The role of HIRA-dependent H3.3 deposition and its modifications in the somatic hypermutation of immunoglobulin variable regions

2021 ◽  
Vol 118 (50) ◽  
pp. e2114743118
Author(s):  
Guojun Yu ◽  
Yongwei Zhang ◽  
Varun Gupta ◽  
Jinghang Zhang ◽  
Thomas MacCarthy ◽  
...  

The H3.3 histone variant and its chaperone HIRA are involved in active transcription, but their detailed roles in regulating somatic hypermutation (SHM) of immunoglobulin variable regions in human B cells are not yet fully understood. In this study, we show that the knockout (KO) of HIRA significantly decreased SHM and changed the mutation pattern of the variable region of the immunoglobulin heavy chain (IgH) in the human Ramos B cell line without changing the levels of activation-induced deaminase and other major proteins known to be involved in SHM. Except for H3K79me2/3 and Spt5, many factors related to active transcription, including H3.3, were substantively decreased in HIRA KO cells, and this was accompanied by decreased nascent transcription in the IgH locus. The abundance of ZMYND11 that specifically binds to H3.3K36me3 on the IgH locus was also reduced in the HIRA KO. Somewhat surprisingly, HIRA loss increased the chromatin accessibility of the IgH V region locus. Furthermore, stable expression of ectopic H3.3G34V and H3.3G34R mutants that inhibit both the trimethylation of H3.3K36 and the recruitment of ZMYND11 significantly reduced SHM in Ramos cells, while the H3.3K79M did not. Consistent with the HIRA KO, the H3.3G34V mutant also decreased the occupancy of various elongation factors and of ZMYND11 on the IgH variable and downstream switching regions. Our results reveal an unrecognized role of HIRA and the H3.3K36me3 modification in SHM and extend our knowledge of how transcription-associated chromatin structure and accessibility contribute to SHM in human B cells.

2021 ◽  
Vol 118 (29) ◽  
pp. e2104013118
Author(s):  
Zhi Duan ◽  
Linda B. Baughn ◽  
Xiaohua Wang ◽  
Yongwei Zhang ◽  
Varun Gupta ◽  
...  

Somatic hypermutation (SHM) and class-switch recombination (CSR) of the immunoglobulin (Ig) genes allow B cells to make antibodies that protect us against a wide variety of pathogens. SHM is mediated by activation-induced deaminase (AID), occurs at a million times higher frequency than other mutations in the mammalian genome, and is largely restricted to the variable (V) and switch (S) regions of Ig genes. Using the Ramos human Burkitt’s lymphoma cell line, we find that H3K79me2/3 and its methyltransferase Dot1L are more abundant on the V region than on the constant (C) region, which does not undergo mutation. In primary naïve mouse B cells examined ex vivo, the H3K79me2/3 modification appears constitutively in the donor Sμ and is inducible in the recipient Sγ1 upon CSR stimulation. Knockout and inhibition of Dot1L in Ramos cells significantly reduces V region mutation and the abundance of H3K79me2/3 on the V region and is associated with a decrease of polymerase II (Pol II) and its S2 phosphorylated form at the IgH locus. Knockout of Dot1L also decreases the abundance of BRD4 and CDK9 (a subunit of the P-TEFb complex) on the V region, and this is accompanied by decreased nascent transcripts throughout the IgH gene. Treatment with JQ1 (inhibitor of BRD4) or DRB (inhibitor of CDK9) decreases SHM and the abundance of Pol II S2P at the IgH locus. Since all these factors play a role in transcription elongation, our studies reinforce the idea that the chromatin context and dynamics of transcription are critical for SHM.


2017 ◽  
Vol 114 (32) ◽  
pp. 8614-8619 ◽  
Author(s):  
Joyce K. Hwang ◽  
Chong Wang ◽  
Zhou Du ◽  
Robin M. Meyers ◽  
Thomas B. Kepler ◽  
...  

Variable regions of Ig chains provide the antigen recognition portion of B-cell receptors and derivative antibodies. Ig heavy-chain variable region exons are assembled developmentally from V, D, J gene segments. Each variable region contains three antigen-contacting complementarity-determining regions (CDRs), with CDR1 and CDR2 encoded by the V segment and CDR3 encoded by the V(D)J junction region. Antigen-stimulated germinal center (GC) B cells undergo somatic hypermutation (SHM) of V(D)J exons followed by selection for SHMs that increase antigen-binding affinity. Some HIV-1–infected human subjects develop broadly neutralizing antibodies (bnAbs), such as the potent VRC01-class bnAbs, that neutralize diverse HIV-1 strains. Mature VRC01-class bnAbs, including VRC-PG04, accumulate very high SHM levels, a property that hinders development of vaccine strategies to elicit them. Because many VRC01-class bnAb SHMs are not required for broad neutralization, high overall SHM may be required to achieve certain functional SHMs. To elucidate such requirements, we used a V(D)J passenger allele system to assay, in mouse GC B cells, sequence-intrinsic SHM-targeting rates of nucleotides across substrates representing maturation stages of human VRC-PG04. We identify rate-limiting SHM positions for VRC-PG04 maturation, as well as SHM hotspots and intrinsically frequent deletions associated with SHM. We find that mature VRC-PG04 has low SHM capability due to hotspot saturation but also demonstrate that generation of new SHM hotspots and saturation of existing hotspot regions (e.g., CDR3) does not majorly influence intrinsic SHM in unmutated portions of VRC-PG04 progenitor sequences. We discuss implications of our findings for bnAb affinity maturation mechanisms.


2021 ◽  
Vol 17 (9) ◽  
pp. e1009323
Author(s):  
Guojun Yu ◽  
Yingru Wu ◽  
Zhi Duan ◽  
Catherine Tang ◽  
Haipeng Xing ◽  
...  

The B cells in our body generate protective antibodies by introducing somatic hypermutations (SHM) into the variable region of immunoglobulin genes (IgVs). The mutations are generated by activation induced deaminase (AID) that converts cytosine to uracil in single stranded DNA (ssDNA) generated during transcription. Attempts have been made to correlate SHM with ssDNA using bisulfite to chemically convert cytosines that are accessible in the intact chromatin of mutating B cells. These studies have been complicated by using different definitions of “bisulfite accessible regions” (BARs). Recently, deep-sequencing has provided much larger datasets of such regions but computational methods are needed to enable this analysis. Here we leveraged the deep-sequencing approach with unique molecular identifiers and developed a novel Hidden Markov Model based Bayesian Segmentation algorithm to characterize the ssDNA regions in the IGHV4-34 gene of the human Ramos B cell line. Combining hierarchical clustering and our new Bayesian model, we identified recurrent BARs in certain subregions of both top and bottom strands of this gene. Using this new system, the average size of BARs is about 15 bp. We also identified potential G-quadruplex DNA structures in this gene and found that the BARs co-locate with G-quadruplex structures in the opposite strand. Using various correlation analyses, there is not a direct site-to-site relationship between the bisulfite accessible ssDNA and all sites of SHM but most of the highly AID mutated sites are within 15 bp of a BAR. In summary, we developed a novel platform to study single stranded DNA in chromatin at a base pair resolution that reveals potential relationships among BARs, SHM and G-quadruplexes. This platform could be applied to genome wide studies in the future.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2704-2704
Author(s):  
Dunja Schneider ◽  
Hendrik Veelken ◽  
Hassan Jumaa

Abstract Abstract 2704 Follicular lymphoma (FL) is an indolent B-cell lymphoma characterized by apoptosis resistance due to overexpression of Bcl-2 as a consequence of the t(14;18) translocation, ongoing somatic hypermutation (SHM), and expression of B-cell receptors (BCR) with glycosylation of the antigen binding sites. Translocation and concomitant Bcl-2 overexpression can be found in healthy human blood B cells and is insufficient to drive lymphoma outgrowth in mouse models. Since most FL cells still express a surface B cell receptor (BCR) despite the disruption of one immunoglobulin heavy chain allele by the t(14;18) translocation, expression of an antigen receptor seems to be indispensable for FL development. Around 80% of FLs possess asparagine (N)-linked glycosylation sites (amino acid sequence: N-X-S/T) in their BCR variable regions that are not encoded in germ-line but are acquired through SHM. In contrast to germ-line-encoded glycosylation sites in the constant BCR region, where normal processing of the glycans results in termination on branched sugars like sialic acid, the variable region glycosylation sites carry mannose-terminating sugars. Recently, it has been shown that C-type lectins bind to and stimulate FL cells. Such lectins are normally expressed on cells of the innate immune system, e.g. dendritic cells (DCs), which also reside in close interaction with the transformed B cells in germinal centers. Importantly, previous studies point to an outstanding role of the tumor microenvironment in survival and proliferation of the FL cells. In this study, we demonstrate that the variable region glycosylation in FL BCRs contribute to stimulation of the cells as well as adhesion to cells of the innate immune system. The BCR from six FL and the appropriate glycosylation-defective controls in which the N-linked glycosylation sequons are removed by replacing the asparagine (N) residues with glutamine (Q) residues were expressed in the tko cellular reconstitution system. In tko cells, the BCR signaling cascade can be rendered functional at will through a tamoxifen-dependent mutant of the signal transducer SLP-65 (Meixlsperger et al., Immunity 2007; Dühren von Minden et al., Nature 2012). Tko cells expressing FL BCRs and their glycosylation-defective controls were tested for binding of a recombinant DC-SIGN/Fc fusion protein by flow cytometry. The mannosylated FL-derived BCR but not glycosylation-mutated receptors bound DC-SIGN. Stepwise mutation of individual glycosylation sites demonstrated variable contribution to the strength of lectin binding. Despite this specific binding to mannosylated FL BCRs, DC-SIGN/Fc failed to induce significant calcium mobilization of transduced tko cells. Crosslinking with anti-IgM, in contrast, led to a readily detectable BCR-mediated signal, thereby demonstrating functionality of the transduced BCR. To study the role of mannosylated FL receptors in interaction with their environment, we co-cultured cells expressing FL receptors containing or lacking N-linked glycans in the variable regions together with macrophages. Western blot analyses with a pan-phosphotyrosine antibody demonstrated higher global tyrosine phosphorylation in the lysates of cells expressing glycosylated receptors, thereby indicating a specific role for mannosylated V-regions in FL stimulation. Glycan-mediated interactions fulfill multiple important functions in the mammalian immune system including pathogen recognition and cell adhesion or trafficking. DC-SIGN serves as receptor for the uptake of mannosylated pathogens and contributes to cell-cell interaction by binding to the heavily glycosylated ICAM-2/3 (intracellular adhesion molecules-2/3). In the case of FL, it is therefore conceivable that DC-SIGN expressed on follicular DCs binds to the heavily mannosylated FL BCRs and serves thereby as adhesion molecule to keep the FL B cells within the follicular structure. We tested this hypothesis using live cell imaging on a DC sublayer and detected slightly slower movement and shorter tracks of cells expressing glycosylated FL BCRs as compared to control cells. Together, our results ascribe a role of the acquired glycosylation sites in FL BCRs for B-cell/DC interaction, thereby keeping the cells in the appropriate environment in a process that involves active signal transduction rather than triggering a classical antigen-induced BCR stimulation. Disclosures: No relevant conflicts of interest to declare.


2002 ◽  
Vol 195 (4) ◽  
pp. 529-534 ◽  
Author(s):  
Hitoshi Nagaoka ◽  
Masamichi Muramatsu ◽  
Namiko Yamamura ◽  
Kazuo Kinoshita ◽  
Tasuku Honjo

Somatic hypermutation (SHM) and class switch recombination (CSR) cause distinct genetic alterations at different regions of immunoglobulin genes in B lymphocytes: point mutations in variable regions and large deletions in S regions, respectively. Yet both depend on activation-induced deaminase (AID), the function of which in the two reactions has been an enigma. Here we report that B cell stimulation which induces CSR but not SHM, leads to AID-dependent accumulation of SHM-like point mutations in the switch μ region, uncoupled with CSR. These findings strongly suggest that AID itself or a single molecule generated by RNA editing function of AID may mediate a common step of SHM and CSR, which is likely to be involved in DNA cleavage.


1998 ◽  
Vol 162 (1) ◽  
pp. 261-280 ◽  
Author(s):  
Ulf Klien ◽  
Tina Goasens ◽  
Motthias Fischer ◽  
Holger Kanzler ◽  
Andreas Braeuninger ◽  
...  

2002 ◽  
Vol 195 (9) ◽  
pp. 1193-1198 ◽  
Author(s):  
F. Nina Papavasiliou ◽  
David G. Schatz

Activation of B cells by antigen fuels two distinct molecular modifications of immunoglobulin (Ig) genes. Class-switch recombination (CSR) replaces the Igμ heavy chain constant region with a downstream constant region gene, thereby altering the effector function of the resulting antibodies. Somatic hypermutation (SHM) introduces point mutations into the variable regions of Ig genes, thereby changing the affinity of antibody for antigen. Mechanistic overlap between the two reactions has been suggested by the finding that both require the activation-induced cytidine deaminase (AID). It has been proposed that AID initiates both CSR and SHM by activating a common nuclease. Here we provide evidence that cells lacking AID, or expressing a dominant negative form of the protein, are still able to incur DNA lesions in SHM target sequences. The results indicate that an intact cytidine deaminase motif is required for AID function, and that AID acts downstream of the initial DNA lesions in SHM.


Autoimmunity ◽  
2012 ◽  
Vol 45 (6) ◽  
pp. 440-448 ◽  
Author(s):  
Chuancang Jiang ◽  
Ming-Lang Zhao ◽  
Katherine M. Waters ◽  
Marilyn Diaz

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Simone Sidoli ◽  
Mariana Lopes ◽  
Peder J. Lund ◽  
Naomi Goldman ◽  
Maria Fasolino ◽  
...  

Abstract Histone post-translational modifications (PTMs) contribute to chromatin accessibility due to their chemical properties and their ability to recruit enzymes responsible for DNA readout and chromatin remodeling. To date, more than 400 different histone PTMs and thousands of combinations of PTMs have been identified, the vast majority with still unknown biological function. Identification and quantification of histone PTMs has become routine in mass spectrometry (MS) but, since raising antibodies for each PTM in a study can be prohibitive, lots of potential is lost from MS datasets when uncharacterized PTMs are found to be significantly regulated. We developed an assay that uses metabolic labeling and MS to associate chromatin accessibility with histone PTMs and their combinations. The labeling is achieved by spiking in the cell media a 5x concentration of stable isotope labeled arginine and allow cells to grow for at least one cell cycle. We quantified the labeling incorporation of about 200 histone peptides with a proteomics workflow, and we confirmed that peptides carrying PTMs with extensively characterized roles in active transcription or gene silencing were in highly or poorly labeled forms, respectively. Data were further validated using next-generation sequencing to assess the transcription rate of chromatin regions modified with five selected PTMs. Furthermore, we quantified the labeling rate of peptides carrying co-existing PTMs, proving that this method is suitable for combinatorial PTMs. We focus on the abundant bivalent mark H3K27me3K36me2, showing that H3K27me3 dominantly represses histone swapping rate even in the presence of the more permissive PTM H3K36me2. Together, we envision this method will help to generate hypotheses regarding histone PTM functions and, potentially, elucidate the role of combinatorial histone codes.


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