Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination.
Variable (V), diversity (D), and joining (J) (V(D)J) recombination is the first determinant of antigen receptor diversity. Understanding how recombination is regulated requires a comprehensive, unbiased readout of V gene usage. We have developed VDJ sequencing (VDJ-seq), a DNA-based next-generation-sequencing technique that quantitatively profiles recombination products. We reveal a 200-fold range of recombination efficiency among recombining V genes in the primary mouse Igh repertoire. We used machine learning to integrate these data with local chromatin profiles to identify combinatorial patterns of epigenetic features that associate with active VH gene recombination. These features localize downstream of VH genes and are excised by recombination, revealing a class of cis-regulatory element that governs recombination, distinct from expression. We detect two mutually exclusive chromatin signatures at these elements, characterized by CTCF/RAD21 and PAX5/IRF4, which segregate with the evolutionary history of associated VH genes. Thus, local chromatin signatures downstream of VH genes provide an essential layer of regulation that determines recombination efficiency.
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Daniel J
DJ
Bolland
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Hashem
H
Koohy
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Andrew L
AL
Wood
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Louise S
LS
Matheson
Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Felix
F
Krueger
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Michael J T
MJ
Stubbington
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Amanda
A
Baizan-Edge
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Peter
P
Chovanec
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Bryony A
BA
Stubbs
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Kristina
K
Tabbada
Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
Simon R
SR
Andrews
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK. Electronic address: mikhail.spivakov@babraham.ac.uk.
Mikhail
M
Spivakov
Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK. Electronic address: anne.corcoran@babraham.ac.uk.
Anne E
AE
Corcoran
D000465:Algorithms; D000818:Animals; D002843:Chromatin / Q000378:metabolism*; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D056426:Genetic Loci; D018398:Homeodomain Proteins / Q000378:metabolism; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics; D007135:Immunoglobulin Variable Region / Q000235:genetics; D051379:Mice; D011946:Receptors, Antigen; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D060152:V(D)J Recombination / Q000235:genetics*
D002843:Chromatin; D018398:Homeodomain Proteins; D007143:Immunoglobulin Heavy Chains; D007135:Immunoglobulin Variable Region; D011946:Receptors, Antigen; C064658:RAG-1 protein