved ?1, ?2, and ?3 helices forming a core histone fold which interlocks histones into an octamer. There are variable non-structure N-terminal regions. Conserved in all organisms.|
|Sites where there is a cytosine followed by a guanine in the DNA sequence. Often DNA methylation occurs in such areas, but not all CpG islands are methylated. Found in gene promoters. Recruits heterochromatin components: histone deacetylases, histone methyltransferases, and chromatin remodeling complexes, by binding to McBPs. Indicates that methylation an affect gene expression. In hemi-methylated DNA, where there is a methylated CpG, DNMT will methylate the cytosine on the opposite strand: the cytosine bound to the guanine next to the originally methylated cytosine.|
|D'Aquila et al (2017)|
Methylation of the ribosomal RNA gene promoter is associated with aging and age-related decline
DNA methylation profiles of ribosomal RNA (rRNA) genes can be used as a biomarker for detecting onset of mammalian age-related diseases and cancers. Methylation of critical housekeeping regions, such as those involved with gene transcription, impacts overall cell function. Hundreds of rRNA loci are silenced by epigenetic mechanisms, due to tendency to recombine in the genome. Studied the effect of methylation of an rRNA gene promoter on rRNA transcription levels across aging. rRNA levels decrease with age in both humans and rats. In humans, there was correlation between methylation of CpG_5 in the promoter and phenotypes of age-related decline. Lack of concordance between methylation and age indicates that profiles are not markers for chronological aging, but are for biological aging. There was correlation between methylation and aging in rat samples; a marker for both biological and chronological aging. This may be due to the more varied environmental conditions in human subjects compared to rat subjects. Emphasized that understanding epigenetic marks can lead to prevention of age-related diseases. Methylation is not necessarily causal to aging. Showed correlation only; direct evidence required to show how methylation leads to age-related decline. Future research may identify functional effects of methylation on rRNA levels and aging. Proposed model:
Methylation of rRNA gene promoter > increased silencing > lack of ribosome biogenesis > less protein synthesized for cellular function
|D'Aquila et al (2017) experimental details|
|DNA was collected from humans and rats of differing ages. Human subjects were 20 to 105 years in age. Amplified rRNA regions of DNA from human blood samples. Identified a region (CpG_25.26) that negatively correlated with age; but this result was unable to be replicated. DNA methylation of rat rDNA homologous to a human sequence was evaluated with bisulfite-treated DNA samples from rat blood, heart, liver, kidney, and testes of differently aged rats. CpG_1 and CpG_8 showed strong positive correlation with age. Most tissue-specific methylation increased with age. Bisulfite treatments resulted in considerable loss of initial DNA input due to DNA degradation during purification; poor bisulfite conversion rates can lead to false positive results. Determined downstream effects of methylating CpG islands within the rDNA promoter. Expression levels were quantified using qPCR.|
|May lead to epigenetic switching of gene activity.|
|Dann et al (2017)|
ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference
Measured imitations switch (ISWI) chromatin remodeler activity in response to a diverse nucleosome library of 115 mutated and modified nucleosomes. Generated a large dataset of remodeling rate kinetics, giving insight into regulation of ISWI interactions. Chromatin remodelers interact with nucleosome post-translational modifications (PTMs), which modulate their activity, controlling gene expression. Found that PTMs generally have similar effect on all seven ISWI complexes analyzed, except NoRC. Each PTM either activates or inactivates all ISWI complexes. The ATPase SNF2h alone has distinct reaction, indicating that reader subunits play an important role in reaction to PTMs. NoRC has different response to PTMs, particularly acetylation marks. Found an association between ISWI complexes and an acidic patch on H2A and H2B histones. Nucleosome library and associated dataset produced represent groundwork upon which there is much potential for future studies on chromatin remodelers. Not an in vivo study; lacks native heterochromatin/euchromatin structure and other regulatory interactions. Uses complete ISWI complexes, which is an improvement from many previous studies which looked at single subunits.
|Dann et al (2017) experimental details|
|Restriction enzyme assay was used, allowing researchers to quickly generate large amounts of information. A 192 bp DNA construct was prepared, with: BC-601 strand, PstI restriction enzyme site, and a unique 6 bp DNA barcode. The modified nucleosome and associated DNA construct are positioned together, so that the nucleosome obscures the PstI restriction site, preventing cleavage. A small amount of each modified nucleosome/DNA construct is added to one sample, along with restriction endonuclease PstI, sufficient ATP, and an ISWI remodeler. If the complex is successful in moving the nucleosome, DNA will be cleaved and produce a short read. If it is unsuccessful, the read will be longer, and uncleaved. DNA was extracted and sequenced with high-throughput multiplexing. Individual strands were distinguished by unique barcodes. Kinetics of the reaction was measured by taking samples at 6 time points in the reaction, and recording proportions of fragments cleaved. PCA was used to interpret the considerable amount of data which was produced.|
|From 1960s to present. Genetic information is encoded by four bases aligned in a DNA polymer.|
|Containing two sets of the genome. S. cerevisiae can grow as diploid cells which grow vegetatively under optimal conditions. Under low nutrient conditions they sporulate to produce haploid spores. Expresses both a and ? mating type genes (a/?), and cannot mate|
|A modification of DNA. Cytosine is methylated. An epigenetic mark. Individual modifications of individual histones and modifications of DNA influence each other. Cytosine is modified after DNA replication by the enzymatic addition of a methyl group to the fifth position of the pyrimidine ring. Produced by DNMT. In eukaryotes, primarily occurs in short symmetrical sites, 5mCpG islands in mammals. Methylation is erased and re-established early in development, and maintained throughout the remainder of development. Establishes differentiation, when cells differentiate into separate cell types. Transmission of MeCpG is coupled to DNA replication; mechanism by DNMT is well understood. Methylation patterns are passed to progeny. Affects gene expression directly by altering the affinity of non-histone DNA binding proteins to their sites, and indirectly through supporting heterochromatin. Usually, but not always, associated with gene silencing. Its role in maintenance of silencing is clear, but its role in establishment of silent states is controversial. Loss of histone H3 methylation abolishes CpG methylation. Connected to histone deacetylation by physical interactions between DNMT and HDAC, and the fact that HDAC inhibitor decreases 5mCpG levels. Decreased cytosine methylation is correlated with increased hyperacetylation. Establishes during development. In certain tissues, certain loci are methylated by a specialized class of DNMTs; this mechanism is not fully elucidated. Methylated DNA binds to MBDs. DNA methylation can cause diseases. Brains of suicide victims had similar DNA methylation patterns, suggesting similar experiences. Signatures can be related to lifestyle. After 6 months of hard exercise, DNA methylation in adipose tissue is altered for months. Can be expensive to analyze populations, requiring huge databases. Not found in yeast.|
|DNA methyltransferase (DNMT)|
|An enzyme which produces the epigenetic mark MeCpG. Adds a methyl group to the 5th position of the pyrimidine ring of cytosine with an unknown mechanism. It methylates replicated DNA de novo, and for maintenance. The mutation dim2 in Neurospora disrupts this gene. Physically interacts with HDAC, forming the connection between DNA methylation and histone deacetylation. It is involved in epigenetic transmission. In vitro, hemi-methylated DNA is a good substrate, and unmethylated DNA is a poor substrate. DNA is most likely methylated during DNA replication using the old methylated strand as a guide to the enzyme. MBDs and DNMTs support this model. Its mechanism is well-known. During DNA replication, DNMT associates with PCNA behind the replication fork. It recognizes the old methylated DNA strand, and transfers the same marks to the new DNA strand, directed by the MBD reader. It methylates CpG islands, adding a methyl group to the cytosine on the opposite strand from the existing mark. Includes DNMT1.|
A model for how old histones are disassembled, and their epigenetic marks transmitted during DNA replication. There is some uncertainty about the mechanism of transfer of histones at the replication fork.
1. Two chaperones, ASG1 and FACT, disassemble the nucleosome right before the passage of the replication fork.
2. ASG1 and FACT ferry the histones to a CAF1 right behind the replication fork. H2A/H2B are transferred as dimers. In most cases H3 and H4 are transferred as un-split tetramers, though there is some evidence that they are split into dimers.
3. New H3/H4 histones are brought to CAF1, which assemble into new and old histones; the mechanism is not firmly established. New histones are recognized by their predisposition marks.
4. Somehow modifications of old histones impose the same modifications on the new histones.
|A fly. Has 120 Mb of DNA, 13,600 genes, 4 chromosomes, and 110 genes/Mb. A model organism. Lifecycle is 20 days. It can have PEV in the eyes. Though the genome is identical in all cells, some eye cells are red and others are white. It is good for studying PEV.|
|Dutch hunger winter|
|During the war, there was a famine in the Netherlands, causing extreme stress during pregnancy. Children gestated in this period had health peculiarities. Sequencing their DNA, there was no correlation, however there was an imprinting on chromatin, from experience of the mother, passed on to progeny.|
|A DNA cis-element silencer. Required for silencing at HMRa and HML?, conferring position effect. Includes ARS317, RAP1, and ABF1. ABF1 and RAP1 recruit SIR3/SIR4.|
|A bacterium. Has 4.5 Mb of DNA, 4,000 genes, 1 chromosome, and 900 genes/Mb.|
Enhancer of variegation
Suppressor genes of whiteV in Drosophila. The fly's eyes are mostly white, with some red patches. It enhances the spread of heterochromatin. Homologues have been identified in all metazoans; key regulators of many epigenetic transactions. Mutated in cancers and various rare diseases. Encodes key readers, writers, and erasers in epigenetic marks. Characterization formed the foundation of modern epigenetics.
|Early childhood stress|
|Can be inherited from epigenetic imprinting. Stress in the mother can affect progeny even before pregnancy.|
|It is heritable, but more flexible than information on DNA, meaning more changes are allowed during development. It governs global gene expression, and the continuity of gene expression landscapes. Confers somatic and trans-generation transmission; the gene expression state is inherited through mitotic and meiotic divisions.|
|Changes in gene activity that are not the result of changes in gene sequence.|
|The establishment of the set of necessary active genes for a tissue. All other genes are silenced for the duration of the life of the organism. It is achieved through histone chaperoning. It is formed early in development, in stem cells as they differentiate. Fully methylated DNA is remethylated after each round of replication. A lot can change during DNA replication. Can be characterized by taking a DNA methylation "snapshot".|
|DNA methylation and histone modifications including methylation, acetylation, phosphorylation, mono-ubiquination, sumoylation, and ADP-ribosylation. Makes up the histone code. Dynamic modifications which can be removed. All interconnected. Once a region is targeted for silencing, all marks are necessary, but not sufficient for maintenance of the domain. Certain modifications can orchestrate formation of certain states of chromatin. Effects of epigenetic marks can lead to cancer developed during the life of the organism. Heritable; the exact same marks are found on daughter cells after mitosis or meiosis.|
|Determined by the balance between activities of HATs and SIRs. It s far less stable than the DNA sequence, but still heritable.|
|The active and silent states of chromatin are heritable. Heritable heterochromatin is critical for repression of transposons, and for the correct set-up of the epigenetic landscape of each cell. The transmission of epigenetic marks onto new histones during DNA replication. The nucleosomes are dispersed in specific ways, dividing into dimers or tetramers. Forms a mixture of new and old histones, but the modifications are made to resemble the old histones. There are mechanisms to rebuild chromatin exactly as the parent cell's during cell division. During DNA replication, chromatin is reconstructed by chaperones, histones, and DNMTs. Any phenomenon discussed in epigenetics is rooted in the transmission of chromatin marks to progeny. Modulation of heritability gives rise to important and sometimes mysterious biological processes.|
|In the 1990s, it was called "transmission genetics". Not to be confused with epistasis. Considers the "flow" of genetic information within the organism from cell to cell, and from one generation to the next. Inheritance of epigenetic marks. Not all genetic information is passed via DNA sequences, but also epigenetically. Mitotically and/or meiotically heritable gene functions that are not encoded by the sequence of DNA. Regulation of gene expression is heritable through epigenetic mechanisms. RNA has a profound effect on the expression of genes. Includes stem cell reprogramming: reversible cell differentiation. Can cause complex phenomena such as variegation, psychic disorders, immune evasion, cancer without DNA mutation, and cell differentiation. Behaviour may be controlled epigenetically, from effects of early childhood environment, or it may be transmitted culturally. All cell types have the same genes, but they are expressed differently in different cell types and tissues. Involves chromatin; DNA and histones can pick up information from the environment, which may be passed on to progeny, especially from the mother. There are models for transmission of epigenetics, but it is still a growing field. Includes histone epigenetic marks, DNA methylation, and position effects. Transmission of histone code and DNA methylation are the core of epigenetics. Can be studied through interesting phenomena including: PEV in Drosophila, TPV, X-chromosomal inactivation in mammals, parental imprinting in mammals, and stem cell epigenetics and insulation.|
|Not to be confused with epigenetics. The enzyme products of different, independently segregating genes interact with each other. The F2 phenotype ratio is 9:7. The C and P genes regulate two consecutive steps in the synthesis of the pigment anthocyanin. A recessive mutation in any of P or C abolishes the process regardless of the allele of the other gene.|
|An enzyme that removes a specific modification from a specific histone.|
|Chromatin which has a relaxed, open structure. Sensitive to nucleases; digested faster. Contains the majority of actively transcribed genes in the cell. Stains when dyed. Nucleosomes are farther apart than in euchromatin, producing less sharp bands when digested with nuclease, because there is greater variation in DNA fragment length.|
|Mutation rates increase in genes that are highly transcribed, and these rates are correlated with the state of chromatin. Gene regulation is controlled by RNA polymerase, repressors, and activators, taking place on chromatin, and adjusting transcription factors; much more complex than in prokaryotes. In differentiated cells, 60 - 70% of genes (in humans, 15,000 genes) are switched off. In the same tissue, patterns of gene expression are maintained through multiple cell divisions. DNA is packed into the nucleus, packaged with proteins to form nucleosomes and chromatin.|
|Facio-scapulo-humeral dystrophy (FSHD)|
|A rare genetic disorder. Symptoms include muscular dystrophy. Caused by TPE in a gene for non-coding RNA and repeat sequences. There is a damaged chromatin insulator (D4Z4) and CTCF sites at 4q35 locus next to the telomere of chromosome IV. These damages expose genes to the silencing effect of the telomere, and prevent their expression in muscles. Shortening of D4Z4 repeats, which usually act as a chromatin boundary, expose the genes (D4S139, FRG1, TUBB4Q), to TPE. FSHD patients have a short "buffer" repeat sequence, so heterochromatin spreads too far, and silences some developmental genes. There is no cure. Genes are not turned completely off, just expressed at a reduced level.|
Facilitates chromatin transcription
A histone chaperone which disassembles the nucleosome right before the passage of the replication fork. Bound to the helicase MCM. It works with H2A and H2B.
|Regions of heterochromatin that exhibit heterochromatic packaging in one subset of cells, but can be converted into euchromatin. Includes sub-telomeric genes in S. cerevisiae, and silenced genes in humans and corn.|
|A helicase studied by Schwab et al (2013). If mutated, can cause Fanconi anemia. Has a novel function of unwinding G4 quadruplexes, a DNA secondary structure which is able to disrupt replication. Limited understanding of how mutations disrupt genetic and epigenetic integrity, and promote tumorigenesis. Prevents the fork from stalling, and inhibits DNA synthesis under conditions of replicative stress. Required to promote replication in the presence of G4 stabilizer telomestatin. Limits accumulation of single-stranded gaps behind the fork. Suppresses reorganization of chromatin structure in a replication-dependent manner. An unscheduled histone H3 incorporation contributes to reorganization of chromatin structure in ?FANCJ cells. Supports global replication fork dynamics by promoting processive DNA synthesis under replicative stress, and past structured DNA on the lagging strand. Does not play a major role in leading strand synthesis. Required to maintain genomic and epigenomic integrity, by facilitating fork movement past DNA replication barriers.|
|Fanconi anemia (FA)|
|A cancer-predisposing disorder characterized by high genomic instability. It is caused by homozygous mutations in the helicase FANCJ.|
|Variability in binding of nucleosomes. Shown by peaks in a graph. Fuzziness increases in yeast cells with age. Not increased by overexpressing H3/H4. Loss of nucleosome fuzziness opens up promoter sites.|
|Term coined by Lamarck. Physical units representing each body part, believed to be gathered from somatic tissues to sex cells, producing heredity. Respond in adaptive ways to an individuals' external environment and experience. Altered gemmules are passed to offspring, allowing for inheritance of acquired characteristics.|
|The basic unit of heredity. Passed from organism to organism via different forms of sexual processes. Produce proteins that determine phenotype. It seems that the state of the gene, its position, its neighbors, and the RNA it makes has no effect on the genetic information and the position, its neighbors, and the RNA it makes has no effect on the genetic information and the activity of the gene, but this is not true. Some genes in stem cells are insulated from others so they can behave differently; activity depends on position. From Mendel's work, and solid evidence from molecular biology, we know that genes reside on DNA, which is faithfully transmitted to future generations. Resides at a specific position on a chromosome, which may be firm or variable. A length of DNA that specifies a product. The number of genes does not reflect the complexity of the organism.|
|Characterized by histone acetylation, and specific patterns of histone methylation. On top, nucleosomes are moved around by chromatin remodelers. Includes hyperacetylated lysine, and glutamine.|
|Gene activity in different depending on if it is transmitted through the male or the female, but is not on a sex chromosome.|
|A fundamental event in cell differentiation. Epigenetically transmitted to daughter cells. Silencing is spread to neighboring regions by spreading of histone modifications. Important for cell differentiation, development, and disease. Requires an interaction between SIR3 and H3. Occurs only in eukaryotes. Level of gene silencing may be a sign of age.|
|Environmental factors can modify DNA, but not its sequence, altering gene expression creating and retaining epigenetic "memories".|
|Mutagenizing an organism, and then screening many of the organisms for mutations, usually loss-of-function mutations.|
|Organisms do not have many genes; the complexity of traits needs to be explained by combinations of genes that are expressed in different tissues.|
|Has the same charge and shape as an acetylated lysine residue. Contributes to gene activation. A K > Q mutation mimics acetylation of lysine residues, disrupting gene silencing.|
|Did work in 1866, calculating pedigrees of pea plants. Was lucky that the organism he studied showed Mendelian Principles, with clear dominance and recessiveness.|
A histone which is associated with linker DNA between nucleosomes. Without H1, nucleosomes are not disrupted, however the tight 30 nm chromatin fibre packaging is lost; it is just "beads on a string". Sits between the nucleosome and the linker DNA.
|A core histone. Can be methylated or acetylated at K9 and K27. When K9 in the N-terminus is methylated, it is mostly found on DNA that is methylated on the 5' position of cytosine.|
|During DNA replication, old H3 and H4 histones are transferred to nascent DNA strands in most cases as a tetramer, but there is some evidence that it transfers in dimers. If transferred in a tetramer, old marks and predisposition marks do not reside in the same nucleosome; there are old nucleosomes and new nucleosomes, and marks would need to be transferred between neighboring nucleosomes. If transferred in a dimer, "mixed" tetramers could form of old and new histone dimers; in this case old marks and predisposition marks reside on the same nucleosome, and marks would be transferred from histone to histone. The latter seems more common-sense, but evidence point to the former model, in which they are transferred as a tetramer. Scientists cannot definitively say which model is true; it is a mystery. There is a possibility that neither of these models are true.|
|Triple methylation of the 36th lysine in H3. Studied in Jiang et al (2013). A modification involves in silencing of var genes in P. falciparum.|
|In insects, it is the functional equivalent of H4K16. A modification of this residue recruits a reader, HP1. Leads to methylation of other histones in the area, determining expression of genes. Loss of this modification disrupts methylation of DNA.|
|H3K9 methyltransferase (MT)|
|Methylates H3K9. The mutation dim5 in Neurospora disrupts this gene. The loss of histone H3 methylation abolishes CpG methylation.|
|Methylated H3K9. A histone modification found mostly on DNA that is methylated on the 5' position of cytosine. Orchestrates the formation of heterochromatin in higher eukaryotes, including Metazoa. Tightly linked to DNA methylation and histone deacetylation. Recognized by the key modifier, HP1. Leads to methylation of other histones in the area, determining expression of genes. Loss of this modification disrupts methylation of DNA.|
|A core histone. Can be methylated or acetylated at K30.|
|The lysine residue which is recognized by SIR3/SIR4 when deacetylated. It is acetylated by SAS2, and deacetylated by SIR2. Acetylation promotes gene activation, and deacetylation promotes silencing. When the lysine is mutated to glutamine (H4K16Q), it results in loss of silencing, but this can be restored by a suppressor mutation in SIR3. The functional equivalent in insects is H3K9. A modification of this residue recruits a reader, SIR3/SIR4.|
|Acetylated H3K16. A modification which is written by SAS2, and erased by SIR2.|
|A mutation in histone H4 which results in loss of silencing. Lysine is replaced by glutamine. A suppressor screen showed that a mutation, sir3, restores genes silencing in H4K16Q mutants.|
|Containing one set of the genome. S. cerevisiae can grow as haploid cells, with an a or an ? mating type. Produced by sporulating diploid cells under low nutrient conditions. Wildtype (homothallic) yeast can switch mating types during haploid growth as they divide. There is both an a and an ? gene, but one is silenced. Capable of combining sexually with another haploid cell of the opposite mating type, to produce a diploid cell.|
|DNA which is partially methylated. There are methylation marks on cytosines only on one strand of the double helix. DNMT reads the methylated strand and adds the same methylation marks to the unmethylated strand.|
|Passed from organism to organisms in genes, encoded in the sequence of DNA. Heritable gene activity can be altered by environmental conditions, such as stress, hunger, addictions, peculiar behaviour, and diet. The idea of heredity has been known as early as 800 BC.|
|Chromatin which has a compact structure. Allows cells to differentiate. Different cell types have heterochromatin in different genes. If the heterochromatin becomes euchromatin, it can cause cancer. Resistant to nucleases; digested slower. Contains sub-telomeres, repetitive DNA, transposons, centromeres, and inactive genes. Found in the nuclear periphery. Nucleosomes are closer together than in euchromatin, producing sharper bands when digested with nuclease, because there is less variation in DNA fragment length. Nuclease accessibility studies show that heterochromatin is not "tighter" than euchromatin, but is more "tidy", with regular spacing of nucleosomes, suggesting less mobility and dynamics. Requires a significant body of proteins to be considered heterochromatin. Hypo-acetylated histone N-termini, and specific patterns of methylated histones. Hallmarks include DNA methylation, histone methylation, and histone deacetylation. A universal mechanism of gene silencing and regulation in eukaryotes. Becomes less tightly packed with age. When most genes from euchromatin are placed near heterochromatin, they exhibit gene silencing to some degree, but will work after it is moved back to euchromatin. It doesn't push away all transcription factors; some genes can be expressed sometimes. There are several types of heterochromatin. Includes facultative and constitutive heterochromatin.|
|A cis element found at a certain position int he genome. Stops the spread of heterochromatin. Where there is a heterochromatin block, there can be expected to be variegation, based on whether genes are active or not.|
|Heterochromatin protein 1 (HP1)|
|Found exclusively in heterochromatin in Metazoa, in which it is highly conserved. A key non-histone component of heterochromatin. It binds to H3K9Me, and recruits HDACs, which deacetylate H3K14, and DNA methyl-transferases which methylate CpG islands, orchestrating formation of heterochromatin in higher eukaryotes. There are homologues found in many eukaryotes. Has a chromo domain and a chromo shadow domain. Mutations result in loss of silencing. Encoded by Su(var)2-5.|
|After H3 and H4 are deacetylated by SIR2, they recruit more SIR3/SIR4, which recruits more SIR2 to deacetylate histones on neighboring nucleosomes. In yeast, RAP1 recruits SIR3/SIR4 to H4K16Ac. SAS2 adds acetyl groups to the histones. It continues along the DNA in this fashion, forming heterochromatin. Begins at the telomeres, where RAP binds to TG3 repeats, and continues into subtelomeric regions. Establishment and spreading of heterochromatin in S. cerevisiae is a paradigm that applies to all eukaryotes, though names of proteins and their activities varies between organisms. Large protein complexes: readers and writers, or readers and erasers, execute similar functions in all eukaryotic nuclei. It is prevented from spreading all the way to the centromere by opposing activity of HATs, and the limited amounts of SIR3/SIR4. The cell has only a certain amount of heterochromatin factors, for which silencers compete. This is how epigenetic switching in PEV and TPE occurs, where there is loss of silencing at loci. Heterochromatin spread is sensitive to other factors in the nucleus. Spreading is not always linear, forming 3D domains of heterochromatin factors.|
|Haploid S. cerevisiae cells which have a mutant allele at HO. Cannot switch mating type.|
|The himalayan allele produces dark fur at the extremities of the body if the rabbit is reared at 20°C or less, but the rabbit has white fur if reared at 30°C or higher. The dark pigment only develops at low temperatures because the enzyme for pigment production is inactivated at higher temperatures.|
|Histone acetyltransferase (HAT)|
|Counteracts the activity of SIR2 and other HDACs, countering spread of silencing, including at telomeres. This interplay determines the state of chromatin (active vs. silent), and produces PEV. Includes SAS2.|
|Not to be confused with translational chaperones. Accompany histones at all times. May transfer epigenetic marks onto new histones during epigenetic transmission. Includes FACT and ASF1. There are no free histones in the nucleus or the cytoplasm. Histones are either in a nucleosome octamer, or associated with chaperones. Accompany the histones during DNA replication, and correctly math them with new histones that arrive from the cytoplasm. Histone codes on the old histones are read by a reader, which recruits writers that eventually impose the same histone code on the new histones.|
|A combination of N-terminal modifications which serve as a "barcode" that is recognized by other proteins, including histone modifying enzymes. Considering that there are four core histones, and more than two modification types, and multiple sites where modifications can occur, the histone code can store thousands of bits of information. A combination of post-translational modifications of the N-termini can be specifically reorganized by histone and chromatin modifiers (readers). Certain modifications can predispose a similar modification on the adjacent nucleosome, because of writers and spreading of heterochromatin. Combinations dictate the state of chromatin and its pertrubations. Modifications are interrelated to prevent drifting away from the state of chromatin and to facilitate its heritability. Modifications maintain other modifications, preventing erosion of the code. Allows for quick and adaptive response to the environment, and reduces need for more genes.|
|Histone deacetylase (HDAC)|
|Recruited by HP1 when it recognizes H3K9Me. Orchestrates the formation of heterochromatin. Recruited to CpG islands by McBPs. Histone deacetylation is connected with DNA methylation. HDAC physically interacts with DNMT. Its inhibitor decreases 5mCpG levels. Increased hyperacetylation of lysine is correlated with decreased cytosine methylation. Histone deacetylation is one of the hallmarks of silent chromatin. Inhibits MeCpG. It is counteracted by HAT; this interplay determines the state of chromatin (active vs. silent). Histone deacetylation is the key post-translation modification found in heterochromatin; plays a critical role in the set-up of the epigenetic landscape of any organism and tissue. Treatment with HDAC inhibitors causes loss of silencing at heterochromatin domains. Gene silencing and hyperacetylated state of unsilenced genes persists much long after the removal of the HDAC inhibitor, because epigenetic marks are heritable.|
|A modification of histone N-termini. Mono- or tri-methylation of H3K4 means the DNA is ready to be expressed. Trimethylation of H3K9 means the DNA is silenced. In Metazoa, it is only observed in H3 and H4.|
|Have post-translational modifications which have a gene regulatory function. Modifications include acetylation, phosphorylation, mono-ubiquination, sumoylation, and ADP-ribosylation. Modifications can signify that DNA has just been replicated, has not been replicated yet, is in a stem cell, or other states; forms the histone code. Extends out from the nucleosome. Highly conserved sequence.|
|There are additional variants to the five major histones that are encoded by different genes. In different organisms, there are different subsets of histone variants. Variants contain minor amino acid alterations, but have a substantially different function. Contribute to the complexity of epigenetic regulation. Substitutions of the individual components of the histone core with structurally distinct histone variants and covalent modifications alter the fabric of the chromatin fibre, resulting in epigenetic changes that can be regulated by the cell. There are fundamental questions that remain unanswered regarding their behaviour and influence on cellular function in the normal and diseased states.|
|Small proteins, 10 - 12 kDA. Rich in lysine (K) and arginine (R). Positively charged, allowing for interaction with negative DNA. Account for 50% of the proteins in the nucleus. Found only in eukaryotes. Highly conserved in all eukaryotes. Includes H1, H2A, H2B, H3, and H4. Form nucleosomes. Among some of the most conserved proteins, but are the most variable in terms of post-translational modifications in histone N-termini. Over 50 years ago, they were considered good candidates as molecules to carry genetic information. After genetic code was cracked, they were thought to have only structural role in packaging DNA. It is now known that they play an important role in carrying epigenetic information. Experimental evidence for their existence include chromatin, digested with micrococcal nuclease, and separated on gel; DNA is in discrete bands, around 180 bp: the 146 around the nucleosome, plus the length of the linker DNA.|
|A mating type loci near the ends of chromosome III in S. cerevisiae. It is always silenced. Genes artificially inserted into this loci are not expressed, because of position effect. Stores the genes that specify the ? mating type. Silenced by compact heterochromatin structure which is heritable. Silencing requires two silencers, E and I. Includes ACS.|
|A mating type loci near the end of chromosome III in S. cerevisiae. It is always silenced. Genes artificially inserted into this loci are not expressed, because of position effect. Stores the genes that specify the a mating type. Silenced by compact heterochromatin structure which is heritable. Silencing requires two silencers, E and I. Includes ACS.|
|An endonuclease which is required for translocation during switching of mating type in S. cerevisiae. Cuts out the MAT locus, and inserts a copy of the previously unexpressed mating type from HML? or HMRa. Won't work if the genes are mismatched (HMLa and HMR?).|
|Haploid S. cerevisiae cells which have a wild-type allele at HO. Can switch mating type.|
|Hu et al (2014)|
Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging
Found that histone protein levels decrease in yeast as they age. Nucleosomes become less well positioned, or move to sequences predicted to better accommodate histone octamers. Altering these epigenetic changes may prevent onset of aging or age-related illnesses in humans. Transcriptional up-regulation of genes leads to shorter lifespan. Retrotransposon transcription increases, leading to greater genomic instability. dsDNA breaks allows mtDNA translocation in genomic DNA. Leads to transcriptional induction of all yeast genes, elevated levels of DNA breakage, mitochondrial DNA transfer to the nuclear genome, large-scale chromosomal alterations, translocations, and retrotransposition during aging. Overexpressing H3 and H4 extends lifespan.
|Hu et al (2014) experimental details|
|Mother cells were biotinylated, and then affinity chromatography was used to sort mother and daughter cells. Ran shotgun RNA sequencing to assess global expression. Gene expression increases during aging, limiting replicative lifespan. Did gel electrophoresis and southern blot, and discovered DNA damage including double stranded breaks and inter/intrachromosomal transposition, except for one intact right segment on chromosome XIII.|
Have 3,300 Mb of DNA, 20,500 genes, 23 chromosomes, and 9 genes/Mb. Have five times as many genes as E. coli. Lifecycle takes around 20 years to complete. There are around 1011 cells in the body. Genome size is 6 x 109 bp. There is a higher order of chromosome structure. Sex is complicated. Sex determination is with X and Y chromosomes.
|A DNA cis-element silencer. Required for silencing at HMRa and HML?, conferring position effect. Includes ABF1 and ARS318. ABF1 recruits SIR3/SIR4.|
|Never completely identical, even though genes are the same. Can have epigenetic differences.|
|Caused by mutagens, such as UV light or radioactivity.|
|Induced pluripotent stem cell (iPSC)|
|Studied in Cheloufi et al (2015). Generating iPSCs involves profound remodeling of chromatin landscape, and reprogramming of mature somatic cells, to produce cells capable of differentiating into any cell type. Can be used for production of patient-specific stem cells, with numerous health applications. Unfortunately, generation is slow and inefficient, suggesting chromatin-associated mechanisms are in place to safeguard somatic cell identity.|
|Induced stem cells (ISC)|
|Differentiated cells, such as skin or fibroblast, can be reprogrammed to become induced stem cells. The cell is entirely reprogrammed to produce a different heritable lineage, without modifying DNA.|
|ISWI chromatin remodeler|
Imitation switch chromatin remodeler
Protein complexes that catalyze ATP-dependent nucleosome sliding along DNA. Includes an ATPase domain (SNF2h), and "reader" subunits which interact with histone post-translational modifications.
|Jeffrey et al (2013)|
Analysis of epigenetic stability and conversions in Saccharomyces cerevisiae reveals a novel role of CAF1 in position effect variegation
PEV phenotypes are characterized by the robust multigenerational repression of a gene located at a certain locus (gene silencing) and occasional conversions to a fully active state. Addressed important aspects of PEV: frequency of conversions. Developed a model for various PEV scenarios based on various states of conversions. Assays revealed that histone chaperone CAF1 is involved in control of epigenetic conversions.
|Jiang et al (2013)|
PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum
Variant antigen in erythrocyte membrane protein 1 (PtEMP1) is expressed on the surface of P. falciparum-infected red blood cells, and is a critical virulence factor for malaria. Each parasite has 60 antigenically distinct VAR genes, encoding a different immune-evasion mechanism. How 59 of the VAR genes are silenced is unknown. Knocking out SET gene controls H4K36Me3 on the VAR gene. Focused on determining the possible regulation mechanisms of var genes through epigenetic factors. Determined that PfSETvs is one mechanism that controls var gene silencing through H3K36Me. Discovered that PfSETvs knockout results in expression of all 60 var genes. Provides insight into mechanisms of PfSETvs ortholog gene repression in other eukaryotes. Parasites containing PfSETvs knockout may lead to development of malaria vaccine. RTS,S recombinant vaccine is currently being tested, and has a success rate of 26 - 50%. Conclusively, the study provided a new target for malaria therapy, and has provided a stepping stone for further research on the relationship between gene silencing and var gene regulation.
|Jiang et al (2013) experimental details|
Six experiments were conducted:
1. Determining if any of the 10 PfHKMTs (PfSET genes) or 3 PfHKDMs contribute to var gene silencing.
2. Determining if multiple var genes can be transcribed at the same time.
3. Determining if var genes are able to translate multiple PfEMP1s on the surface of an infected red blood cell.
4. Determining the effect of PfSETvs knockout on methylation of P. falciparum genome, and identify a relationship between histone methylation and location of var genes.
5. Determine if the reduction of H3K36Me3 by PfSETvs? is specifically associated with activation of parasite clonally variant genes.
6. Determine the role of H3K36Me3 in var gene silencing in active vs. silent var genes.
|Joshua and Esther Lederberger|
|Performed experiments on the nature of mutation and adaptation in microorganisms. What confers heritable adaptation and evolution? Are mutations a meaningful source for variation? Are mutations induced, and therefore adaptive? Conducted replica plating of bacteria in benign environments, and transferred to restrictive media with antibiotics. Found that most colonies died. Survivors got the mutation before exposure. Concluded that mutations that confer resistance to streptomycin was not acquired during exposure to streptomycin; it is spontaneous, and not adaptive. Won the Nobel Prize for this experiment.|
|Used in D'Aquila et al (2017). Survival curves of 60 - 89-year old human samples. There was over 20% methylation levels vs 20% methylation levels at CpG_5. Observed chance of survival after a 9-year period. Survival chance was significantly lower in subjects with methylation levels over 20%; mortality was twice that of subjects with methylation levels below or equal to 20%. Methylation of other CpG units had no effect on survival chances in a 9-year period; no association between methylation variability and survival in the 90 and over age group.|
|There is an ongoing dispute on whether mutation rates in certain bacterial genes can be enhanced by exposure to a specific environment.|
|Thought that under selective pressure, organisms acquire or lose characteristics that then become heritable. Believed that organisms had "gemmules". His theories were forgotten because they didn't work with other theories, and were disproved.|
|Luria and Delbruck|
|Performed experiments on the nature of mutation and adaptation in microorganisms. What confers heritable adaptation and evolution? Are mutations a meaningful source for variation? Are mutations induced, and therefore adaptive? Produced colonies from one cell each, and found several million cells were resistant; less if the mutation is more recent. Mutations can occur at any point. Concluded that mutations were not acquired during exposure to selective agents; mutations are rare and non-adaptive. Won the Nobel Prize for this experiment.|
|A positively charged amino acid, which is important for binding to DNA. Acetylation reduces its charge, reducing its bond to DNA, allowing for easier access of transcription machinery for gene expression. Can be methylated or acetylated. In histone tail mutants, when it is hypoacetylated it contributes to gene silencing, but when hyperacetylated, contributes to gene activation. Acetylation facilitates the spread of heterochromatin marks along DNA.|
|Majocchi et al (2014)|
Epigenetic regulatory elements associate with specific histone modifications to prevent silencing of telomeric genes
Evaluated different epigenetic regulators for their ability to protect transgene expression at telomeres. Found that matrix attachment regions (MARs), ubiquitous chromatin opening elements (UCOE), and chicken cHS4 insulator acted as barrier elements.
|Caused by a parasitic plasmodium which evades host immune response. The number one killer of humans worldwide. It is spread by mosquitoes. It kills 1 million people each year. Once a person survives malaria, they may have a certain amount of immunity. Children do not often survive.|
|A DNA locus in S. cerevisiae which ontrols mating type. Can be MATa or MAT?, which controls which type of pheromone and receptor is expressed during shmooing, thus controlling mating type. Mating type haploid cells is determined by whether HMRa or HML? is translocated into this locus, and expressed from this position. There are two transcripts, both required for mating: either a1 and a2, or ?1 and ?2.|
|An allele of the MAT locus. Translocated from HML?. Confers an ? mating type in S. cerevisiae. An ?-factor pheromone is expressed, and an a-factor receptor. Contains the two transcripts ?1 and ?2.|
|An allele of the MAT locus. Translocated from HMRa. Confers an a mating type in S. cerevisiae. An a-factor pheromones is expressed, and an ?-factor receptor. Contains the transcripts a1 and a2.|
|Haploid S. cerevisiae cells have either a or ? mating type. Wild type yeast can switch mating types during haploid growth. There are both an a and an ? gene, but the haploid cells express only one. Mating can happen only between an a and an ? cell, to form a diploid cell. Controlled by MAT locus. Mating type genes, a or ?, are positioned in two mating type loci, HMRa and HML?, near the ends of chromosome III; these genes are always silenced, never expressed. These loci store the genes that specify mating type. Kept silenced by compact heterochromatin structure. Loss of silencing and expression of both a and ? will prevent cells from mating, but not from shmooing. Silencing requires two silencers, E and I. Ability to switch mating type is conferred by HO.|
Methyl-CpG binding domain
Supports the model that DNMT methylates using the old methylated strand as a guide for the enzymes. Binds to hemi-methylated DNA. It reads for CpG islands, and directs the activity of DNMT, copying methylation onto the other DNA strand. In Neurospora, it is NP95. Includes MBD1, MBD2, and MBD3, which are reader proteins that direct DNMT1 to the newly synthesized DNA strand. MBD2 and MBD3 are interchangeable subunits of NuRD nucleosome modeling complex; mutations in these impair cell differentiation and cause cancer.
|A replicative helicase which travels ahead of the replicative fork. It is bound to ASF1 and FACT. It unwinds the DNA double helix during DNA replication.|
|What would happen in a "perfect Mendelian world". There are independent dominant and recessive alleles of genes. Alleles segregate independently of each other and of other genes. Genes don't change location on the chromosome. You can build pedigree charts and calculate probability of phenotypes of progeny based on phenotype of parents. Mendel was lucky that the organism he studied showed such principles. Mendelian alleles in diploid organisms follow the rules of dominance.|
|In yeast, silenced in the presence of nutrients, and active in the absence of nutrients. A form of adaptation and plasticity.|
|Kind of stable. When there is random silencing of a gene early in development. Occurs for the White gene in Drosophila, when it is found in the chromatin boundary, causing PEV. Once established, the silencing is heritable and stable in all progeny cells. However, rare conversions of state are possible, and reflect developmental history. Large sectors of cells of one type mean there was an early conversion event, and smaller sectors mean later events.|
|Heterochromatin has histone deacetylation, trimethylation of histone H3K9, DNA methylation (on CpG islands in mammals), and HP1.|
|Methyl-cytosine-binding proteins (McBP)|
|Binds to CpG islands and recruits histone deacetylases, histone methyltransferases, and chromatin remodeling complexes. Binds to methylated DNA. Always found in a complex with a reader molecule and HDAC. Deacetylates histones.|
|Micrococcal nuclease (MN)|
|An enzyme which makes cuts in DNA that is not protected by proteins; in between nucleosomes. It works faster on euchromatin than heterochromatin. It digests chromatin into discrete bands, around 180 bp in length: the 146 around the nucleosome, plus the length of the linker DNA. Bands are not sharp, because there is variation in fragment size.|
|A modification of histone N-termini.|
|A water organism. In a genetic screen, researchers found two mutants with defective silencing. Both had no 5mCpG methylation on the unsilenced gene.|
|Nucleosome acidic patch|
|A unique surface feature which was analysed by Dann et al (2017). Created by a cluster of acidic residues within the core region of histones H2A and H2B. Together creates a negatively charged cleft on each face of the nucleosome dicsc. In H2A, three residues form a binding pocket for arginine residues. Modification or mutation inhibits or enhances remodeling activity. LANA peptide binds to the arginine residues, inhibiting modeling. H2A.Z has additional residues which extend the acidic patch, and enhance remodeling. The SNF2h ATPase subunts needs an intact acidic patch to function, suggesting that it is generally required for chromatin remodeling.|
|Can be seen under an electron microscope, after extracting chromatin from nuclei without dissociating DNA in mild salt conditions. Seen as "beads on a string". Consist of repeating units of 146 bp of DNA. There are two each of the four core histones, H2A, H2B, H3, and H4, forming an 8-subunit octameric structure, 11 nm in diameter. There is one (H3-H4)2 tetramer and two (H2A-H2B) dimers. Can be compactly or loosely spaced on the DNA, depending on the chromatin type. The DNA is wrapped around the outside of the nucleosome.|
|A nucleosome remodeling complex which has interchangeable subunits, MBD2 and MBD3. Mutations in these subunits impair cell differentiation, and cause cancer.|
|The amount of time that a nucleosome spends at a DNA locus. Not increased by overexpressing H3/H4.|
|Ohm et al (2010)|
Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells
Ability to induce pluripotent stem cells from committed, somatic human cells provides tremendous potential for regenerative medicine. Neoplastic potential inherent to reprogramming must be understood; provides a model for tumorigenesis. Used genome-wide assays. Identified cancer-related epigenetic abnormalities which arise early during reprogramming and persist in induced pluripotent stem cell clones.
|Transcription factors studied in Cheloufi et al (2015). Four are sufficient to reprogram cells into iPSCs. Enhanced reprogramming depends on OKSM dosage.|
Origin recognition complex
Binds to ACS in mating type loci, and recruits SIR1, allowing for recruitment of SIR2.
|An idea used by Darwin to explain heritable variation. Adopted from Lamarck's theory of adaptation. In organisms there are "gemmules" which are gathered from somatic tissues into sex cells.|
Proliferating cell nuclear antigen
A replicative clamp which travels right behind the replication fork. Associates with CAF1 and DNMT. A "sliding clamp". It is often a mark of cancer, found in proliferating cells. A lot of proteins may bind to it, but it can only have three bound to it at a time. Regardless of how many factors are bound to it, it knows when to replicate.
|If only half of individuals with a genotype show the phenotype, there is 50% penetrance.|
|Heterochromatin in the periphery of the nucleus. Genes may be pulled into it by proto-silencers, and silenced. Genes on protruding loops may still be expressed, causing PEV. The nuclear pore pushes domains out of the heterochromatin block.|
|A modification of histone N-termini. Serine (S) and threonine (T) residues are phosphorylated. Phosphorylation of H4T45 means the DNA is damaged. Phosphorylation on H2A means that DNA is being repaired, and shouldn't be replicated.|
|Blood intracellular parasites. Studied in Jiang et al (2013). Live inside erythrocytes, but will burst out and be exposed to the immune system. Cause malaria. Contains 60 VAR genes which control which PfEMP is transcribed and expressed as a singular antigen. Invades human immune systems by cycling through expression of 60 surface antigens.|
|Can produce several cell types, but is not fully totipotent. Many differentiated cells can reset to a pluripotent cell.|
|Extra fingers and toes. Can have incomplete penetrance, and variable expressivity. A person with the genotype may not display the phenotype. Expression depends on many complex factors.|
|When a locus is permanently silenced. Genes spliced into this locus will be silenced. When the chromatin neighborhood determines the state of expression. Found in all eukaryotes. Happens all the time naturally. There is position effect at HMRa and HML?.|
|Position effect variegation (PEV)|
|When subtelomeric genes convert their state (silent vs. active). Occurs about one every 20 generations. Caused by competition between SIRs and HATs. States may persist for many cell generations. Discovered in Drosophila in the 1930s by Muller. He X-rayed Drosophila flies to cause mutations. Mechanism was elucidated later: a chromosome rearrangement (inversion) moves the gene for synthesis of red eye pigment (White) to a different location. The gene is not mutated. White is now at the boundary between centromeric heterochromatin and euchromatin; the chromatin boundary. Causes variegated pigmentation in the eye, caused by infrequent conversions between silenced and active state of White during development. The effect is dependent on the position of White: normally it is expressed from another position in the genome. It is a one-time movement of the gene caused by the X-rays, and is passed on to progeny. All facets of the eye have identical genomes, but position effect causes White to be expressed only in some facets of the eye; expression is metastable. By studying PEV, we learned that gene silencing is caused by tightly packed heterochromatin. PEV is caused by a centromeric block of heterochromatin with infrequent, random switches in expression. Additional evidence indicates that things are not so simple. Genes in Drosophila which normally exist in heterochromatin exhibit PEV when moved into euchromatin; some genes prefer heterochromatin neighborhoods. Genetic screens were conducted with a whiteV gene; loss of patched eyes indicate loss of genes which regulate PEV. Two genes were classified: Su(var) and E(var).|
A mark which is used to recognize new histones during DNA replication and epigenetic transmission. There is a reader which directs enzymes to modify the new, and not the old histones.
|Principal components analysis (PCA)|
|A technique used in Dann et al (2017). Uses computer software to search large datasets for correlations between variables. Splits variables into dimensions, and finds planes upon which there is the highest level of variation. Information is used to produce 2D graphs which identify proteins of similar activity, which cluster together.|
|Genes are regulated in the absence of chromatin by a simple interplay of RNA polymerase, repressors, and activators. There are upstream regulatory sequences. -10 is a synthase, and -35 is a regulatory factor.|
|A large protein bound to the DNA. During DNA replication, as it is pushed away, some histone marks may be lost, and the replication fork is slowed. This can lead to epigenetic switching of gene activity state. Any tightly bound protein can act as a protein barrier. There are 100,000s in humans, and each with dedicated factors.|
|A weak silencer. Does not work on its own; requires several factors to work. It can push the signal of heterochromatin further away from other silencers. A cis element that is weak and cannot work on its own, but relays and enhances signals by strong silencers. Includes isolated ACS, and binding sites for Abf1 and Rap1. Supports other silencers, but is not a silencer itself.|
|Can be inherited from epigenetic imprinting.|
|A breed of sheep which has a large butt. The trait has no gene; it is epigenetic.|
|Not directed by anything. The rate of random mutations is too low to provide for evolution; this is a recent idea. Higher rates of random mutations jeopardizes genomic stability. Life is unsustainable if mutations happened at a rate that is necessary for evolution. Some genetic components must have adaptive mutations in DNA.|
|Binds to TG3 repeats in the telomere, recruiting SIR3/SIR4, which recruits SIR2. Deacetylation spreads, producing heterochromatin.|
|A protein that recognizes a specific modification on a specific residue of a histone. Histone and chromatin modifiers. Includes HP1.|
|Replication-coupled epigenetic switch|
|A model for how heterochromatin can reversibly activate nearby genes (causing epigenetic changes during PEV and TPE). During DNA replication, the chromatin is completely disassembled and reassembled. Replication forks temporarily pause at a promoter of active genes. Different genes can use this opportunity to independently switch their state. If gene A switches, and gene B does not, there is independent variegation of the two neighboring genes.|
|Can be caused by several things. Generates conditions for epigenetic switching. Cancer cells are in a constant state of replication stress. Checkpoints are damaged. Signalling is compromised, but not malignant. Can lead to epigenetic switching of gene activities.|
|A huge complex which travels and replicates the DNA, and transfers epigenetic marks. Includes the replication fork, and all the associated components. The replication fork will move slowly through tight heterochromatin.|
|Ronn et al (2013)|
A six months exercise intervention influences the genome-wide DNA methylation pattern in human adipose tissue
The epigenome differs between cell types, characterized for a few human tissues. Environmental factors potentially alter the epigenome. Describes genome-wide patterns of DNA methylation in human adipose tissue, and concludes that exercise induces genome-wide changes, potentially affecting adipocyte metabolism.
|A mutation reduces the frequency of conversions at the telomere. A non-replicative DNA helicase that helps the fork pass sites which are difficult to replicate. Pushes away proteins which are tightly bound to the DNA, allowing passage of the replication fork. It unwinds the DNA.|
A single-celled eukaryote. Has 15 Mb of DNA, 6,200 genes, 17 chromosomes, and 400 genes/Mb. Genome size is 12 x 106 bp. Heterochromatin has histone deacetylation (SIR2), no trimethylation of histone H3K9, trimethylation of H3K79, no DNA methylation, and no HP1. Not everything found in yeast applies to Metazoa. Used in the making of beer and bread. A model organism; became popular in research in the 1970s, especially in cancer research. Lifecycle takes 90 minutes to complete; very fast. Billions can live in a petri dish. There is higher order of chromosome structure. Has very simple sexual reproduction. Can be used to study gene silencing at mating loci. Sex determination (a or ? mating type) is with four genes in two loci: MAT, HML, HMR, and HO. Can grow and divide as either diploid or haploid cells. Undergo standard eukaryotic cell cycle. Its stage in cell cycle can be determined under a microscope. In S phase, there is a bump on the cell surface, which becomes two cells during mitosis. Daughter cells may remain attached after mitosis. Sporulates during bad conditions, undergoing meiosis, in which four haploid cells burst from the cell: two each of a and ? mating types. After budding, there is a scar on the cell, which can be used to determine the age of the cell. Disadvantages to studying PEV include no DNA methylation, and no HP1. Advantages include estimating frequency of epigenetic switches can be observed forwards and backwards. Its lack of DNA methylation can be good for epigenetic research, because it removes "background noise". We learned that genes regulate chromatin structure, with many writers, readers, and erasers. Proteins at the replication fork regulate epigenetic switching, especially when stalled.
|Salvi et al (2013)|
Enforcement of a lifespan-sustaining distribution of SIR2 between telomeres, mating-type loci, and rDNA repeats by RIF1
Showed that RIF1 maintains replicative lifespan by stabilizing another age-related chromosomal domain, harbouring ribosomal DNA (rDNA) repeats. Siruin histone deacetylases, including SIR2 and mammalian SIRT6, operate at multiple age-related loci, and limiting their location to these loci can promote lifespan-sustaining roles elsewhere in the genome.
Something about silencing 2
SIR2 is a suppressor mutation of sir3. An H4K16 acetyltransferase (HAT); a writer of H4K16Ac. It is constantly competing with SIR2. A mutation reduces frequency of conversions at the telomere. A HAT that travels behind the replication fork. It travels with CAF1. Has an unknown relationship to replication.
|Schwab et al (2013)|
FANCJ couples replication past natural fork barriers with maintenance of chromatin structure
Homozygous mutations in the helicase FANCJ cause Fanconi anemia. Replicative stress, caused by replication fork barriers, can negatively impact the epigenome. Researchers propose that FANCJ plays a crucial role in maintenance of genomic and epigenomic stability by facilitating replication or movement past DNA-structure mediated replication barriers. Stalled forks were replication competent and capable of restarting DNA synthesis upon removal of replicative stress. Guanine rich sequences were found in promoter regions of many tumour suppressor genes; changes in chromatin compaction may result in their silencing.
|Enzymes dedicated to modifying residues. A writer.|
|When haploid cells of S. cerevisiae display their preference for a or ? mating types, before sexual reproduction. Release pheromones of their own mating type, and display receptors of the opposite. Mating can occur only between an a mating type and an ? mating type. If the mating type is the same, or something is interfering with mating, the cells will continue to shmoo. Can be observed visually. If the mating type is opposite, the cells may merge together for sexual reproduction, forming a diploid cell. Genes that regulate silencing of mating type loci can be observed during prolonged shmooing. The word Shmoo is also the name of a friendly cartoon character.|
Non-active genes. In differentiated eukaryotic cells, 60 - 70% of genes (in humans, 15,000 genes) are switched off In the same tissue, the pattern of gene expression is maintained through multiple cell divisions. Different sets of genes are silenced in different cell lineages. The silenced genes are very rarely unsilenced, which can lead to pathology such as cancer.
|Specialized DNA cis elements which establish strong gene silencing. Includes E and I in HMRa and HML?. Silencing is spread to neighboring regions by spreading of histone modifications. Establishes a heterochromatin domain. Includes telomeres. Includes clusters of ACS and binding sites for Abf1 and Rap1. Can have variable strength. Includes 96 genes, including ORC and RAP1.|
|Silent information region (SIR)|
|Genes required for silencing at HMRa and HML?. Includes SIR1, SIR2, and SIR3/SIR4. The SIR3/SIR4 complex binds to ABF1 and RAP1 in the E and I silencing elements, and SIR1 binds to ACS. SIR3/SIR4 and SIR1 recruit SIR2, which acts as a histone deacetylase. This causes a spreading of SIRs and histone deacetylation, critical for silencing. The repressed state is heritable.|
|A silent information region. Brings SIR2 to ACS, in HMRa and HML?, leading to deacetylation.|
|A silent information region. Acts as a histone deacetylase (HDAC). Deacetylates H4K16Ac. An eraser. It is recruited by SIR1 and SIR3/SIR4. Its activity is countered by SAS2. Competes with HATs, producing PEV. Its method of deacetylation is conserved.|
|A silent information region. A reader of H4K16; it reads that the lysine is acetylated (H4K16Ac), it brings the HDAC SIR2 to the site, leading to deacetylation. When it reads deacetylated histones, it recruits SIR2 for adjacent nucleosomes, contributing to heterochromatin spreading. A dimer. One complex binds to RAP1, and the other to Abf1. Screens for suppressors of SIR3 mutants identified several genes, including SAS2. A mutation, sir3, can restore gene silencing in H4K16Q mutants. Both SIR3 and SIR4 bind to H3 and H4. H3/H4 tail mutants, such as H4K16Q, disrupt histone deacetylation which is crucial for silencing.|
|Caused by trypanosome parasites which evade host immune response by expressing one gene at a time. The person is sick for three days, and then they seem to get better. But then they develop a fever and die from exhaustion. The blood parasite eats everything in the blood. Strategies for combating it might include: stopping epigenetic switches, developing a vaccine for all 1,000 VSG genes, or turning off all silencing.|
|A model for how heterochromatin can reversibly activate nearby genes (causing epigenetic changes during PEV and TPE). A gene is positioned close to a proto-silencer, which flips over to come into proximity with a strong silencer. Heterochromatin factors (SIRs) spill over from the silencer onto the proto-silencer, so now the gene next to the proto-silencer are off, and genes between the silencer and proto-silencer are on.|
|Occurring without an identified cause. Joshua and Esther Lederberger concluded that mutations that confer resistance to streptomycin were spontaneous.|
Suppressor of variegation
Suppressor genes of whiteV (PEV) in Drosophila, found in a genetic screen. The fly's eyes are mostly red, with some white patches. It inhibits the spread of heterochromatin. Includes Su(var)2-5 and Su(var)3-9; both encode proteins related to the histone mark H3K9Me. Homologues have been identified in all Metazoans; key regulators of many epigenetic transactions. Mutated in cancers and various rare diseases. Encodes key readers, writers, and erasers in epigenetic marks. Characterization formed the foundation of modern epigenetics.
|A Su(var) gene which encodes HP1, a key component of heterochromatin.|
DNA sequences adjacent to the telomeres. Contain histones which are highly condensed into heterochromatin. In east, there are short TGGG (TG3) repeats, as well as ACS and Abf1 sites. There are 1,000 repeats, scattered in the subtelomere. Repetitive and conserved, but not as conserved as the telomeres. Genes are silenced in yeast. Genes can convert their state (silent vs. active) about once every 20 divisions: PEV and TPV. There is variegation. Allows cells in the population to express genes based on the environment. In yeast, most transposons are found in the subtelomere.
|A modification of histone N-termini.|
|A mutation which restores a function to a mutation at another loci. Detected with a suppressor screen.|
A substitution mutation is inserted into H3 and H4 histones to perform mechanistic studies on histone modifications. For example, a K > Q mutation mimics acetylation of lysine residues. Can be used to look at gene silencing function in yeast. Identifies proteins that act through positions of the histones when H4K16 is mutated to Q. The phenotype, due to loss of silencing, is observed. The whole genome of H4K16Q mutant cells is mutagenized to find cells with restored silencing using a genetic screen; this is the suppressor mutation. Identifies SIRs and RAP1 as proteins needed to silence mating type loci in yeast, if silencing is impaired.
1. Create a mutation that disrupts a function.
2. Produce a cell culture with mutant cells.
3. Treat this culture with a mutagen so that every cell contains about one additional mutation in any gene.
4. Identify a cell that has regained the function; this cell has a secondary suppressor mutation, which suppresses the effect of the first mutation. If gene silencing is impaired, the yeast cells will express ADE3 gene, and form white colonies. Look for rare red colonies which suppress the defect, and ADE2 gene is silenced.
5. Identify the gene that carries the secondary mutation. Cells are transformed with a library of plasmids, each expressing one gene. Each cell normally acquires one plasmid. Isolate the plasmid and sequence the gene.
|When homothallic haploid S. cerevisiae cells switch mating type. Requires translocation of genes from silent HML? or HMRa locus into the active MAT locus. Wild-type HO endonuclease is required, which cuts out the MAT locus, and inserts a copy of the previously unexpressed mating type from HML? or HMRa.|
|A component of the telomere. There is an area with 3-stranded DNA, with a free loop that can reposition next to other parts of the chromosome, away from the telomere. Acts as a very strong silencer. Silencing switches over and comes into another region, near a proto-silencer. Explains discontinuous silencers.|
|All eukaryotic chromosomes end with a highly repetitive stretch of DNA. Protects the ends of linear DNA molecules from deoxyribonucleases. Prevents fusion of chromosomes during mitosis. Facilitates complete replication of the ends of linear DNA molecules. Heterochromatic. Has position effect; the telomere itself is a powerful silencer. Silencing is counteracted by several HATs. The most vulnerable part of the chromosome. Difficult to replicate. There are no nucleosomes in the T-loop. A sign of aging, the integrity of the genome, and proliferation state of the cell. Lengths of telomeres reduces with age. Repetitive sequences generate structures including the T-loop, R-loop, and G-quadruplex DNA. Wrapped in the telosome. In yeast, it contains TG3 repeats. In humans, it contains T2AG3 repeats. Telomeric clusters are found in the nuclear periphery. Maintenance of telomeric (and other) heterochromatin can be related to aging, in yeast and other species including humans. Contains different histone variants from heterochromatin or euchromatin.|
|Telomere position effect (TPE)|
|When subtelomeric genes convert their state (silent vs. active). Occurs about one every 20 generations. Used by blood parasites to evade immune response. Used in yeast for adaptation: S. cerevisiae displays typical PEV phenotypes. All eukaryotes have some TPE. There are heterochromatin blocks that silence repetitive DNA. It causes genetic disorders including FSHD.|
|A large, non-histone protein complex which wraps the telomere.|
|Repeats found in the telomere of yeast. Binds to RAP1.|
|Theory of Natural Selection|
|Put forth by Darwin to explain the cause of evolutionary change. A big gap in the theory was a lack of understanding of the genetic basis for variation and inheritance. Darwin borrowed to ideas to explain heritable variation: pangenesis and inheritane of acquired characteristics.|
|Genetic information is known to be encoded on DNA, but other levels of complexity exist, depending on chromosome architecture, proteins, et cetera. Something like a complex blob.|
|Can produce a whole organism.|
|A copy-and-paste mechanism. An HO endonuclease is required.|
|Transmission of histone modifications|
A model for how epigenetic marks transfer to new histones. All steps are highly speculative.
1. Reading and copying of histone code. Epigenetic marks (H3K9Me or H4K16A) recruit a specific dedicated reader/enzyme pair. The reader and writer may be separate complexes, the reader directing the enzyme's work, which would otherwise be random. Concomitant with this step is the recognition of the new histones by their predisposition mark (H3K56Ac); a reader directs enzymes to modify only new histones.
2. The enzyme catalyzes the same modification on the residue of the new histone.
3. The histone code is in action. H4K16Ac and H3K56Ac are recognized by another enzyme, which catalyzes mon-methylation of K3K9.
4. The predisposition mark is removed. The histone is no longer "new", and is recognized as carrying the same histone code as the hold histones.
|Mobile genes that can cause trouble. In yeast, most are found in the subtelomeric region, where they are silenced by heterochromatin. Often found in heterochromatin. May be metabolic genes.|
|Derivatives of this molecule may be used as anti-cancer drugs. Reduces silencing by mutating HDAC.|
|A parasite which lives in the blood, and causes sleeping sickness. Transmitted by the tsetse fly, which lives in Africa. Contains VSG genes which have TPE that enables them to evade immune response; this leaves the host unable to produce an antibody for the disease.|
|Very old days|
|The 1950s and earlier. Genetic information was thought to be carried on complex, amorphous blobs of proteins, nucleic acids, and who-knows-what.|
Variable surface glycoprotein
Genes found in trypanosome blood parasites. Coat the parasite, and are exposed to the immune system. There are about 1,000 VSGs, even though it only uses 50 - 60. Most are subtelomeric genes, silenced and variegated by a TPE mechanism similar to that of yeast. While the immune response to VSGx builds up, the parasite has an epigenetic switch to another VSG. Subtelomeres contain assemblies of proto-silencers, anti-silencers, and insulators that compromise a sophisticated and seemingly indestructible switching mechanism. If we suppress switching, the immune system will overwhelm the parasites.
|The stem cells (zygotes) are undifferentiated. The cells chose paths of irreversible cell differentiation to become tissues. In actuality, there can be resetting of epigenetic marks in development.|
|The gene for synthesis of red eye pigment in Drosophila. Wild type (W+) flies have red eyes, and deletion mutant (w) have white eyes. Can display PEV (whiteV) when it is moved towards the chromatin boundary at the centromere; the flies have eyes with red and white patches. It will have less variegation if transferred to the telomere.|
|An enzyme that confers a specific modification on a specific residue of a histone. Includes SET.|
A plant. Has around 3,500 Mb of DNA, around 50,000 genes, and 10 chromosomes. Can have variegation where kernels have identical genotypes, but one is solid colour and the other is spotted.