Bromodomain -> acetyllysine in H4 Lys16

Lysine Methylation H3K4me3 -> active transcription start sites H3K9me3 -> constitutive heterochromatin H3K27me3 -> silent genes in euchromatic regions or facultative heterochromatin Bivalent domains -> stem-cell development H3K4me3 + H3K27me3 Histone lysine methylation in the recruitment of DNA damage repair proteins H3K4me3 -> near the promoters and 5 ends of highly transcribed genes, H3K4me2 -> coding region of genes that are either active or poised for transcription H3K36me3-> highly enriched throughout the entire transcribed region Chromodomains -> di- and trimethyllysine in H3K9 and H3K27 contexts Heterochromatin protein-1 (HP1) --> H3K9me3 + H3K9me2 Polycomb --> H3K27me3 Double chromodomains Chromo helicase DNA-binding (CHD) proteins includes SWI/SNF nucleosome remodeling complex target methyllysine in H3K4 Double tudor domains Jumonji domaincontaining protein-2A (JMJD2A) H3K4me3 Plant homeodomain (PHD) fingers bind H3K4me3 -> recruiting or stabilizing downstream complexes BPTF -> largest subunit of the nucleosomal remodeling factor (NURF) ATP-dependent chromatinremodeling complex Yng1p -> part of Nucleosomal acetyltransferase of histone H3 (NuA3) complex NuA3 -> H3-specific H3K14 HAT -> acetylation for TFIID basal transcription machinery

Cysteine-rich ADD domain ->Unmodified H3K4 DNMT3L -> lacks intrinsic methyltransferase Germline-specific DNA methylation defective in mice deficient in the DNMT3L

WD40 protein WDR5 -> Unmodified H3R2 WD40-repeat protein WDR5 - common component of SET1-family histone methyltransferase complexes Binding to H3R2 promotes H3K4 3Xme

Phosphoserine marks On all core histone tails & linker histone H1 Important in cell-cycle control, DNA damage repair and transcriptional regulation 14-3-3 Proteins -> phosphoserine in H3S10 There are many examples of two or more putative histone-binding modules linked within the same protein or within the same multisubunit complex, allowing for combinatorial PTM readout at the histone or nucleosomal level. 2 Domains, 1 binding site double chromodomains of CHD1 double tudor domains of JMJD2A tandem tudor domains of 53BP1 tandem BRCT domains of MDC1 TAF1 double bromodomain -> 2 x acetylated histones on H4 tail MBT repeats of L3MBTL1: two of the three repeats may be used simultaneously to engage two sites/marks in a histone tail

modules that bind H3K4me3 are found in both complexes that activate transcription and complexes that repress it. The biophysics of multivalency may resolve this conundrumfor example, an activating complex might bind H3K4me3 and additional activating PTMs, whereas a silencing complex might also bind H3K4me3 but simultaneously engage silencing PTMs.