Chromatin organisation

• The nucleosome is the basic unit of chromatin structure, consisting of two copies of each histone protein (H2A, H2B, H3, and H4) wrapped around DNA.
• Agouti mice are phenotypically distinct due to differential methylation of their genomes.
• The diet of pregnant mice (F0) can affect the epigenome and phenotype of their offspring (F1) without altering the DNA sequence of F1.
• The ENCODE project is one of the projects involved in high-throughput sequencing.
• Finally, use high-throughput sequencing to identify IP’d DNA sequences.
• Folate, a component of the diet of pregnant mice (F0), feeds into the methionine cycle for the biosynthesis of S-adenosine methionine (SAM), which is the co-factor that donates methyl group for both DNA and histone methylation.
• The ChIP assay is a very important technique to identify and quantify the DNA sequence associated with specific histone modifications or bound by specific DNA-binding proteins in vivo.
• Chromatin, histone modifications and epigenetics are also studied in the development and use of ChIP assays and ChIP-seq.
• The number of HDAC inhibitors under clinical trials are being used as anti-cancer drugs.
• The development and usage of histone-modification-specific antibodies greatly facilitated the studies of histone modifications, useful for tracking nuclear localization or changes in the levels of modified histones.
• Competitive HDAC inhibitors resemble acetyl-lysine chain and bind to the same pocket as K-Ac substrates, physically blocking the interactions between HDACs and K-Ac substrates.
• There are two main types of DNA methyltransferases: DNMT1 and DNMT3a/3b.
• Genome-wide alterations of DNA methylation are linked to cancer.
• DNA methylation involves writing methyl marks on DNA.
• DNA methylation can be read by methyl-DNA binding proteins.
• Epigenetic cancer drugs, inhibitors of DNMT and HDAC, show synergy in clinical trials.
• Passive DNA methylation is coupled to replication and cell division, meaning without active methylation, genome are progressively de-methylated over multiple rounds of replication.
• Cancer cells have higher levels of hyper-methylated CpG islands and are hypomethylated at the pericentromeric heterochromatin, indicating transcription repression and genome instability.
• Transgenerational epigenetic inheritance of phenotype is supported by the observation that yellow fur, obesity, and diabetes are associated with dark fur, skinny (lean) and healthy phenotypes.
• Gel shift assay is used to measure DNA methylation.
• DNA methylation mediates transcription repression by three mechanisms: steric hinderance, recruitment of DNA-methyl binding protein and co-repressor, and change in chromatin structure to inactive chromatin (heterochromatin).
• DNA repair enzymes (TDG and BER) remove mismatched thymine, 5fC, 5caC, and restore cytosine.
• 5-aza-cytidine inhibition results in irreversible binding and degradation of DNA, leading to passive loss of DNA methylation.
• Base excision repair (BER) is a method of DNA repair that removes damage caused by oxidation, alkali, and other agents.
• Ten-eleven translocation enzymes (TET) convert 5mC to 5hmC and other derivatives through oxidation of -CH3 group and lead to eventual removal of the methyl group.
• 5hmC is found in high abundance in neural cell and embryonic stem cell lines.
• 5hmC is thought to antagonize methylation mediated by DNA methylation and function in transcriptional activation.
• Epigenetic and chromatin regulation:Active DNA de-methylation:For a long time, it was unclear whether active DNA de-methylation occurs in vivo.
• An alternative pathway involves deamination of 5mC, catalyzed by AID/APOBEC enzymes.
• Epigenetic and chromatin regulation:Active DNA de-methylation:5hmC is associated with transcriptional activation.
• Thymine DNA glycosylase (TDG) is an enzyme that removes thymine from DNA.
• Other modifications include A, P, U.
• Some lysine residues can be modified with one or the other PTM, but mutual exclusive (one type at a time).
• Phosphorylation mainly occurs on serine (S) and threonine (T) residues.
• Histone PTMs are often written in short hand - H3K4me3, H3K3me3, H3K2me3, H3K1me3, H3K0me3, H3K2me2, H3K1me2, H3K0me2, H3K2me1, H3K1me1, H3K0me1, H3K2me0, H3K1me0, H3K2me-c, H3K1me-c, H3K2me-p, H3K1me-p, H3K2me-x, H3K1me-x, H3K2me-y, H3K1me-y, H3K2me-z, H3K1me-z.
• Phosphorylated H2A.X is enriched at DNA damage site.
• Lysines can be modified by acetylation, methylation, ubiquitylation and others.
• Histones and histone post-translational modifications (PTMs) include acetylation, phosphorylation, methylation, ubiquitylation and others.
• Histone acetylation and transcriptional regulation: Histone acetylation founding paradox for how reversible histone PTMs regulate chromatin structure and biological processes.
• Methylation can also occur on arginine (R) and threonine (T) residues.