Antisense Intergenic Transcription Precedes <i>Igh</i> D-to-J Recombination and Is Controlled by the Intronic Enhancer E<sub>μ</sub>

Bolland, Daniel J.; Wood, Andrew L.; Afshar, Roshi; Featherstone, Karen; Oltz, Eugene M.; Corcoran, Anne E.

doi:10.1128/mcb.02407-06

Cited by 76 publications

(93 citation statements)

References 69 publications

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“…However, it has been shown that sense and antisense transcription in the distal V H region does not depend upon Eμ (32,33), and we showed here that PAIR antisense transcription is also independent of Eμ. Thus, we predicted that it is likely that YY1 has an additional, and perhaps a more direct, effect on the regulation of antisense transcription.…”

Section: Discussionsupporting

confidence: 49%

Noncoding transcription within the Igh distal V _H region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells

Verma-Gaur

Torkamani

Schaffer

et al. 2012

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

102

122

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Noncoding sense and antisense germ-line transcription within the Ig heavy chain locus precedes V(D)J recombination and has been proposed to be associated with Igh locus accessibility, although its precise role remains elusive. However, no global analysis of germline transcription throughout the Igh locus has been done. Therefore, we performed directional RNA-seq, demonstrating the locations and extent of both sense and antisense transcription throughout the Igh locus. Surprisingly, the majority of antisense transcripts are localized around two Pax5-activated intergenic repeat (PAIR) elements in the distal IghV region. Importantly, long-distance loops measured by chromosome conformation capture (3C) are observed between these two active PAIR promoters and Eμ, the start site of Iμ germ-line transcription, in a lineage-and stage-specific manner, even though this antisense transcription is Eμ-independent. YY1 −/− pro-B cells are greatly impaired in distal V H gene rearrangement and Igh locus compaction, and we demonstrate that YY1 deficiency greatly reduces antisense transcription and PAIR-Eμ interactions. ChIP-seq shows high level YY1 binding only at Eμ, but low levels near some antisense promoters. PAIR-Eμ interactions are not disrupted by DRB, which blocks transcription elongation without disrupting transcription factories once they are established, but the looping is reduced after heat-shock treatment, which disrupts transcription factories. We propose that transcription-mediated interactions, most likely at transcription factories, initially compact the Igh locus, bringing distal V H genes close to the DJ H rearrangement which is adjacent to Eμ. Therefore, we hypothesize that one key role of noncoding germ-line transcription is to facilitate locus compaction, allowing distal V H genes to undergo efficient rearrangement.A ntigen receptors in lymphocytes are assembled in the highly regulated lineage-specific process of V(D)J recombination, which creates a diverse repertoire of Ig and T-cell receptors. In each precursor lymphocyte, one each of the many V, D, and J gene segments at the appropriate receptor loci are juxtaposed to create a V(D)J exon encoding the variable region of the antigen receptor. In B-lineage progenitors, rearrangement occurs first at the Ig heavy chain (Igh) locus, where D H to J H rearrangement occurs first on both alleles, followed by V H to DJ H rearrangement (1). After successful rearrangement of the Igh locus, rearrangement at the Igk light chain locus begins. These successive stages of rearrangement have been proposed to be regulated by differential accessibility of different portions of the loci at the appropriate time for rearrangement (2). Early indications of this stage-specific and lineage-specific accessibility came from the observation that unrearranged gene segments underwent noncoding transcription at the stage immediately preceding their rearrangement (3, 4).The murine Igh locus spans ∼2.8 Mb, of which ∼2.4 Mb contains the 195 V H gene segments (5). The V H genes are divided i...

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Section: Discussionsupporting

confidence: 49%

Noncoding transcription within the Igh distal V _H region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells

Verma-Gaur

Torkamani

Schaffer

et al. 2012

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

102

122

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“…Notably, both B and T lymphocytes have germ-line "μ0" transcripts that initiate from a promoter upstream of the most 3′ D segment (D H Q52) and run downstream through the J H segments, consistent with T lymphocytes making low levels of DJ H rear- rangements (16). In addition, pro-B lymphocytes express low levels of antisense transcripts from the D portion of the locus (17,18). Additional epigenetic modifications associated with V(D)J recombinational accessibility include DNA and/or histone modifications of particular regions and chromosomal positioning of the Ig or TCR loci within the nucleus (15,19,20).…”

mentioning

confidence: 85%

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

Giallourakis

Franklin²,

Guo³

et al. 2010

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

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Ig and T-cell receptor (TCR) variable-region gene exons are assembled from component variable (V), diversity (D) and joining (J) gene segments during early B and T cell development. The RAG1/2 endonuclease initiates V(D)J recombination by introducing DNA double-strand breaks at borders of the germ-line segments. In mice, the Ig heavy-chain (IgH) locus contains, from 5′ to 3′, several hundred V H gene segments, 13 D segments, and 4 J H segments within a several megabase region. In developing B cells, IgH variable-region exon assembly is ordered with D to J H rearrangement occurring on both alleles before appendage of a V H segment. Also, IgH V H to DJ H rearrangement does not occur in T cells, even though DJ H rearrangements occur at low levels. In these contexts, V(D)J recombination is controlled by modulating substrate gene segment accessibility to RAG1/2 activity. To elucidate control elements, we deleted the 100-kb intergenic region that separates the V H and D clusters (generating ΔV H -D alleles). In both B and T cells, ΔV H -D alleles initiated high-level antisense and, at lower levels, sense transcription from within the downstream D cluster, with antisense transcripts extending into proximal V H segments. In developing T lymphocytes, activated germ-line antisense transcription was accompanied by markedly increased IgH D-to-J H rearrangement and substantial V H to DJ H rearrangement of proximal IgH V H segments. Thus, the V H -D intergenic region, and likely elements within it, can influence silencing of sense and antisense germ-line transcription from the IgH D cluster and thereby influence targeting of V(D)J recombination. The activity of the common V(D)J recombinase is regulated in several contexts (8, 9). First, V(D)J recombination is regulated in a lineage-specific manner. Thus, Ig variable-region exons are completely assembled in B cells and not in T cells, whereas TCR variable-region exons are assembled in T but not B cells (6). Second, within a given lineage, V(D)J recombination is highly ordered. The IgH locus contains a large cluster of V H segments, a cluster of 13 D segments, and a cluster of 4 J H segments in a several-megabase region (1). In progenitor (pro) B lymphocytes, IgH variable-region exons are assembled via a process in which D to J H rearrangements occur first and on both alleles, followed by appendage of a V H segment to the DJ H complex (10). Direct joining of a V H to a D is not observed, even though permitted by the 12/23 rule (10). Although not strictly ordered, the most Dproximal V H families and, in particular, the most D-proximal V H 81X gene segment, rearrange more frequently than the most distal V H gene families, such as the V H J558 family (11). After assembly of a productive IgH variable-region exon and expression of a μ heavy chain, pro-B cells advance to the precursor (pre) stage at which Ig light-chain (IgL) variable-region assembly occurs. Similarly ordered V(D)J recombination occurs during assembly of TCR variable-region exons in developing T lineage cells (12). F...

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“…Following D to J recombination, non-coding transcripts are generated from the V genes (7,8). Furthermore, extensive antisense intergenic transcription occurs throughout the D and J domains before D to J, and then throughout the V domain before V to DJ recombination (9,10). Nuclear positioning may also play a role in ordered V(D)J recombination.…”

mentioning

confidence: 99%

“…E is required for efficient D to J recombination (18,19). It acts in part by activation of antisense intergenic transcription, which is abrogated in the DJ region by E deletion (10). It is unclear whether E is required for V to DJ recombination.…”

mentioning

confidence: 99%

“…It is unclear whether E is required for V to DJ recombination. However, the V region is transcribed in its absence (10,18,19), suggesting that additional elements that activate the V region are present in the Igh locus. The only other element identified in the V-D-J region, the PDQ52 promoter/enhancer, is unlikely to play a role because its deletion does not affect germ line V gene transcription (19) or V to DJ recombination (20).…”

mentioning

confidence: 99%

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The Mouse Immunoglobulin Heavy Chain V-D Intergenic Sequence Contains Insulators That May Regulate Ordered V(D)J Recombination

Featherstone¹,

Wood²,

Bowen³

et al. 2010

Journal of Biological Chemistry

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V(D)J recombination of the multigene antigen receptor loci is essential for the generation of a diverse antigen receptor repertoire. Recombination is strictly regulated, occurring only in lymphocytes due to restricted expression of the recombination activating gene enzymes, RAG1 and RAG2, therein. Further, T cell receptors only recombine in T cells, B cell receptors only recombine in B cells, and the loci only recombine at specific stages in lymphocyte differentiation. In B cells, the Igh recombines before the Ig light chains. Finally some antigen receptor loci (e.g. the Igh) have two ordered recombination events. A D gene first recombines with a J gene on both alleles, followed by recombination of a V gene to the DJ recombined segment. Once a productive VDJ rearrangement has been generated, further V to DJ recombination is prevented on the second allele, a process termed allelic exclusion, which in B cells ensures that each B cell expresses a monoclonal IgH (1).Ordered recombination is crucial for antigen receptor integrity, but key questions remain: how is recombination order achieved, and how is it regulated? Numerous studies have suggested that order is achieved through alterations in the chromatin conformation of individual gene domains at sequential stages of lymphocyte development (2). In the mouse Igh locus, the D-J-C region acquires histone post-translational modifications characteristic of open chromatin before the V region (3, 4). Non-coding RNA transcripts, including I, generated from E, located 3Ј of the J genes (5), and o, transcribed from the promoter of the most 3Ј D gene, DQ52, occur on germ line alleles (6). Following D to J recombination, non-coding transcripts are generated from the V genes (7,8). Furthermore, extensive antisense intergenic transcription occurs throughout the D and J domains before D to J, and then throughout the V domain before V to DJ recombination (9, 10). Nuclear positioning may also play a role in ordered V(D)J recombination. The Igh locus is tethered at the nuclear periphery via the V region in non-B cells (11,12). Relocation toward euchromatic regions occurs preferentially from the DJC end, favoring D to J recombination. Furthermore, locus compaction through DNA looping is required for distal V gene recombination (13,14). Several transcription factors, including Pax5 (13), YY1 (15), and Ikaros (16), play a role in looping, and in their absence, only the D-proximal V genes recombine. Following productive V(D)J recombination and cell surface expression of an IgH polypeptide, several of the above processes are reversed to silence V to DJ recombination of the second allele by allelic exclusion. Both Igh V regions decontract, V region germ line transcription is lost, and the second Igh allele is recruited to pericentric heterochromatin via the D-distal V genes (1). In contrast, both DJC regions remain transcriptionally active (9, 17). Thus, there is differential chromatin regulation of both activation and inactivation of the DJC versus V regions of the Igh locus.

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Antisense Intergenic Transcription Precedes Igh D-to-J Recombination and Is Controlled by the Intronic Enhancer E_μ

Cited by 76 publications

References 69 publications

Noncoding transcription within the Igh distal V _H region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells

Noncoding transcription within the Igh distal V _H region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells

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

The Mouse Immunoglobulin Heavy Chain V-D Intergenic Sequence Contains Insulators That May Regulate Ordered V(D)J Recombination

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Antisense Intergenic Transcription Precedes Igh D-to-J Recombination and Is Controlled by the Intronic Enhancer Eμ

Cited by 76 publications

References 69 publications

Noncoding transcription within the Igh distal V H region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells

Noncoding transcription within the Igh distal V H region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells

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

The Mouse Immunoglobulin Heavy Chain V-D Intergenic Sequence Contains Insulators That May Regulate Ordered V(D)J Recombination

Contact Info

Product

Resources

About

Antisense Intergenic Transcription Precedes Igh D-to-J Recombination and Is Controlled by the Intronic Enhancer E_μ

Noncoding transcription within the Igh distal V _H region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells

Noncoding transcription within the Igh distal V _H region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells