title: Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies.
abstract: A diverse Ab repertoire is formed through the rearrangement of V, D, and J segments at the IgH (Igh) loci. The C57BL/6 murine Igh locus has >100 functional VH gene segments that can recombine to a rearranged DJH. Although the nonrandom usage of VH genes is well documented, it is not clear what elements determine recombination frequency. To answer this question, we conducted deep sequencing of 5'-RACE products of the Igh repertoire in pro-B cells, amplified in an unbiased manner. Chromatin immunoprecipitation-sequencing results for several histone modifications and RNA polymerase II binding, RNA-sequencing for sense and antisense noncoding germline transcripts, and proximity to CCCTC-binding factor (CTCF) and Rad21 sites were compared with the usage of individual V genes. Computational analyses assessed the relative importance of these various accessibility elements. These elements divide the Igh locus into four epigenetically and transcriptionally distinct domains, and our computational analyses reveal different regulatory mechanisms for each region. Proximal V genes are relatively devoid of active histone marks and noncoding RNA in general, but having a CTCF site near their recombination signal sequence is critical, suggesting that being positioned near the base of the chromatin loops is important for rearrangement. In contrast, distal V genes have higher levels of histone marks and noncoding RNA, which may compensate for their poorer recombination signal sequences and for being distant from CTCF sites. Thus, the Igh locus has evolved a complex system for the regulation of V(D)J rearrangement that is different for each of the four domains that comprise this locus.
authors.affiliation: Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Nancy M
authors.initials: NM
authors.lastname: Choi
authors.forename: Salvatore
authors.initials: S
authors.lastname: Loguercio
authors.forename: Jiyoti
authors.initials: J
authors.lastname: Verma-Gaur
authors.forename: Stephanie C
authors.initials: SC
authors.lastname: Degner
authors.forename: Ali
authors.initials: A
authors.lastname: Torkamani
authors.forename: Andrew I
authors.initials: AI
authors.lastname: Su
authors.forename: Eugene M
authors.initials: EM
authors.lastname: Oltz
authors.forename: Maxim
authors.initials: M
authors.lastname: Artyomov
authors.forename: Ann J
authors.initials: AJ
authors.lastname: Feeney
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D015326:Gene Rearrangement, B-Lymphocyte, Heavy Chain / Q000235:genetics*; D050438:Genes, Immunoglobulin Heavy Chain / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D007135:Immunoglobulin Variable Region / Q000235:genetics*; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D017422:Sequence Analysis, DNA
chemical_list: D007135:Immunoglobulin Variable Region
references.citation: Nature. 2011 Sep 11;477(7365):424-30
references.pmid: 21909113
references.citation: J Immunol. 2005 Nov 15;175(10):6668-75
references.pmid: 16272322
references.citation: Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):E3493-502
references.pmid: 23169622
references.citation: Immunity. 2011 Feb 25;34(2):175-87
references.pmid: 21349430
references.citation: Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):17004-9
references.pmid: 23027941
references.citation: Science. 1987 Nov 20;238(4830):1134-8
references.pmid: 3120312
references.citation: Genome Biol. 2008;9(9):R137
references.pmid: 18798982
references.citation: J Immunol. 1995 Dec 1;155(11):5268-72
references.pmid: 7594539
references.citation: Science. 2002 Apr 5;296(5565):158-62
references.pmid: 11935030
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W262-7
references.pmid: 20478831
references.citation: Nature. 1979 Jul 26;280(5720):288-94
references.pmid: 111144
references.citation: Genome Biol. 2002;3(12):RESEARCH0072
references.pmid: 12537561
references.citation: Curr Opin Cell Biol. 2011 Jun;23(3):318-24
references.pmid: 21169003
references.citation: Nat Immunol. 2003 Feb;4(2):124-31
references.pmid: 12496962
references.citation: Nat Immunol. 2010 Jul;11(7):635-43
references.pmid: 20543837
references.citation: J Clin Invest. 1996 May 15;97(10):2277-82
references.pmid: 8636407
references.citation: J Exp Med. 1990 Mar 1;171(3):843-59
references.pmid: 2261012
references.citation: J Immunol. 2005 Nov 15;175(10):6624-32
references.pmid: 16272317
references.citation: EMBO J. 2001 Nov 15;20(22):6394-403
references.pmid: 11707410
references.citation: Cell. 2010 Apr 30;141(3):419-31
references.pmid: 20398922
references.citation: Genes Dev. 2005 Feb 1;19(3):322-7
references.pmid: 15687256
references.citation: Science. 2001 Aug 10;293(5532):1074-80
references.pmid: 11498575
references.citation: Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9566-71
references.pmid: 21606361
references.citation: Immunity. 2007 Oct;27(4):561-71
references.pmid: 17936034
references.citation: J Immunol. 2012 Jun 1;188(11):5547-60
references.pmid: 22544934
references.citation: J Immunol. 2006 Apr 1;176(7):4221-34
references.pmid: 16547259
references.citation: Mol Cell Biol. 2003 Apr;23(7):2438-50
references.pmid: 12640127
references.citation: J Immunol. 2003 Nov 15;171(10):5296-304
references.pmid: 14607931
references.citation: Adv Exp Med Biol. 2009;650:73-81
references.pmid: 19731802
references.citation: Nature. 1984 Oct 25-31;311(5988):727-33
references.pmid: 6092962
references.citation: Annu Rev Immunol. 2012;30:337-56
references.pmid: 22224771
references.citation: Genes Dev. 2007 May 15;21(10):1179-89
references.pmid: 17504937
references.citation: J Immunol. 1990 Mar 1;144(5):1983-7
references.pmid: 2106560
references.citation: J Immunol. 2001 Jul 1;167(1):257-63
references.pmid: 11418657
references.citation: Annu Rev Immunol. 1986;4:339-68
references.pmid: 3085692
references.citation: Cell. 2011 Oct 14;147(2):332-43
references.pmid: 21982154
references.citation: Nature. 2007 Dec 13;450(7172):1106-10
references.pmid: 18033247
references.citation: Genes Dev. 2004 Feb 15;18(4):411-22
references.pmid: 15004008
references.citation: J Immunol. 2009 Feb 1;182(3):1362-9
references.pmid: 19155482
references.citation: Genes Dev. 2003 Jan 1;17(1):37-42
references.pmid: 12514097
references.citation: Proc Natl Acad Sci U S A. 1979 Jul;76(7):3450-4
references.pmid: 115000
references.citation: J Exp Med. 2003 Jan 20;197(2):207-20
references.pmid: 12538660
references.citation: Nucleic Acids Res. 1994 May 25;22(10):1785-96
references.pmid: 8208601
references.citation: Mol Immunol. 2000 Jan-Feb;37(1-2):29-39
references.pmid: 10781833
references.citation: Cell. 1985 Feb;40(2):271-81
references.pmid: 2578321
references.citation: Proc Natl Acad Sci U S A. 2008 Jun 24;105(25):8685-90
references.pmid: 18562282
references.citation: Science. 1985 Mar 29;227(4694):1597-601
references.pmid: 3975629
references.citation: Nat Genet. 2007 Mar;39(3):311-8
references.pmid: 17277777
references.citation: Science. 2000 Jan 21;287(5452):495-8
references.pmid: 10642553
references.citation: J Immunol. 2009 Jan 1;182(1):44-8
references.pmid: 19109133
references.citation: Mol Cell. 2007 Sep 7;27(5):842-50
references.pmid: 17803947
references.citation: Genes Dev. 1989 Jul;3(7):1053-61
references.pmid: 2777075
references.citation: Cell. 2008 Apr 18;133(2):265-79
references.pmid: 18423198
references.citation: Nature. 2011 Aug 10;476(7361):467-71
references.pmid: 21832993