Altered 3D chromatin structure permits inversional recombination at the IgH locus

Different mechanisms govern the first and second steps of IgH gene recombination. Immunoglobulin heavy chain (IgH) genes are assembled by two sequential DNA rearrangement events that are initiated by recombination activating gene products (RAG) 1 and 2. Diversity (DH) gene segments rearrange first, followed by variable (VH) gene rearrangements. Here, we provide evidence that each rearrangement step is guided by different rules of engagement between rearranging gene segments. DH gene segments, which recombine by deletion of intervening DNA, must be located within a RAG1/2 scanning domain for efficient recombination. In the absence of intergenic control region 1, a regulatory sequence that delineates the RAG scanning domain on wild-type IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA. We propose that VH gene segments find their targets by distinct mechanisms from those that apply to DH gene segments. These distinctions may underlie differential allelic choice associated with each step of IgH gene assembly.

[1]  Erez Lieberman Aiden,et al.  The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination , 2019, Nature.

[2]  M. Krangel,et al.  A Lamina-Associated Domain Border Governs Nuclear Lamina Interactions, Transcription, and Recombination of the Tcrb Locus. , 2018, Cell reports.

[3]  F. Alt,et al.  CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning , 2018, Cell.

[4]  Hongkai Ji,et al.  Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus. , 2018, Molecular cell.

[5]  F. Alt,et al.  An Ectopic CTCF Binding Element Inhibits Tcrd Rearrangement by Limiting Contact between Vδ and Dδ Gene Segments , 2016, The Journal of Immunology.

[6]  Richard L. Frock,et al.  Orientation-specific RAG activity in chromosomal loop domains contributes to Tcrd V(D)J recombination during T cell development , 2016, The Journal of experimental medicine.

[7]  James T. Robinson,et al.  Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. , 2016, Cell systems.

[8]  Neva C. Durand,et al.  Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.

[9]  F. Alt,et al.  Highly sensitive and unbiased approach for elucidating antibody repertoires , 2016, Proceedings of the National Academy of Sciences.

[10]  Louise S. Matheson,et al.  Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination , 2016, Cell reports.

[11]  Richard L. Frock,et al.  Detecting DNA double-stranded breaks in mammalian genomes by linear amplification–mediated high-throughput genome-wide translocation sequencing , 2016, Nature Protocols.

[12]  Jie Liang,et al.  Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire. , 2016, Cell reports.

[13]  C. Bassing.  Faculty Opinions recommendation of A discrete chromatin loop in the mouse Tcra-Tcrd locus shapes the TCRδ and TCRα repertoires. , 2015 .

[14]  Philip A. Ewels,et al.  HiCUP: pipeline for mapping and processing Hi-C data , 2015, F1000Research.

[15]  Richard L. Frock,et al.  Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes , 2015, Cell.

[16]  A. Feeney,et al.  A structural hierarchy mediated by multiple nuclear factors establishes IgH locus conformation , 2015, Genes & development.

[17]  Liang Chen,et al.  A discrete chromatin loop in the murine Tcra-Tcrd locus shapes the TCRδ and TCRα repertoires , 2015, Nature Immunology.

[18]  Aaron N. Chang,et al.  Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth , 2015, Nature Immunology.

[19]  F. Alt,et al.  CTCF-binding elements 1 and 2 in the Igh intergenic control region cooperatively regulate V(D)J recombination , 2015, Proceedings of the National Academy of Sciences.

[20]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[21]  Olivia I. Koues,et al.  Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element , 2015, The Journal of experimental medicine.

[22]  W. Garrard,et al.  A Major Deletion in the Vκ–Jκ Intervening Region Results in Hyperelevated Transcription of Proximal Vκ Genes and a Severely Restricted Repertoire , 2014, The Journal of Immunology.

[23]  Yaojun Zhang,et al.  3D Trajectories Adopted by Coding and Regulatory DNA Elements: First-Passage Times for Genomic Interactions , 2014, Cell.

[24]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[25]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[26]  A. Feeney,et al.  Deep Sequencing of the Murine Igh Repertoire Reveals Complex Regulation of Nonrandom V Gene Rearrangement Frequencies , 2013, The Journal of Immunology.

[27]  P. Ferrier.  Faculty Opinions recommendation of Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. , 2012 .

[28]  F. Alt,et al.  Localized Epigenetic Changes Induced by DH Recombination Restricts Recombinase to DJH Junctions , 2012, Nature Immunology.

[29]  Vivek Chandra,et al.  Global changes in nuclear positioning of genes and intra- and inter-domain genomic interactions that orchestrate B cell fate , 2012, Nature immunology.

[30]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[31]  Boris Lenhard,et al.  The DNA-binding protein CTCF limits proximal Vκ recombination and restricts κ enhancer interactions to the immunoglobulin κ light chain locus. , 2011, Immunity.

[32]  Haiping Hao,et al.  Two Forms of Loops Generate the Chromatin Conformation of the Immunoglobulin Heavy-Chain Gene Locus , 2011, Cell.

[33]  F. Alt,et al.  CTCF Binding Elements Mediate Control of V(D)J Recombination , 2011, Nature.

[34]  C. Bassing,et al.  Repair of Chromosomal RAG-Mediated DNA Breaks by Mutant RAG Proteins Lacking Phosphatidylinositol 3-Like Kinase Consensus Phosphorylation Sites , 2011, The Journal of Immunology.

[35]  Nicholas J. Schork,et al.  CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells , 2011, Proceedings of the National Academy of Sciences.

[36]  Galt P. Barber,et al.  BigWig and BigBed: enabling browsing of large distributed datasets , 2010, Bioinform..

[37]  David G. Schatz,et al.  The In Vivo Pattern of Binding of RAG1 and RAG2 to Antigen Receptor Loci , 2010, Cell.

[38]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[39]  Adam J. Bowen,et al.  The Mouse Immunoglobulin Heavy Chain V-D Intergenic Sequence Contains Insulators That May Regulate Ordered V(D)J Recombination , 2010, The Journal of Biological Chemistry.

[40]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[41]  F. Alt,et al.  A 220-nucleotide deletion of the intronic enhancer reveals an epigenetic hierarchy in immunoglobulin heavy chain locus activation , 2009, The Journal of experimental medicine.

[42]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[43]  M. Schlissel,et al.  Chromosomal position of a VH gene segment determines its activation and inactivation as a substrate for V(D)J recombination , 2007, The Journal of experimental medicine.

[44]  R. Sen,et al.  Repeat organization and epigenetic regulation of the DH-Cmu domain of the immunoglobulin heavy-chain gene locus. , 2007, Molecular cell.

[45]  T. Pandita,et al.  ATM stabilizes DNA double-strand-break complexes during V(D)J recombination , 2006, Nature.

[46]  E. Oltz,et al.  Regulation of IgH Gene Assembly: Role of the Intronic Enhancer and 5′DQ52 Region in Targeting DHJH Recombination1 , 2006, The Journal of Immunology.

[47]  F. Alt,et al.  Elucidation of IgH intronic enhancer functions via germ-line deletion. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  A. Marshall,et al.  Frequency of VH81x usage during B cell development: initial decline in usage is independent of Ig heavy chain cell surface expression. , 1996, Journal of immunology.

[49]  G. Wu,et al.  Inversions produced during V(D)J rearrangement at IgH, the immunoglobulin heavy-chain locus , 1995, Molecular and cellular biology.

[50]  M. Lieber,et al.  The basis for the mechanistic bias for deletional over inversional V(D)J recombination. , 1992, Genes & development.

[51]  P. Gearhart,et al.  Adult B-cell repertoire is biased toward two heavy-chain variable-region genes that rearrange frequently in fetal pre-B cells. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[52]  L. Hood,et al.  Developmentally controlled expression of immunoglobulin VH genes. , 1985, Science.

[53]  F. Alt,et al.  Preferential utilization of the most JH-proximal VH gene segments in pre-B-cell lines , 1984, Nature.

[54]  F. Alt,et al.  Joining of immunoglobulin heavy chain gene segments: implications from a chromosome with evidence of three D-JH fusions. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[55]  F. Alt,et al.  RAG Chromatin Scanning During V(D)J Recombination and Chromatin Loop Extrusion are Related Processes. , 2018, Advances in immunology.

[56]  D. Schatz,et al.  Regulation and Evolution of the RAG Recombinase. , 2015, Advances in immunology.

[57]  R. Sen,et al.  Chromatin Interactions in the Control of Immunoglobulin Heavy Chain Gene Assembly. , 2015, Advances in immunology.