Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4

Abstract

In the earliest stages of antigen receptor assembly, D and J segments of the Ig heavy chain and T cell receptor ␤ loci are recombined in B and T cells, respectively, whereas the V segments are not. Distinct distribution patterns of various histone modifications and the nucleosome-remodeling factor BRG1 are found at ''active'' (DJ) and ''inactive'' (V) regions. Striking ''hotspots'' of histone H3 dimethylated at lysine 4 (di-Me H3-K4) are localized at the ends of the active DJ domains of both the Ig heavy chain and T cell receptor ␤ loci. BRG1 is not localized to specific sequences, as it is with transcriptional initiation, but rather associates with the entire active locus in a pattern that mirrors acetylation of histone H3. Within some inactive loci marked by H3-K9 dimethylation, two distinct levels of methylation are found in a nonrandom genesegment-specific pattern. We suggest that the hotspots of di-Me H3-K4 are important marks for locus accessibility. The specific patterns of modification imply that the regulation of V(D)J recombination involves recruitment of specific methyltransferases in a localized manner.T he chromatin in the nucleus of eukaryotic cells is regulated to permit or exclude access of the enzymatic machinery for processes such as transcription and recombination. Specific regulatory sequences in the DNA are ultimately responsible for this regulation, serving as binding sites for proteins or protein complexes that recruit specific chromatin-modifying activities. In the case of transcriptional regulation, specific DNA-binding activators or repressors recruit histone-modifying enzymes and nucleosome remodeling complexes, generating localized modifications of the chromatin that govern the access of the transcription machinery (reviewed in refs. 1 and 2). In addition to such localized chromatin modifications, there are developmentally regulated large-scale reorganizations of chromatin structure into active and inactive domains [e.g., ␤-globin genes in chickens (3) and the mating-type locus in Schizosaccharomyces pombe (4)] (reviewed in ref. 5).A variety of covalent histone modifications are associated with active or inactive chromatin (6-8). Acetylation of histones H3 and H4 is well known to mark transcriptionally active chromatin. Dimethylation of histone H3 on lysine 4 (di-Me H3-K4) is often observed at active loci in yeast (4), Tetrahymena (9), and chicken (3), although associations with silent loci have also been reported (10). In contrast, dimethylation of histone H3 on lysine 9 (di-Me H3-K9) is often, if not always, correlated with regions of silent inactive chromatin (11).Coordination of the series of DNA rearrangement events required to assemble Ig and TCR genes from component V, D, and J segments presents a highly complex regulatory problem (reviewed in refs. 12 and 13). There are seven structurally unique antigen receptor loci, some spanning 3 or 4 megabases, each composed of multiple V, J, and sometimes D segments, along with nonrearranging constant (C) gene segments. Rearrangement is ...

Elements between the IgH variable (V) and diversity (D) clusters influence antisense transcription and lineage-specific V(D)J recombination

“…The large intergenic region between the most 3′ functional V H segment (V H 81X) (11) and the most 5′ D segment (DFL16.1) (27) has a number of properties suggestive of a potential regulatory function, including multiple DNase I hypersensitivity sites, differential histone modifications in V H and D regions in pro-B versus pro-T cells, and two defined CTCF binding sites located several kilobases upstream of DFL16.1 (25,(28)(29)(30). To evaluate potential regulatory properties of the V H to D intergenic region, we used the Velocigene technology (31) to create an IgH allele termed ΔV H -D that harbors a 109.8-kb deletion that encompasses the region from 6.4 kb 5′ of V H 81X (V H 7183.a2.3) to 847 bp 3′ of DFL16.1 ( Fig.…”

The PHD domain of the sea urchin RAG2 homolog, SpRAG2L, recognizes dimethylated lysine 4 in histone H3 tails

“…These can be categorized as "writers" (adding modifications), "erasers" (removing such modification), or "readers" (recognizing such modifications) [ 21 ]. One chromatin mark that correlates well with accessible areas in antigen receptor gene loci is hypermethylation of H3K4 [ 24,27,[35][36][37]. Recently, strong experimental evidence was provided that the RAG2 PHD domain is a histone code reader, rendering the recombinase highly active when in contact with nucleosomes displaying H3K4me3 [ 24,27 ].…”

The SWI/SNF complex and cancer

“…BRM and BRG1 play important roles in the immune system SWI/SNF plays an important role in immune responses, T-cell development and recombination events (Golding et al, 1999;Agalioti et al, 2000;Kwon et al, 2000;Spicuglia et al, 2002;Morshead et al, 2003). The SWI/ SNF complexes have been shown to remodel chromatin in such a way as to drive consecutive developmental transitions in T cells in response to external stimuli.…”

“…Variable-diversity-joining (V(D)J) recombination has also been shown to be mediated by SWI/SNF. BRG1 stimulates in vitro recombination of chromatin and is also bound to regions in the T-cell receptor (TCR) and immunoglobulin loci that take part in recombination events (Golding et al, 1999;Kwon et al, 2000;Spicuglia et al, 2002;Morshead et al, 2003;Patenge et al, 2004). More recent studies have shown SWI/SNF to be fundamental to the promoter-directed assembly of TCR-b (TCRB) genes (Osipovich et al, 2007); SWI/ SNF is recruited to promoters and then facilitates recombination by exposing segments of genomic DNA to V(D)J recombinase.…”