scholarly journals Noncoding RNA transcription alters chromosomal topology to promote isotype-specific class switch recombination

2020 ◽  
Vol 5 (44) ◽  
pp. eaay5864 ◽  
Author(s):  
Gerson Rothschild ◽  
Wanwei Zhang ◽  
Junghyun Lim ◽  
Pankaj Kumar Giri ◽  
Brice Laffleur ◽  
...  
Keyword(s):  
B Cells ◽  
Regulatory Region ◽  
Noncoding Rnas ◽  
Class Switch Recombination ◽  
Regulatory Elements ◽  
Specific Class ◽  
Antibody Diversity ◽  
Variable Regions ◽  
Class Switch ◽  
Super Enhancer

B cells undergo two types of genomic alterations to increase antibody diversity: introduction of point mutations into immunoglobulin heavy- and light-chain (IgH and IgL) variable regions by somatic hypermutation (SHM) and alteration of antibody effector functions by changing the expressed IgH constant region exons through IgH class switch recombination (CSR). SHM and CSR require the B cell–specific activation-induced cytidine deaminase (AID) protein, the transcription of germline noncoding RNAs, and the activity of the 3′ regulatory region (3′RR) super-enhancer. Although many transcription regulatory elements (e.g., promoters and enhancers) reside inside the IgH and IgL sequences, the question remains whether clusters of regulatory elements outside IgH control CSR. Using RNA exosome–deficient mouse B cells where long noncoding RNAs (lncRNAs) are easily detected, we identified a cluster of three RNA-expressing elements that includes lncCSRIgA (that expresses lncRNA-CSRIgA). B cells isolated from a mouse model lacking lncRNA-CSRIgA transcription fail to undergo normal levels of CSR to IgA both in B cells of the Peyer’s patches and grown in ex vivo culture conditions. lncRNA-CSRIgA is expressed from an enhancer site (lncCSRIgA) to facilitate the recruitment of regulatory proteins to a nearby CTCF site (CTCFlncCSR) that alters the chromosomal interactions inside the TADlncCSRIgA and long-range interactions with the 3′RR super-enhancer. Humans with IgA deficiency show polymorphisms in the lncCSRIgA locus compared with the normal population. Thus, we provide evidence for an evolutionarily conserved topologically associated domain (TADlncCSRIgA) that coordinates IgA CSR in Peyer’s patch B cells through an lncRNA (lncRNA-CSRIgA) transcription-dependent mechanism.

Genomic deletion of the whole IgH 3′ regulatory region (hs3a, hs1,2, hs3b, and hs4) dramatically affects class switch recombination and Ig secretion to all isotypes

Blood ◽  
2010 ◽  
Vol 116 (11) ◽  
pp. 1895-1898 ◽  
Author(s):  
Christelle Vincent-Fabert ◽  
Remi Fiancette ◽  
Eric Pinaud ◽  
Véronique Truffinet ◽  
Nadine Cogné ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
B Cells ◽  
Plasma Cell ◽  
Regulatory Region ◽  
Class Switch Recombination ◽  
B Cell Differentiation ◽  
Plasma Cell Differentiation ◽  
Heavy Chains ◽  
Class Switch ◽  
Transcriptional Changes

Abstract The immunoglobulin heavy chain locus (IgH) undergoes multiple changes along B-cell differentiation. In progenitor B cells, V(D)J assembly allows expression of μ heavy chains. In mature B cells, class switch recombination may replace the expressed constant (C)μ gene with a downstream CH gene. Finally, plasma cell differentiation strongly boosts IgH transcription. How the multiple IgH transcriptional enhancers tune these changes is unclear. Here we demonstrate that deletion of the whole IgH 3′ regulatory region (3′RR) allows normal maturation until the stage of IgM/IgD expressing lymphocytes, but nearly abrogates class switch recombination to all CH genes. Although plasma cell numbers are unaffected, we reveal the role of the 3′RR into the transcriptional burst normally associated with plasma cell differentiation. Our study shows that transcriptional changes and recombinations occurring after antigen-encounter appear mainly controlled by the 3′RR working as a single functional unit.

scholarly journals IgH 3’ regulatory region increases ectopic class switch recombination

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009288
Author(s):  
Sandrine Le Noir ◽  
Amélie Bonaud ◽  
Bastien Hervé ◽  
Audrey Baylet ◽  
François Boyer ◽  
...  
Keyword(s):  
Somatic Hypermutation ◽  
Regulatory Region ◽  
Class Switch Recombination ◽  
Dna Lesions ◽  
Reporter System ◽  
Long Distance ◽  
Class Switch ◽  
Super Enhancer ◽  
Switch Regions ◽  
Activation Induced Deaminase

DNA lesions inflicted by activation-induced deaminase (AID) instrumentally initiate the processes reshaping immunoglobulin genes in mature B-cells, from local somatic hypermutation (SHM) to junctions of distant breaks during class switch recombination (CSR). It remains incompletely understood how these divergent outcomes of AID attacks are differentially and temporally focused, with CSR strictly occurring in the Ig heavy chain (IgH) locus while SHM concentrates on rearranged V(D)J regions in the IgH and Ig light chain loci. In the IgH locus, disruption of either the 3’Regulatory Region (3’RR) super-enhancer or of switch (S) regions preceding constant genes, profoundly affects CSR. Reciprocally, we now examined if these elements are sufficient to induce CSR in a synthetic locus based on the Igκ locus backbone. Addition of a surrogate “core 3’RR” (c3’RR) and of a pair of transcribed and spliced Switch regions, together with a reporter system for “κ-CSR” yielded a switchable Igκ locus. While the c3’RR stimulated SHM at S regions, it also lowered the local SHM threshold necessary for switch recombination to occur. The 3’RR thus both helps recruit AID to initiate DNA lesions, but then also promotes their resolution through long-distance synapses and recombination following double-strand breaks.

scholarly journals IgD class switch recombination is not controlled through the immunoglobulin heavy chain 3′ regulatory region super-enhancer

2017 ◽  
Vol 14 (10) ◽  
pp. 871-874 ◽  
Author(s):  
Hussein Issaoui ◽  
Nour Ghazzaui ◽  
Alexis Saintamand ◽  
Yves Denizot ◽  
François Boyer
Keyword(s):  
Heavy Chain ◽  
Regulatory Region ◽  
Class Switch Recombination ◽  
Immunoglobulin Heavy Chain ◽  
Class Switch ◽  
Super Enhancer

scholarly journals The IgH 3′ regulatory region super-enhancer does not control IgA class switch recombination in the B1 lineage

2017 ◽  
Vol 15 (3) ◽  
pp. 289-291 ◽  
Author(s):  
Hussein Issaoui ◽  
Nour Ghazzaui ◽  
Alexis Saintamand ◽  
Claire Carrion ◽  
Christelle Oblet ◽  
...  
Keyword(s):  
Regulatory Region ◽  
Class Switch Recombination ◽  
Class Switch ◽  
Super Enhancer

scholarly journals Mapping of a Functional Recombination Motif that Defines Isotype Specificity for μ→γ3 Switch Recombination Implicates NF-κB p50 as the Isotype-specific Switching Factor

2004 ◽  
Vol 199 (5) ◽  
pp. 617-627 ◽  
Author(s):  
Amy L. Kenter ◽  
Robert Wuerffel ◽  
Carmen Dominguez ◽  
Ananth Shanmugam ◽  
Hongmei Zhang
Keyword(s):  
B Cells ◽  
Binding Site ◽  
Class Switch Recombination ◽  
Interleukin 4 ◽  
Specific Factor ◽  
Wild Type ◽  
Class Switch ◽  
Activation Induced Deaminase ◽  
Necessary And Sufficient

Ig class switch recombination (CSR) requires expression of activation-induced deaminase (AID) and production of germline transcripts to target S regions for recombination. However, the mechanism of CSR remains unclear. Here we show that an extrachromosomal S plasmid assay is AID dependent and that a single consensus repeat is both necessary and sufficient for isotype-specific CSR. Transfected switch substrates specific for μ→γ3 and μ→γ1 are stimulated to switch with lipopolysaccharide (LPS) alone or LPS and interleukin-4, respectively. An Sγ3/Sγ1 substrate containing only three Sγ3-associated nucleotides reconstituted LPS responsiveness and permitted mapping of a functional recombination motif specific for μ→γ3 CSR. This functional recombination motif colocalized with a binding site for NF-κB p50, and p50 binding to this site was previously established. We show a p50 requirement for plasmid-based μ→γ3 CSR using p50-deficient B cells. Switch junctions from p50-deficient B cells showed decreased lengths of microhomology between Sμ and Sγ3 relative to wild-type cells, indicating a function for p50 in the mechanics of CSR. We note a striking parallel between the affects of p50 and Msh2 deficiency on Sμ/Sγ3 junctions. The data suggest that p50 may be the isotype-specific factor in μ→γ3 CSR and epistatic with Msh2.

MicroRNA-directed pathway discovery elucidates an miR-221/222–mediated regulatory circuit in class switch recombination

2021 ◽  
Vol 218 (11) ◽  
Author(s):  
Eric J. Wigton ◽  
Yohei Mikami ◽  
Ryan J. McMonigle ◽  
Carlos A. Castellanos ◽  
Adam K. Wade-Vallance ◽  
...  
Keyword(s):  
B Cells ◽  
B Cell ◽  
Cell Fate ◽  
Cell Activation ◽  
Class Switch Recombination ◽  
Cell Fate Decisions ◽  
Class Switch ◽  
Mrna Targets ◽  
Regulatory Circuit ◽  
Pathway Discovery

MicroRNAs (miRNAs, miRs) regulate cell fate decisions by post-transcriptionally tuning networks of mRNA targets. We used miRNA-directed pathway discovery to reveal a regulatory circuit that influences Ig class switch recombination (CSR). We developed a system to deplete mature, activated B cells of miRNAs, and performed a rescue screen that identified the miR-221/222 family as a positive regulator of CSR. Endogenous miR-221/222 regulated B cell CSR to IgE and IgG1 in vitro, and miR-221/222–deficient mice exhibited defective IgE production in allergic airway challenge and polyclonal B cell activation models in vivo. We combined comparative Ago2-HITS-CLIP and gene expression analyses to identify mRNAs bound and regulated by miR-221/222 in primary B cells. Interrogation of these putative direct targets uncovered functionally relevant downstream genes. Genetic depletion or pharmacological inhibition of Foxp1 and Arid1a confirmed their roles as key modulators of CSR to IgE and IgG1.

scholarly journals Correction: Exosomes Derived from Burkitt’s Lymphoma Cell Lines Induce Proliferation, Differentiation, and Class-Switch Recombination in B Cells

2019 ◽  
Vol 203 (3) ◽  
pp. 769-770
Author(s):  
Cindy Gutzeit ◽  
Noemi Nagy ◽  
Maurizio Gentile ◽  
Katarina Lyberg ◽  
Janine Gumz ◽  
...  
Keyword(s):  
B Cells ◽  
Cell Lines ◽  
Class Switch Recombination ◽  
Burkitt’S Lymphoma ◽  
Lymphoma Cell ◽  
Burkitt's Lymphoma ◽  
Class Switch

scholarly journals The Balance Between Pax5 and Id2 Activities Is the Key to AID Gene Expression

2003 ◽  
Vol 198 (9) ◽  
pp. 1427-1437 ◽  
Author(s):  
Hiroyuki Gonda ◽  
Manabu Sugai ◽  
Yukiko Nambu ◽  
Tomoya Katakai ◽  
Yasutoshi Agata ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cells ◽  
Cytidine Deaminase ◽  
Regulatory Region ◽  
Binding Activity ◽  
Class Switch ◽  
Dna Binding Activity ◽  
Activation Induced Cytidine Deaminase ◽  
Putative Regulatory Region ◽  
Kinetics Of

Pax5 activity is enhanced in activated B cells and is essential for class switch recombination (CSR). We show that inhibitor of differentiation (Id)2 suppresses CSR by repressing the gene expression of activation-induced cytidine deaminase (AID), which has been shown to be indispensable for CSR. Furthermore, a putative regulatory region of AID contains E2A- and Pax5-binding sites, and the latter site is indispensable for AID gene expression. Moreover, the DNA-binding activity of Pax5 is decreased in Id2-overexpressing B cells and enhanced in Id2−/− B cells. The kinetics of Pax5, but not E2A, occupancy to AID locus is the same as AID expression in primary B cells. Finally, enforced expression of Pax5 induces AID transcription in pro–B cell lines. Our results provide evidence that the balance between Pax5 and Id2 activities has a key role in AID gene expression.

scholarly journals Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination

2016 ◽  
Vol 213 (3) ◽  
pp. 303-312 ◽  
Author(s):  
Anne-Sophie Thomas-Claudepierre ◽  
Isabelle Robert ◽  
Pedro P. Rocha ◽  
Ramya Raviram ◽  
Ebe Schiavo ◽  
...  
Keyword(s):  
B Cells ◽  
Long Range ◽  
Transcriptional Activation ◽  
Transcription Initiation ◽  
Structural Changes ◽  
Class Switch Recombination ◽  
Mediator Complex ◽  
Loop Formation ◽  
Class Switch ◽  
Igh Locus

Immunoglobulin (Ig) class switch recombination (CSR) is initiated by the transcription-coupled recruitment of activation-induced cytidine deaminase (AID) to Ig switch regions (S regions). During CSR, the IgH locus undergoes dynamic three-dimensional structural changes in which promoters, enhancers, and S regions are brought to close proximity. Nevertheless, little is known about the underlying mechanisms. In this study, we show that Med1 and Med12, two subunits of the mediator complex implicated in transcription initiation and long-range enhancer/promoter loop formation, are dynamically recruited to the IgH locus enhancers and the acceptor regions during CSR and that their knockdown in CH12 cells results in impaired CSR. Furthermore, we show that conditional inactivation of Med1 in B cells results in defective CSR and reduced acceptor S region transcription. Finally, we show that in B cells undergoing CSR, the dynamic long-range contacts between the IgH enhancers and the acceptor regions correlate with Med1 and Med12 binding and that they happen at a reduced frequency in Med1-deficient B cells. Our results implicate the mediator complex in the mechanism of CSR and are consistent with a model in which mediator facilitates the long-range contacts between S regions and the IgH locus enhancers during CSR and their transcriptional activation.

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