Spt5 accumulation at variable genes distinguishes somatic hypermutation in germinal center B cells from ex vivo–activated cells

Maul, Robert W.; Cao, Zheng; Venkataraman, Lakshmi; Giorgetti, C A; Press, Joan L.; Denizot, Yves; Du, Huarui; Sen, Ranjan; Gearhart, Patricia J.

doi:10.1084/jem.20131512

Cited by 44 publications

(56 citation statements)

References 55 publications

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“…First, SHM seems strongly dependent on the proximal module. The drastic reduction in SHM frequency in germinal center (GC) B cells from 3′PAL Δ/Δ mice (0.005 mutations per base pair downstream from the J H introns, excluding unmutated sequences) was similar to that observed in 3′RR-deficient animals (31), a model described as deficient for recruiting activation-induced cytidine deaminase (AID) in IgH variable regions (43). In our 3′PAL Δ mice, the SHM defect was also correlated with a decrease (at least twofold) in IgH primary transcription, a defect comparable to that seen in 3′RR-deficient mice (31).…”

Section: Discussionmentioning

confidence: 60%

Sequential activation and distinct functions for distal and proximal modules within the IgH 3′ regulatory region

Garot

Marquet

Saintamand

et al. 2016

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

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As a master regulator of functional Ig heavy chain (IgH) expression, the IgH 3′ regulatory region (3′RR) controls multiple transcription events at various stages of B-cell ontogeny, from newly formed B cells until the ultimate plasma cell stage. The IgH 3′RR plays a pivotal role in early B-cell receptor expression, germ-line transcription preceding class switch recombination, interactions between targeted switch (S) regions, variable region transcription before somatic hypermutation, and antibody heavy chain production, but the functional ranking of its different elements is still inaccurate, especially that of its evolutionarily conserved quasipalindromic structure. By comparing relevant previous knockout (KO) mouse models (3′RR KO and hs3b-4 KO) to a novel mutant devoid of the 3′RR quasi-palindromic region (3′PAL KO), we pinpointed common features and differences that specify two distinct regulatory entities acting sequentially during B-cell ontogeny. Independently of exogenous antigens, the 3′RR distal part, including hs4, fine-tuned B-cell receptor expression in newly formed and naïve B-cell subsets. At mature stages, the 3′RR portion including the quasi-palindrome dictated antigen-dependent locus remodeling (global somatic hypermutation and class switch recombination to major isotypes) in activated B cells and antibody production in plasma cells.immunoglobulin gene regulation | enhancers | B-cell development I mmunoglobulin heavy chain (IgH) expression is critical for B-cell development and survival. In developing B-lineage cells, accessibility to the major remodeling events [VDJ recombination, somatic hypermutation (SHM), class switch recombination (CSR), and locus suicide recombination] depends on epigenetic changes and germ-line transcription of many regions, including V H promoters, I/switch region promoters, cis-regulatory region enhancers, and chromatin insulators (1-3). A focus on knockout (KO) models for IgH cis-regulatory regions (enhancers and chromatin insulators) is a means to simplify the regulation picture. At the preproB stage, the IgH locus undergoes long-range looping in a "rosette-like" structure that brings into close proximity major IgH regulatory regions, such as the V H to D H intergenic control regions (IGCR1 and -2), the Eμ intronic enhancer, the 3′ regulatory region (3′RR), and the 3′IgH CTCF-binding elements (CBEs) (4-6). Initiation of VDJ recombination is assisted by the Eμ enhancer, which provides efficient transcription and accessibility to initiate D H to J H rearrangements (7-10), as well as the IGCR1 and -2 elements that ordinate the V H to DJ H second recombination step (5, 11-13). Devoid of enhancer activity (14, 15), 3′CBE (hs5 to hs8) likely participate in IgH folding before VDJ recombination because deletion of hs5 to -7 only impacts use of proximal V H regions (16). In pre-B cells, once a functional H chain is expressed as a component of the pre-B-cell recptor (BCR), the Eμ enhancer function switches from DJ H region accessibility to Igμ chain expression, and consequent...

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Section: Discussionmentioning

confidence: 60%

Sequential activation and distinct functions for distal and proximal modules within the IgH 3′ regulatory region

Garot

Marquet

Saintamand

et al. 2016

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

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“…This suggests that AID-dependent demethylation is coupled to the rate of SHM, which is much lower in the ex vivo system than in GCB (McKean et al, 1984; Robbiani et al, 2008). In this regard, it has recently been demonstrated that ex vivo stimulated B cells are defective in SHM because the initiating form of RNA polymerase II is not retained in the variable regions of the Ig genes, hampering the recruitment of the cofactor Spt5 and AID (Maul et al, 2014). Another attempt to delineate the demethylation function of AID in GCB was made by Hogenbirk et al using Methyl-Cap-Seq and failed to find any AID-dependent changes (Hogenbirk et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID

et al. 2015

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Summary Changes in DNA methylation are required for the formation of germinal centers (GC), but the mechanisms of such changes are poorly understood. Activation-induced cytidine deaminase (AID) has been recently implicated recently in DNA demethylation through its deaminase activity coupled with DNA repair. We investigated the epigenetic function of AID in vivo in germinal center B cells (GCB) isolated from wild type (WT) and AID-deficient (Aicda-/-) mice. We determined that the transit of B cells through the GC is associated with marked locus-specific loss of methylation and increased methylation diversity, both of which are lost in Aicda-/- animals. Differentially methylated cytosines (DMCs) between GCB and naïve B cells (NB) are enriched in genes that are targeted for somatic hypermutation (SHM) by AID and these genes form networks required for B cell development and proliferation. Finally, we observed significant conservation of AID-dependent epigenetic reprogramming between mouse and human B cells.

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“…Importantly, the paused polymerases generate ssDNA, an efficient target for AID. RNA polII abundance also correlates with SHM in germinal center cells 112 . At this time AID can act on the non-transcribed strand but cannot access the transcribed strand, although access to the transcribed strand is necessary to introduce DSB at S regions.…”

Section: Rna Exosome Cooperates With Aid To Promote Dna Deamination Dmentioning

confidence: 97%

RNA Exosome and Non-coding RNA-Coupled Mechanisms in AID-Mediated Genomic Alterations

Laffleur

Basu

Lim

2017

Journal of Molecular Biology

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The eukaryotic RNA exosome is a well-conserved protein complex with ribonuclease activity implicated in RNA metabolism. Various families of non-coding RNAs (ncRNAs) have been identified as substrates of the complex, underscoring its role as a ncRNA processing/degradation unit. However, the role of RNA exosome and its RNA processing activity on DNA mutagenesis/alteration events have not been investigated until recently. B lymphocytes use two DNA alteration mechanisms, class switch recombination (CSR) and somatic hypermutation (SHM), to re-engineer their antibody gene expressing loci until a tailored antibody gene for a specific antigen is satisfactorily generated. CSR and SHM require the essential activity of the DNA activation induced cytidine deaminase (AID). Causing collateral damage to the B cell genome during CSR and SHM, AID induces unwanted (and sometimes oncogenic) mutations at numerous non-immunoglobulin gene sequences. Recent studies have revealed that AID’s DNA mutator activity is regulated by the RNA exosome complex, thus providing an example of a mechanism that relates DNA mutagenesis with RNA processing. Here, we review the emergent functions of RNA exosome during CSR, SHM and other chromosomal alterations in B cells, and discuss implications relevant to mechanisms that maintain B cell genomic integrity.

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Spt5 accumulation at variable genes distinguishes somatic hypermutation in germinal center B cells from ex vivo–activated cells

Abstract: Maul et al. show that proteins associated with variable gene hypermutation, such as Spt5 and AID, are recruited to the initiating form of RNA polymerase II specifically in cells activated in germinal centers but not in culture.

Cited by 44 publications

References 55 publications

Sequential activation and distinct functions for distal and proximal modules within the IgH 3′ regulatory region

Sequential activation and distinct functions for distal and proximal modules within the IgH 3′ regulatory region

DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID

RNA Exosome and Non-coding RNA-Coupled Mechanisms in AID-Mediated Genomic Alterations

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