Jacob L. Glass and Ross L. Levine
Heritable DNA-associated regulatory info, often tissue specific, that does not involve the DNA sequence itself
Types of Epigenetic Information
• DNA methylation: Addition of a methyl group to the cytosine of a CG pair
DNMT1: DNMT that primarily maintains DNA methylation during cell division
DNMT3a + DNMT3b: De-novo DNMTs
Methyl binding domain proteins: Bind to/recognize methylated DNA
• Histone modification: Chemical modification of amino acids w/in a histone tail altering the accessibility of the surrounding DNA. Modifications include:
Nucleosomes: Generally comprises 8 histones, 2 each of H2A, H2B, H3, & H4. 147 base pairs of DNA are wrapped around each histone, providing a structural organization to the DNA in the cell nucleus
Histone structure: Globular portion + tail. Modifications of the tail include residue acetylation, mono-, di-, & tri-methylation, phosphorylation, & ubiquitination. These are abbreviated in a format including the histone type, modified residue position, & modification type. Eg, H3K4me3 = histone H3 lysine position 4 trimethylation; H3K9ac = histone H3 lysine 9 acetylation.
Histone code: The idea that combinations of histone modifications convey unique info. However, modifications are generally simply categorized as “activating” or “repressive”.
Activating marks: H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K9ac, H3K14ac, H3K27me1, H3K36me3, H3K79me1, H3K79me2, H3K79me3 (also repressive), H4K20me1, H2BK5me1
Repressive marks: H3K9me2, H3K9me3, H3K27me2, H3K27me3, H3K79me3 (also activating), H4K20me2, H4K20me3, H2BK5me3. (Cell 2007;823–837)
Bivalent domain: Both activating + repressive; H3K4me3 + H3K27me3. (Cell 2006;315–326)
• Nucleosome positioning: Changes in positioning that can occur w/DNA methylation & histone modification changes. This is mediated by protein complexes including the SWI-SNF complex, the NuRD complex, & others.
• Noncoding RNAs: RNA transcripts affecting gene expression via modification of other RNA transcripts (snoRNAs), mediation of specific RNA transcript degradation (siRNA, microRNA), & mediation of chromatin remodeling (lncRNA)
Epigenetic Changes in Cancer
• Promoter methylation changes: Aberrant promotor methylation has been a/w oncogenic changes
Promoter hypermethylation: Generally a/w gene silencing. Methylation of TSGs such as Rb in retinoblastoma (Hum Genet 1989;155–158), MLH1 in CRC (Nature 2012;330–337), BRCA1 in breast CA + ovarian CA (Carcinogenesis2000;147–151), & p16 in multiple malignancies (J Clin Oncol 1998;197–206).
Promoter hypomethylation: Generally a/w gene activation. Hypomethylation of growth-promoting genes has been observed in R-Ras in gastric CA (Cancer Res 2005;2115–2124), MAPSIN in CRC (J Pathol 2005;606–614), & BRCA2 in ovarian CA (Cancer Res 2002;4151–4156)
Loss of imprinting: Hypomethylation of imprinted loci has been a/w biallelic instead of monoallelic expression of growth factors such as IGF2 in Wilms tumor (Nature 1993;749–751) & CRC (Science 2003;1753–1755)
• Methylation patterning changes: Global hypomethylation is a typical feature of CA cells, w/c in some cases is a/w Mt in DNMTs (Carcinogenesis 2010;27–36) or dysregulation of demethylation also occurs (Cancer Cell 2010;553–567). More specific patterns also exist, such as the CIMP in w/c normally hypomethylated CpG islands become aberrantly methylated.
• Repetitive DNA hypomethylation: A/w genomic instability at these sites as well as retrotransposon reactivation (Int J Cancer 2008;81–87)
• Global changes in histone modifications: Histone modification changes w/c occur on a broad, genome-wide basis. One is broad loss of H4K16ac + H4K20me3 resulting in gene repression + perturbation of nl H3K9 & H3K27 methylation patterning. These can be mediated by Mt/aberrant expression of histone acetyl transferases, HDAC, & histone methyltransferases (Nat Genet 2005;391–400).
• Epigenetic switching: A change in epigenetic marks from reversible histone-modification to heritable changes in DNA methylation. This has been observed at developmentally important genes in w/c the H3K27me3 repressive mark is maintained by EZH2 (Nat Genet 2007;232–236).
• Aberrant nucleosome positioning: Occurs w/other epigenetic marks, but also can be a consequence of chromatin remodeling complex suppression or gene Mt. Eg, two subunits of SWI-SNF are silenced in 15–20% of 1° NSCLC (Cancer Res. 2003;560–566).
• Altered expression of histone variants: Histone variants have a limited scope under biologic conditions. Eg, H2A.Z functions as a chromatin boundary element, appearing on either side of nucleosome free regions around transcription start sites & facilitates transcription. Overexpression of H2A.Z results in promotion of cell cycle progression. H2A.Z loss is a/w spreading of repressive chromatin marks, w/c can result in hypermethylation of tumor suppressors (Mol Cell 2009;271–284).
• Altered microRNA expression: Multiple microRNAs can be dysregulated. Egs include repression of miRNAs targeting growth-promoting genes such as BCL2 in CLL (mir-15 + mir-16), RAS in lung ca (let-7), BCL6 in prostate & bladder ca (mir-127), & EZH2 in bladder ca (mir-101). Upregulation of miRNAs targeting growth inhibitory pathways also occurs such as PTEN in glioblastoma (mir-21), & likely AID in breast, lung, & various heme malignancies (mir-155). These expression level changes can be mediated epigenetically as well (Carcinogenesis 2010;27–36).
• 5-azacytidine, decitabine: Prevent propagation of cytosine methylation, FDA approved for tx of MDS. Also cytotoxic.
• Vorinostat, romidepsin: Pan-HDAC inhibitors, FDA approved for tx of CTCL
Figure 4-9 http://commonfund.nih.gov/epigenomics/figure.aspx