Greater Than the Sum of Parts: Complexity of the Dynamic Epigenome

Abstract

Information encoded in DNA is interpreted, modified, and propagated as chromatin. The diversity of inputs encountered by eukaryotic genomes demands a matching capacity for transcriptional outcomes provided by the combinatorial and dynamic nature of epigenetic processes. Advances in genome editing, visualization technology, and genome-wide analyses have revealed unprecedented complexity of chromatin pathways, offering explanations to long-standing questions and presenting new challenges. Here, we review recent findings, exemplified by the emerging understanding of crossregulatory interactions within chromatin, and emphasize the pathologic outcomes of epigenetic misregulation in cancer.

Figure 1. Hierarchical organization of epigenetic regulation

Dynamic and reversible epigenetic processes generate diverse regulatory environment. DNA methylation (1) (mC, methylcytosine – closed circle) may result in eviction of DNA-binding proteins, or recruitment of methyl-binding factors. mC oxidation (shown is hydroxymethylcytosine, hmC) generates additional diversity. Core and linker histone exchange, including variant histone incorporation (2), regulate local DNA accessibility, and, together with histone modifications (3), introduce local variations to chromatin structure. These are interpreted by the “reader” machinery (3) and drive higher-order chromatin organization and nuclear topology (4). Red arrows above and below indicate crosstalk between regulatory layers.

Figure 2. Structural basis of histone variant dynamics: implications of single amino acid differences

(A-C) Glycine at position 90 is critical for H3.3 recognition by chaperone DAXX. (A) Amino acid sequence of histone H3.1 and variant H3.3 α2 helix, with three distinct residues in bold. G90 is highlighted in red. (B, C) Ribbon diagram of DAXX-H3.3-H4 complex structure, with DAXX shown in gray, H3.3 in blue and H4 in green [PDB 4H9N (Elsasser et al., 2012)]. Variant-specific interface is shown is expanded in (C). G90 is highlighted in red, nearby amino acid side chains are shown. (D-F) Structural basis for H2A.Z eviction by chaperone ANP32E. (D) Amino acid sequence of histone H2A and variant H2A.Z αC-helix. Glycine in position 98 (highlighted) prevents the helix extension in canonical H2A; five additional amino acids can extend the helix (αC-ext) in H2A.Z variant. Distinct amino acid residues are shown in bold. (E) Within the nucleosome, H2A.Z αC-helix is short and accommodates contacts with C-terminus of H4 [PDB: 1F66 (Suto et al., 2000)]. (F) Bound by ANP32E (teal), H2A.Z αC-helix is extended (red) and is incompatible with the H4 interface, resulting in eviction from the nucleosome [PDB: 4CAY (Obri et al., 2014)].

Figure 3. Diverse processes are defined by extensive cross-talk between epigenetic circuits

(A) Regulation of DNA methylation. Heterochromatin protein 1 (HP1) binds H3 K9me2/3 (gray circle) and recruits de novo and maintenance DNA methyltransferases (1), which in turn associate with H3 K9-specific methyltransferases Suv39h1, Setdb1 and G9a (2). Other targeting mechanisms include unmodified H3 tail recognition by Dnmt3 ADD domain (3) and linker histone-dependent recruitment (4). Histone H3 K4 methylation (green circle) (5) prevents Dnmt3 association and protects transcription factor (TF) binding sites from methylation (6). Additionally, PWWP domain of Dnmt3 reads H3 K36 methylation (orange circle) and is required for Dnmt recruitment to the gene bodies (7). (B) Hierarchical recruitment and spreading of Polycomb complexes PRC1 and PRC2. Unmethylated CpG islands are bound by KDM2B (1), which recruits variant PRC1 complex; the RING1B E3 ubiquitin ligase then monoubiquitylates H2A K119 (red circle) (2), which facilitates recruitment of PRC2 (3) and methylation of H3 K27 (blue circle) (4). Processive PRC2 spreading (5) expands the K27me domain, which in turn facilitates PRC1 recruitment, which recognizes K27me via CBX subunit (6) and in turn, expands the K119 ubiquitylation (7). This may counteract histone replacement by chaperone FACT (8) and result in chromatin compaction (8). For clarity, some labels are omitted from the schematic. (C) DNA double-stranded break response relies on a cascade of dynamic core and linker histone modifications. Initiated by ATM recruitment to the DSB site (1) and phosphorylation of H2A.X variant at serine 139 (2), the cascade is amplified by ATM1-MDC1 positive feedback loop (3), which facilitates recruitment of ubiquitin ligases RNF8/UBC13 (4). K63-linked polyubiquitylation of linker histone then recruits RNF168 (5), which, together with yet unidentified E2 ligase, monoubiquitylates H2A (6). RNF8 then extends the H2A ubiquitylation placed by RNF168 (7), which serves as recruitment platform for many DNA damage response factors (BRCA1 and RAP80 are shown) (8).

Figure 4. Binary switches and cooperative activators: roles of histone phosphorylation

(A) Sequences of H3 and H1E N-terminal tails, with stereotypical ARKS motifs highlighted. (B) H3K9me2/3 and H1E K26me2/3 (gray circles) recruit HP1 in interphase cells. phosphorylation of adjacent lysines by cell-cycle dependent kinase Aurora B (yellow circles) (2) results in HP1 eviction from mitotic chromosomes (3). (C) MYC recruits PIM1 kinase to facilitate H3 S10 phosphorylation (1). Bound by 14-3-3 proteins (2) which in turn recruit histone acetyltransferase MOF, or by GCN5 acetyltransferase (3), S10 phosphorylation facilitates acetylation-dependent transcriptional activation, recruiting bromodomain-containing factors (BRD4 is shown) (4).

Figure 5. Reciprocal misregulation of Polycomb-dependent silencing by alterations of H3 K36 methyltransferase function: the yin and yang of histone methylations

(A) In wild type cells, gene expression is correlated positively with histone H3 K36 methylation (yellow circles) and negatively with K27 methylation (blue circles). The domains demarcated by these two modifications (yellow and blue rectangles) are non-overlapping. (B) NSD2 overexpression in t(4;14) multiple myeloma leads to expansion of H3 K36me, which counteracts PcG complex activity and causes PcG relocalization to few highly methylated ectopic domains (darker shade of blue), resulting in aberrant gene repression. (C) Histone H3 K36M mutation in chondroblastoma dominantly inhibits NSD2 methyltransferase activity, resulting in global loss of H3 K36 methylation. Loss of counterbalancing signal causes spreading of PcG from well-demarcated repressed regions to intergenic “sinks” (lighter shade of blue), resulting in ectopic gene activation.