Nucleosome structure completely inhibits in vitro cleavage by the V(D)J recombinase

Golding, Amit; Chandler, Simon; Ballestar, Esteban; Wolffe, Alan P.; Schlissel, Mark S.

doi:10.1093/emboj/18.13.3712

Cited by 133 publications

(98 citation statements)

References 60 publications

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“…Recent data suggests that nucleosomal remodeling may be the critical change required to allow the V(D)J recombinase access to target sites (15,38,39). The role of demethylation may be to alter the chromatin structure of the kappa locus, providing a permanent change in the accessibility of the locus for transcription.…”

Section: Discussionmentioning

confidence: 99%

V(D)J recombination is not activated by demethylation of the kappa locus

Cherry

Beard

Jaenisch

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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V(D)J recombination is thought to be regulated by changes in the accessibility of target sites, such as modulation of methylation. To test whether demethylation of the kappa locus can activate recombination, we generated two recombinationally active B cell lines in which the gene for maintenance of genomic DNA methylation, Dnmt1, was flanked with loxP sites. Transduction with a retrovirus expressing both the cre recombinase and green fluorescent protein allowed us to purify recombinationally active cells devoid of methylation. Loss of methylation of the kappa locus was not sufficient to activate recombination, although transcription was activated in one line. It appears that demethylation of the kappa locus is not the rate-limiting step for altering accessibility and thus regulated demethylation does not generate specificity of recombination.T he V(D)J recombination machinery assembles antigen receptor genes during lymphoid development from gene segments flanked by recombination signal sequences (1). This nonhomologous site-specific recombination process is precisely controlled by a number of different regulatory mechanisms. For one thing, the coexpression of the lymphoid-specific Rag-1 and Rag-2 genes occurs restrictively in developing B and T cells, ensuring that only the appropriate cell types are recombinationally active (2). A second level of regulation also controls lineage specificity: complete Ig gene rearrangement occurs only in B cells, whereas T cell receptor genes rearrange exclusively in T cells (3). Moreover, within developing B and T cells there are temporal controls over specific gene segment usage (4, 5). Additionally, allelic exclusion ensures that each B or T cell generates only one functional antigen receptor even though two alleles exist at each locus (6).This remarkable ability of the recombination machinery to target only a very small subset of substrates within a given cell together with the fact that a single recombinase is required for this process has led to the hypothesis that the accessibility of DNA targets to the recombination machinery is tightly controlled (7-9). Recombination loci are thought to be inaccessible until they are modified to allow the recombination machinery access to target sites. Changes in chromatin structure, transcriptional activity, or DNA methylation at each locus have been identified that correlate with recombinational activity. Many studies have attempted to define the cis-acting sequences and trans-acting factors required to regulate this process. Distinct enhancer sequences present within individual loci must be controlled by different trans-acting proteins to allow developmentally regulated changes in the accessibility of each locus to occur.DNA methylation has been shown to regulate chromatin structure, leading to changes of gene expression (10). Additionally, methylation has been correlated with Ig gene regulation: both the heavy chain and light chain are hypermethylated in cells in which they are not recombined (11,12). Concomitant with V(D)J rearrang...

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Section: Discussionmentioning

confidence: 99%

V(D)J recombination is not activated by demethylation of the kappa locus

Cherry

Beard

Jaenisch

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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“…In vitro studies have confirmed that nucleosome position can influence V(D)J cleavage (20,21). An RSS assembled into a mononucleosome is refractory to cleavage by the Rag1/2 recombinase, but the precise position of the RSS with respect to the dyad axis governs the extent of inhibition.…”

Section: Significancementioning

confidence: 93%

Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination

Pulivarthy

Lion

Kuzu

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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We show that the physical distribution of nucleosomes at antigen receptor loci is subject to regulated cell type-specific and lineagespecific positioning and correlates with the accessibility of these gene segments to recombination. At the Ig heavy chain locus (IgH), a nucleosome in pro-B cells is generally positioned over each IgH variable (VH) coding segment, directly adjacent to the recombination signal sequence (RSS), placing the RSS in a position accessible to the recombination activating gene (RAG) recombinase. These changes result in establishment of a specific chromatin organization at the RSS that facilitates accessibility of the genomic DNA for the RAG recombinase. In contrast, in mouse embryonic fibroblasts the coding segment is depleted of nucleosomes, which instead cover the RSS, thereby rendering it inaccessible. Pro-T cells exhibit a pattern intermediate between pro-B cells and mouse embryonic fibroblasts. We also find large-scale variations of nucleosome density over hundreds of kilobases, delineating chromosomal domains within IgH, in a cell typedependent manner. These findings suggest that developmentally regulated changes in nucleosome location and occupancy, in addition to the known chromatin modifications, play a fundamental role in regulating V(D)J recombination. Nucleosome positioning-which has previously been observed to vary locally at individual enhancers and promoters-may be a more general mechanism by which cells can regulate the accessibility of the genome during development, at scales ranging from several hundred base pairs to many kilobases.T he diverse repertoire of antigen receptors in vertebrates is generated by an ordered series of somatic site-specific DNA rearrangement events, collectively termed V(D)J recombination. Antigen receptor genes are assembled from V, D, and J gene segments organized into seven different loci [T-cell receptor (TCR) α, β, γ, and δ, and Ig H, κ, and λ], each of which undergoes a series of recombination reactions to generate a functional TCR or B-cell receptor (BCR) (1, 2) Rearrangement is lineage-specific, such that BCR genes are fully rearranged only in B cells and TCR genes are assembled only in T cells. Rearrangement also occurs in a preferred temporal order. For example, at the human and murine IgH loci, joining of D to J segments precedes V to DJ joining, and IgH joining precedes joining at Igκ (or Igλ) (3). In addition, recombination at several loci shows "allelic exclusion": Functional VDJH or VJκ/Jλ joining occurs only on one allele (4).Recombination is initiated by the lymphocyte-specific recombination activating gene (RAG)1/RAG2 endonuclease. RAG1/2 cleaves at the recombination signal sequences (RSSs) flanking all antigen receptor gene segments. The consensus RSS consists of a heptamer sequence directly adjacent to the coding element and an A/T-rich nonamer separated from the heptamer by a spacer region of conserved length (12 or 23 bp) but relatively nonconserved sequence. The broken ends are then joined with the aid of DNA repair proteins,...

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“…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.…”

Section: Brm and Brg1 Control The Expression Of Genes That Are Involvmentioning

confidence: 99%

“…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.…”

Section: Brm and Brg1 Control The Expression Of Genes That Are Involvmentioning

confidence: 99%

The SWI/SNF complex and cancer

2009

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The mammalian SWI/SNF complexes mediate ATPdependent chromatin remodeling processes that are critical for differentiation and proliferation. Not surprisingly, loss of SWI/SNF function has been associated with malignant transformation, and a substantial body of evidence indicates that several components of the SWI/SNF complexes function as tumor suppressors. This review summarizes the evidence that underlies this conclusion, with particular emphasis upon the two catalytic subunits of the SWI/SNF complexes, BRM, the mammalian ortholog of SWI2/SNF2 in yeast and brahma in Drosophila, and Brahma-related gene-1 (BRG1).

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Nucleosome structure completely inhibits in vitro cleavage by the V(D)J recombinase

Cited by 133 publications

References 60 publications

V(D)J recombination is not activated by demethylation of the kappa locus

V(D)J recombination is not activated by demethylation of the kappa locus

Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination

The SWI/SNF complex and cancer

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