Germline Deletion of <i>Igh</i> 3′ Regulatory Region Elements hs 5, 6, 7 (hs5–7) Affects B Cell-Specific Regulation, Rearrangement, and Insulation of the <i>Igh</i> Locus

Volpi, Sabrina A.; Verma-Gaur, Jiyoti; Hassan, Rabih; Zhang, Ju; Roa, Sergio; Chatterjee, Sanjukta; Werling, Uwe; Hou, Harry; Will, Britta; Steidl, Ulrich; Scharff, Matthew D.; Edelman, Winfried; Feeney, Ann J.; Birshtein, Barbara K.

doi:10.4049/jimmunol.1102763

Cited by 45 publications

(50 citation statements)

References 66 publications

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“…Downstream of HS1-4 localizes another subset of hypersensitive sites (HS5-7) that possess conserved, overlapping CTCF and cohesin binding sites [30]. The deletion of HS5-7 region had no effect on CSR [31].…”

Section: Resultsmentioning

confidence: 99%

Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation

et al. 2014

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The immunoglobulin heavy chain locus (Igh) features higher-order chromosomal interactions to facilitate stage-specific assembly of the Ig molecule. Cohesin, a ring-like protein complex required for sister chromatid cohesion, shapes chromosome architecture and chromatin interactions important for transcriptional regulation and often acts together with CTCF. Cohesin is likely involved in B cell activation and Ig class switch recombination. Hence, binding profiles of cohesin in resting mature murine splenic B lymphocytes and at two stages after cell activation were elucidated by chromatin immunoprecipitation and deep sequencing. Comparative genomic analysis revealed cohesin extensively changes its binding to transcriptional control elements after 48 h of stimulation with LPS/IL-4. Cohesin was clearly underrepresented at switch regions regardless of their activation status, suggesting that switch regions need to be cohesin-poor. Specific binding changes of cohesin at B-cell specific gene loci Pax5 and Blimp-1 indicate new cohesin-dependent regulatory pathways. Together with conserved cohesin/CTCF sites at the Igh 3′RR, a prominent cohesin/CTCF binding site was revealed near the 3′ end of Cα where PolII localizes to 3′ enhancers. Our study shows that cohesin likely regulates B cell activation and maturation, including Ig class switching.

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Section: Resultsmentioning

confidence: 99%

Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation

et al. 2014

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“…Thus, recombination of distal but not proximal V H genes is inhibited in mice deficient in the histone-modifying enzyme EZH2 and in different transcription factors involved in V(D)J recombination, such as PAX5, YY1, and Ikaros (35)(36)(37)(38). Mutations targeting various cis-acting elements at the IgH locus similarly showed a differential effect on germ line transcription and recombination of proximal versus distal V H genes (12,16,(39)(40)(41)(42). Importantly, deletion of the 3=RR in the context of the 120-kb deletion had no effect on long-range interactions across the IgH locus in RAG2-deficient pro-B cells (22).…”

Section: Discussionmentioning

confidence: 97%

Developmental Switch in the Transcriptional Activity of a Long-Range Regulatory Element

Braikia

Conte

Moutahir

et al. 2015

Molecular and Cellular Biology

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e Eukaryotic gene expression is often controlled by distant regulatory elements. In developing B lymphocytes, transcription is associated with V(D)J recombination at immunoglobulin loci. This process is regulated by remote cis-acting elements. At the immunoglobulin heavy chain (IgH) locus, the 3= regulatory region (3=RR) promotes transcription in mature B cells. This led to the notion that the 3=RR orchestrates the IgH locus activity at late stages of B cell maturation only. However, long-range interactions involving the 3=RR were detected in early B cells, but the functional consequences of these interactions were unknown. Here we show that not only does the 3=RR affect transcription at distant sites within the IgH variable region but also it conveys a transcriptional silencing activity on both sense and antisense transcription. The 3=RR-mediated silencing activity is switched off upon completion of V H -DJ H recombination. Our findings reveal a developmentally controlled, stage-dependent shift in the transcriptional activity of a master regulatory element. The spatial and temporal control of gene expression in metazoans is effected by regulatory elements that are often located far from gene promoters (1). This pattern of gene expression regulation is a hallmark of antigen receptor loci, whose expression involves both transcription and recombination. The mouse IgH locus contains ϳ195 variable (V H ) genes subdivided into domainorganized gene families, including the distal V H family, by far the largest, and the proximal V H family. The V H genes are followed by a dozen diversity (D) segments, 4 joining (J H ) segments, and 8 constant (C H ) genes (2, 3) (Fig. 1A, top scheme). The assembly of an IgH variable region exon through V(D)J recombination occurs in early developing B cells in an ordered manner, first D to J H and then V H to DJ H . While the first recombination step (D-J H ) can also be detected in developing T cells, V H -DJ H recombination is strictly B cell specific (4).In addition to its B cell lineage specificity, V H -DJ H rearrangement is regulated by allelic exclusion, which enables monoallelic expression of only one IgH locus by a given B cell (4, 5). In this process, a productive V(D)J rearrangement on one allele ultimately leads to surface expression of a heavy chain which signals arrest of V H -DJ H recombination on the second allele. If the first rearrangement is not productive (i.e., no heavy chain production), then the second allele can undergo V H -DJ H recombination (4, 5). There is considerable evidence to support the notion that V H -DJ H rearrangement is the regulated step in IgH allelic exclusion and its maintenance through a feedback mechanism (4, 5), although the molecular mechanisms through which feedback signaling inhibits V H -DJ H recombination remain unclear.Another level of regulation of V H -DJ H recombination relates to the physical location of V H gene segments within the variable domain. Indeed, several gene-targeted studies showed that recombinations of the distal and p...

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“…Hence, intrachromosomal interactions that facilitate the spatial proximity of various V segments with the RC are a necessary prerequisite for VDJ recombination at the AgR loci (20) and are manifested as "locus contraction," toward which CTCF/cohesin complexes can contribute. At the Igh locus, a long-range interaction between IGCR1 and CBS located downstream of the 3= regulatory region (3=RR) influences the Vh segments for VDJ recombination; the Vh usage gets altered upon the deletion of CBS from either of these elements (16,21,22). Further, CTCF/cohesin complex contributes to the organization of the Igh locus into rosettes whose spatial proximity to the RC provides equal opportunity for distal and proximal Vh segments for VDJ recombination (23)(24)(25).…”

mentioning

confidence: 99%

Chromatin Domain Organization of the TCRb Locus and Its Perturbation by Ectopic CTCF Binding

Rawat

Jalan

Sadhu

et al. 2017

Molecular and Cellular Biology

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CTCF-mediated chromatin interactions influence organization and function of mammalian genome in diverse ways. We analyzed the interactions among CTCF binding sites (CBS) at the murine TCRb locus to discern the role of CTCFmediated interactions in the regulation of transcription and VDJ recombination. Chromosome conformation capture analysis revealed thymocyte-specific long-range intrachromosomal interactions among various CBS across the locus that were relevant for defining the limit of the enhancer Eb-regulated recombination center (RC) and for facilitating the spatial proximity of TCRb variable (V) gene segments to the RC. Ectopic CTCF binding in the RC region, effected via genetic manipulation, altered CBS-directed chromatin loops, interfered with RC establishment, and reduced the spatial proximity of the RC with Trbv segments. Changes in chromatin loop organization by ectopic CTCF binding were relatively modest but influenced transcription and VDJ recombination dramatically. Besides revealing the importance of CTCF-mediated chromatin organization for TCRb regulation, the observed chromatin loops were consistent with the emerging idea that CBS orientations influence chromatin loop organization and underscored the importance of CBS orientations for defining chromatin architecture that supports VDJ recombination. Further, our study suggests that in addition to mediating long-range chromatin interactions, CTCF influences intricate configuration of chromatin loops that govern functional interactions between elements.KEYWORDS antigen receptor loci, CTCF, VDJ recombination, chromatin loop, chromatin organization S patial and temporal regulation of nuclear processes is intricately related to chromatin structure and organization since it can influence the interactions among regulatory elements. The mechanisms underlying these complex interactions are not completely understood. CTCF was identified to be the trans-acting factor that can organize an insulator and block enhancer-promoter interaction in a position dependent manner (1-3). Subsequently, CTCF has emerged as an important architectural protein that can influence interchromosomal and intrachromosomal interactions and impact nuclear functions largely in collaboration with cohesin (4, 5). Genome-wide investigations, including chromatin immunoprecipitation (ChIP), 4C, Hi-C, and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), etc., have established an important role of CTCF in organization of topologically associated domains (TADs) (6, 7). In addition, CTCF binding sites (CBS) located within TADs can contribute to celltype-specific chromatin loop organization by facilitating, as well as inhibiting, the interactions between regulatory elements. Locus-specific genetic analysis relying on deletion and inversion of CBS has revealed CBS orientation-dependent chromatin loop organization and its influence on transcriptional regulation (8-11). However, several aspects regarding the ability of CBS to organize chromatin and regulate function

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Germline Deletion of Igh 3′ Regulatory Region Elements hs 5, 6, 7 (hs5–7) Affects B Cell-Specific Regulation, Rearrangement, and Insulation of the Igh Locus

Cited by 45 publications

References 66 publications

Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation

Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation

Developmental Switch in the Transcriptional Activity of a Long-Range Regulatory Element

Chromatin Domain Organization of the TCRb Locus and Its Perturbation by Ectopic CTCF Binding

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