Two Forms of Loops Generate the Chromatin Conformation of the Immunoglobulin Heavy-Chain Gene Locus

Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA.
Cell (Impact Factor: 32.24). 10/2011; 147(2):332-43. DOI: 10.1016/j.cell.2011.08.049
Source: PubMed


The immunoglobulin heavy-chain (IgH) gene locus undergoes radial repositioning within the nucleus and locus contraction in preparation for gene recombination. We demonstrate that IgH locus conformation involves two levels of chromosomal compaction. At the first level, the locus folds into several multilooped domains. One such domain at the 3' end of the locus requires an enhancer, Eμ; two other domains at the 5' end are Eμ independent. At the second level, these domains are brought into spatial proximity by Eμ-dependent interactions with specific sites within the V(H) region. Eμ is also required for radial repositioning of IgH alleles, indicating its essential role in large-scale chromosomal movements in developing lymphocytes. Our observations provide a comprehensive view of the conformation of IgH alleles in pro-B cells and the mechanisms by which it is established.

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    • "With growing appreciation for how three-dimensional structural changes at the locus may bring V genes into proximity of the (D)J rearrangement to which one V gene will ultimately rearrange, current studies are employing cutting edge technologies to further understand this process. Chromatin conformation capture (3C) and its more recent modifications, 4C, 5C, and Hi-C (1–3), have allowed the identification of long-range chromosomal interactions, which facilitate the rearrangement of distant V genes by making critical connections between the V genes and enhancers downstream (4). Next generation sequencing technologies coupled with chromatin immunoprecipitation (ChIP) (ChIP-seq) have allowed us to determine the binding sites of transcription factors throughout the genome as well as the genome-wide epigenetic landscape. "
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    ABSTRACT: At both the immunoglobulin heavy and kappa light chain loci, there are >100 functional variable (V) genes spread over >2 Mb that must move into close proximity in 3D space to the (D)J genes to create a diverse repertoire of antibodies. Similar events take place at the T cell receptor (TCR) loci to create a wide repertoire of TCRs. In this review, we will discuss the role of CTCF in forming rosette-like structures at the antigen receptor (AgR) loci, and the varied roles it plays in alternately facilitating and repressing V(D)J rearrangements. In addition, non-coding RNAs, also known as germline transcription, can shape the 3D configuration of the Igh locus, and presumably that of the other AgR loci. At the Igh locus, this could occur by gathering the regions being transcribed in the VH locus into the same transcription factory where Iμ is being transcribed. Since the Iμ promoter, Eμ, is adjacent to the DJH rearrangement to which one V gene will ultimately rearrange, the process of germline transcription itself, prominent in the distal half of the VH locus, may play an important and direct role in locus compaction. Finally, we will discuss the impact of the transcriptional and epigenetic landscape of the Igh locus on VH gene rearrangement frequencies.
    Frontiers in Immunology 02/2014; 5:49. DOI:10.3389/fimmu.2014.00049
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    • "The mechanisms that control Ig locus contraction are unknown. A small number of transcription factors or protein complexes (YY1, Pax5, CTCF, IKAROS, cohesin, condensin, EZH2) are implicated in the DNA loops needed for V(D)J rearrangement (59, 78, 81–86), but the molecular details and regulatory processes that control this mechanism are not clear. Pax5 binds to multiple repeat sequences in the distal region of the IgH locus (PAIR sequences) and is believed to participate in rearrangement of distal VH genes (83). "
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    ABSTRACT: During B cell development, long-distance DNA interactions are needed for V(D)J somatic rearrangement of the immunoglobulin (Ig) loci to produce functional Ig genes, and for class switch recombination (CSR) needed for antibody maturation. The tissue-specificity and developmental timing of these mechanisms is a subject of active investigation. A small number of factors are implicated in controlling Ig locus long-distance interactions including Pax5, Yin Yang 1 (YY1), EZH2, IKAROS, CTCF, cohesin, and condensin proteins. Here we will focus on the role of YY1 in controlling these mechanisms. YY1 is a multifunctional transcription factor involved in transcriptional activation and repression, X chromosome inactivation, Polycomb Group (PcG) protein DNA recruitment, and recruitment of proteins required for epigenetic modifications (acetylation, deacetylation, methylation, ubiquitination, sumoylation, etc.). YY1 conditional knock-out indicated that YY1 is required for B cell development, at least in part, by controlling long-distance DNA interactions at the immunoglobulin heavy chain and Igκ loci. Our recent data show that YY1 is also required for CSR. The mechanisms implicated in YY1 control of long-distance DNA interactions include controlling non-coding antisense RNA transcripts, recruitment of PcG proteins to DNA, and interaction with complexes involved in long-distance DNA interactions including the cohesin and condensin complexes. Though common rearrangement mechanisms operate at all Ig loci, their distinct temporal activation along with the ubiquitous nature of YY1 poses challenges for determining the specific mechanisms of YY1 function in these processes, and their regulation at the tissue-specific and B cell stage-specific level. The large numbers of post-translational modifications that control YY1 functions are possible candidates for regulation.
    Frontiers in Immunology 02/2014; 5:45. DOI:10.3389/fimmu.2014.00045
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    • "The CCCTC-binding factor CTCF (22) and cohesin were implicated in these loops, which appear to create a topological subdomain that covers the region from 3′RR to IGCR1 (5,21). The proximal and distal VH region also adopt distinct topological substructures that then merge with the 3′ domain to maximize DHJH contacts with the full VH gene repertoire (16,23). Thus, in early B cell development, IgH topology ensures that proximal and distal VH genes have equal opportunites to interact with Eµ. "
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    ABSTRACT: In developing B cells, the immunoglobulin heavy chain (IgH) locus is thought to move from repressive to permissive chromatin compartments to facilitate its scheduled rearrangement. In mature B cells, maintenance of allelic exclusion has been proposed to involve recruitment of the non-productive IgH allele to pericentromeric heterochromatin. Here, we used an allele-specific chromosome conformation capture combined with sequencing (4C-seq) approach to unambigously follow the individual IgH alleles in mature B lymphocytes. Despite their physical and functional difference, productive and non-productive IgH alleles in B cells and unrearranged IgH alleles in T cells share many chromosomal contacts and largely reside in active chromatin. In brain, however, the locus resides in a different repressive environment. We conclude that IgH adopts a lymphoid-specific nuclear location that is, however, unrelated to maintenance of allelic exclusion. We additionally find that in mature B cells—but not in T cells—the distal VH regions of both IgH alleles position themselves away from active chromatin. This, we speculate, may help to restrict enhancer activity to the productively rearranged VH promoter element.
    Nucleic Acids Research 06/2013; 41(14). DOI:10.1093/nar/gkt491 · 9.11 Impact Factor
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