DNA methylation, histone code, chromatin remodeling, X-inactivation, imprinting.
Epigenetics And Chromatin
Epigenetics
Heritable changes in gene expression not caused by DNA sequence change. Mediated by DNA methylation, histone modifications, chromatin…
DNA methylation (5mC)
Covalent methyl group on cytosine C5, primarily in CpG dinucleotides in mammals. Written by DNMT3A/B (de novo) + DNMT1 (maintenance); read…
CpG island
~500-2000 bp region with elevated CpG frequency (>50%) and lower methylation, commonly at promoters of ~70% of mammalian genes. Aberrant…
Histone post-translational modification
Covalent tags on histone tails (H3/H4 Lys/Arg/Ser): acetylation, methylation, phosphorylation, ubiquitination, SUMOylation. Form a 'histone…
H3K4me3
Trimethylation of H3 Lys4 — active-promoter mark. Written by SET1/MLL; bound by TAF3/CHD1 (PHD, chromo). Rare at repressed genes; bivalent…
H3K27me3
Trimethylation of H3 Lys27 — Polycomb-mediated silencing mark. Written by PRC2 (EZH2 catalytic); read by PRC1 (CBX). Broad repression of…
Histone acetylation
Lysine acetylation (Kac) by HATs (p300, CBP, GCN5) neutralises positive charge, loosens chromatin, recruits bromodomain readers (BET…
X-chromosome inactivation
Dosage-compensation mechanism in female mammals: one of two X chromosomes randomly silenced per cell via XIST lncRNA-mediated spreading of…
Genomic imprinting
Parent-of-origin-specific silencing via differentially methylated regions (DMRs) set in the germline. ~100 imprinted loci in mammals;…
Chromatin remodeller
ATP-dependent complexes (SWI/SNF, ISWI, CHD, INO80) slide or eject nucleosomes. Frequently mutated in cancer (SMARCA4, ARID1A). Regulates…
Histone-code framework
Strahl & Allis 2000: combinatorial post-translational histone modifications (H3K4me3, H3K9me3, H3K27me3, H3K36me3, H3K27ac, H4K16ac, …)…
DNA methylation / CpG-island framework
CpG dinucleotides are mostly methylated (5-methylcytosine) in mammalian genomes; CpG islands (~70% of gene promoters) are unmethylated. …
Histone code (Jenuwein-Allis 2001)
Jenuwein-Allis 2001 histone-code hypothesis; modern Suganuma-Workman 2011 + chromatin-code 100+ modifications mapped.
DNA methylation (Bird 1985)
A Bird 1985 CpG islands; modern DNMT1/3 + TET enzymes; methylation-clock Horvath 2013.
Polycomb-Trithorax (Pirrotta 1997)
Pirrotta 1997 + Schwartz-Pirrotta 2007 PcG/TrxG developmental memory; modern PRC1 + PRC2 cancer-targets EZH2.
X-inactivation (Lyon 1961)
M Lyon 1961 X-chromosome inactivation in females; XIST RNA + Tsix antisense; modern Plath review 2002 chromatin-mechanism.
Imprinting (Bartolomei 1991)
Bartolomei-Webber-Brunkow 1991 H19/IGF2 imprinting; modern parent-of-origin disorders Prader-Willi + Angelman.
Hi-C (Lieberman-Aiden 2009)
Lieberman-Aiden 2009 Hi-C 3D genome; A/B compartments + TADs + loops; modern Micro-C + ChIA-PET fine-mapping.
Waddington landscape (1957)
C Waddington 1957 epigenetic-landscape; modern modern Wang 2011 quantitative-landscape + 2024 single-cell-velocity reconstruction.
DNA methylation (Bird 1985)
A Bird 1985 CpG-island; modern modern foundational + DNMT1/3a/3b + TET-active-demethylation Tahiliani 2009.
Polycomb/Trithorax (Paro 1991)
R Paro 1991 + Müller 2002 PRC2-EZH2-H3K27me3; modern modern foundational + EED-bound-allosteric + tazemetostat-DLBCL approval 2020.
Nucleosome (Luger 1997)
K Luger-T Richmond 1997 nucleosome 2.8Å; modern modern hexasome + 2024 cryo-EM mononucleosome dynamic + chromatosome H1.
TAD (Dixon 2012)
J Dixon-B Ren 2012 + Nora 2012 topologically-associating-domain; modern modern Hi-C + Micro-C + 2024 single-cell-Hi-C dynamics.
Paramutation (Coe 1959)
E Coe 1959 + Chandler 2010 paramutation maize-RdDM; modern modern small-RNA-mediated transgenerational-inheritance + Drosophila MERVL.