دورية أكاديمية
Addressing Technical Pitfalls in Pursuit of Molecular Factors That Mediate Immunoglobulin Gene Regulation.
| العنوان: | Addressing Technical Pitfalls in Pursuit of Molecular Factors That Mediate Immunoglobulin Gene Regulation. |
|---|---|
| المؤلفون: | Engelbrecht E; Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY., Rodriguez OL; Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY., Watson CT; Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY. |
| المصدر: | Journal of immunology (Baltimore, Md. : 1950) [J Immunol] 2024 Sep 01; Vol. 213 (5), pp. 651-662. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Association of Immunologists Country of Publication: United States NLM ID: 2985117R Publication Model: Print Cited Medium: Internet ISSN: 1550-6606 (Electronic) Linking ISSN: 00221767 NLM ISO Abbreviation: J Immunol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: Bethesda, MD : American Association of Immunologists Original Publication: Baltimore : Williams & Wilkins, c1950- |
| مواضيع طبية MeSH: | Gene Expression Regulation*, Humans ; Immunoglobulin Heavy Chains/genetics ; Haplotypes ; V(D)J Recombination/genetics ; Genes, Immunoglobulin |
| مستخلص: | The expressed Ab repertoire is a critical determinant of immune-related phenotypes. Ab-encoding transcripts are distinct from other expressed genes because they are transcribed from somatically rearranged gene segments. Human Abs are composed of two identical H and L chain polypeptides derived from genes in IGH locus and one of two L chain loci. The combinatorial diversity that results from Ab gene rearrangement and the pairing of different H and L chains contributes to the immense diversity of the baseline Ab repertoire. During rearrangement, Ab gene selection is mediated by factors that influence chromatin architecture, promoter/enhancer activity, and V(D)J recombination. Interindividual variation in the composition of the Ab repertoire associates with germline variation in IGH, implicating polymorphism in Ab gene regulation. Determining how IGH variants directly mediate gene regulation will require integration of these variants with other functional genomic datasets. In this study, we argue that standard approaches using short reads have limited utility for characterizing regulatory regions in IGH at haplotype resolution. Using simulated and chromatin immunoprecipitation sequencing reads, we define features of IGH that limit use of short reads and a single reference genome, namely 1) the highly duplicated nature of the DNA sequence in IGH and 2) structural polymorphisms that are frequent in the population. We demonstrate that personalized diploid references enhance performance of short-read data for characterizing mappable portions of the locus, while also showing that long-read profiling tools will ultimately be needed to fully resolve functional impacts of IGH germline variation on expressed Ab repertoires. (Copyright © 2024 by The American Association of Immunologists, Inc.) |
| References: | Elife. 2019 Jan 16;8:. (PMID: 30650056) J Immunol. 2017 May 1;198(9):3371-3373. (PMID: 28416712) Front Immunol. 2021 May 18;12:682589. (PMID: 34084176) Science. 2020 Sep 11;369(6509):. (PMID: 32913075) Science. 2020 Aug 28;369(6507):1119-1123. (PMID: 32661058) Mol Cell. 2018 Apr 5;70(1):21-33.e6. (PMID: 29576529) Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12776-81. (PMID: 26417104) Genes Immun. 2021 Dec;22(7-8):335-338. (PMID: 34667305) Nature. 2011 Sep 11;477(7365):424-30. (PMID: 21909113) Nat Rev Immunol. 2020 May;20(5):294-307. (PMID: 31988391) Nat Rev Genet. 2023 Oct;24(10):687-711. (PMID: 36737647) Immunol Cell Biol. 2019 Nov;97(10):888-901. (PMID: 31441114) Science. 2022 Apr;376(6588):eabj5089. (PMID: 35357915) J Clin Invest. 1996 May 15;97(10):2277-82. (PMID: 8636407) Front Immunol. 2018 Oct 08;9:2249. (PMID: 30349529) Cell Rep. 2016 Feb 2;14(4):896-906. (PMID: 26804913) Nat Immunol. 2023 Feb;24(2):320-336. (PMID: 36717722) Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):1815-20. (PMID: 25624508) Trends Immunol. 2017 Jul;38(7):459-470. (PMID: 28539189) J Immunol. 2005 Nov 15;175(10):6668-75. (PMID: 16272322) Nat Methods. 2021 Jun;18(6):588-591. (PMID: 34002093) Genome Res. 2024 Jun 7;:. (PMID: 38849157) J Immunol. 2013 Sep 1;191(5):2393-402. (PMID: 23898036) Science. 2002 Aug 9;297(5583):1003-7. (PMID: 12169732) Nat Commun. 2021 Aug 25;12(1):5118. (PMID: 34433829) Adv Exp Med Biol. 2009;650:73-81. (PMID: 19731802) Front Immunol. 2020 Sep 23;11:2136. (PMID: 33072076) Nat Rev Genet. 2023 May;24(5):314-331. (PMID: 36599936) Hum Mol Genet. 2001 Oct 1;10(20):2215-23. (PMID: 11673404) Nat Immunol. 2024 Jun;25(6):1073-1082. (PMID: 38816615) Immunol Rev. 2010 Sep;237(1):22-42. (PMID: 20727027) J Immunol. 2012 Feb 1;188(3):1333-40. (PMID: 22205028) Proc Natl Acad Sci U S A. 2023 Jun 27;120(26):e2306564120. (PMID: 37339228) Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6. (PMID: 14681465) Nature. 2024 Jun;630(8016):447-456. (PMID: 38839969) Cell. 2018 Jun 28;174(1):102-116.e14. (PMID: 29804837) Nat Commun. 2023 Mar 3;14(1):1225. (PMID: 36869028) Science. 2020 Sep 11;369(6509):1318-1330. (PMID: 32913098) Cell. 2017 May 04;169(4):597-609.e11. (PMID: 28475892) Nat Commun. 2023 Jul 8;14(1):4054. (PMID: 37422489) Sci Adv. 2020 Aug 14;6(33):eaaz8850. (PMID: 32851160) Science. 2020 Sep 11;369(6509):. (PMID: 32913073) Nat Methods. 2019 Jan;16(1):88-94. (PMID: 30559433) Immunity. 2013 Aug 22;39(2):229-44. (PMID: 23973221) Curr Opin Syst Biol. 2020 Dec;24:100-108. (PMID: 37008538) Annu Rev Biomed Data Sci. 2023 Aug 10;6:419-441. (PMID: 37196356) Immunology. 2018 Sep;155(1):3-17. (PMID: 29574826) Nat Ecol Evol. 2017;1(3):69. (PMID: 28580430) Nat Commun. 2023 May 29;14(1):3090. (PMID: 37248219) Nature. 2020 Jul;583(7818):693-698. (PMID: 32728248) Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20066-71. (PMID: 22123975) Nat Methods. 2022 Jun;19(6):711-723. (PMID: 35396487) Annu Rev Genomics Hum Genet. 2024 Apr 25;:. (PMID: 38663087) Bioinformatics. 2020 Jun 1;36(12):3687-3692. (PMID: 32246826) IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1983-92. (PMID: 26356912) Nat Genet. 2020 Dec;52(12):1355-1363. (PMID: 33199916) Cell. 2023 Mar 30;186(7):1493-1511.e40. (PMID: 37001506) Nat Commun. 2023 Apr 21;14(1):2316. (PMID: 37085514) Am J Hum Genet. 2013 Apr 4;92(4):530-46. (PMID: 23541343) Immunity. 2016 Nov 15;45(5):1108-1121. (PMID: 27851912) Nat Commun. 2023 Jul 21;14(1):4419. (PMID: 37479682) Am J Hum Genet. 2005 Jul;77(1):78-88. (PMID: 15918152) Cell. 2016 Oct 6;167(2):341-354.e12. (PMID: 27667684) Nat Methods. 2020 Dec;17(12):1191-1199. (PMID: 33230324) Sci Immunol. 2022 Feb 25;7(68):eabm2508. (PMID: 35213211) Science. 2022 Apr;376(6588):eabj6965. (PMID: 35357917) Proc Biol Sci. 2007 Nov 22;274(1627):2801-10. (PMID: 17785269) Immunol Cell Biol. 2017 May;95(5):473-477. (PMID: 28244489) Genome Res. 2022 Jun;32(6):1152-1169. (PMID: 35545447) Genes Immun. 2012 Jul;13(5):363-73. (PMID: 22551722) Genome Res. 2001 Jun;11(6):1005-17. (PMID: 11381028) Am J Hum Genet. 2018 Sep 6;103(3):421-430. (PMID: 30100087) Cell Rep. 2016 Jun 14;15(11):2475-87. (PMID: 27264181) Nucleic Acids Res. 2023 Sep 8;51(16):e86. (PMID: 37548401) Nat Rev Genet. 2021 Oct;22(10):658-671. (PMID: 34302145) Nat Rev Genet. 2020 Mar;21(3):171-189. (PMID: 31729472) Immunogenetics. 2020 Jul;72(5):279-294. (PMID: 32367185) Genome Biol. 2020 May 25;21(1):124. (PMID: 32450900) Nat Biotechnol. 2011 Jan;29(1):24-6. (PMID: 21221095) Trends Genet. 2001 Nov;17(11):661-9. (PMID: 11672867) Trends Immunol. 2024 Jan;45(1):62-74. (PMID: 38151443) Am J Hum Genet. 2021 Aug 5;108(8):1436-1449. (PMID: 34216551) NPJ Vaccines. 2024 Mar 11;9(1):58. (PMID: 38467663) Sci Rep. 2016 Feb 16;6:20842. (PMID: 26880249) Trends Genet. 2022 Sep;38(9):895-903. (PMID: 35410794) Nat Commun. 2019 Feb 7;10(1):628. (PMID: 30733445) NPJ Vaccines. 2021 Sep 6;6(1):113. (PMID: 34489473) Nat Rev Genet. 2011 Nov 29;13(1):36-46. (PMID: 22124482) Nature. 2023 May;617(7960):325-334. (PMID: 37165237) Acta Neuropathol Commun. 2022 Oct 28;10(1):154. (PMID: 36307868) Comput Struct Biotechnol J. 2021 Jul 28;19:4207-4216. (PMID: 34527193) J Exp Med. 1998 Dec 7;188(11):2151-62. (PMID: 9841928) Hum Mol Genet. 1994 Jun;3(6):853-60. (PMID: 7951227) Mol Immunol. 2007 Apr;44(10):2675-85. (PMID: 17218014) Genes Immun. 2024 Feb;25(1):92-94. (PMID: 38097744) J Immunol. 1998 Dec 1;161(11):6068-73. (PMID: 9834090) Nat Commun. 2021 Jun 7;12(1):3394. (PMID: 34099641) Nat Commun. 2023 Mar 6;14(1):1250. (PMID: 36878904) Genes Immun. 2015 Jan-Feb;16(1):24-34. (PMID: 25338678) Genes Immun. 2024 Aug;25(4):297-306. (PMID: 38844673) BMC Genomics. 2011 Jan 27;12:78. (PMID: 21272357) Immunol Rev. 2018 Jul;284(1):120-131. (PMID: 29944759) J Bone Miner Res. 2022 Sep;37(9):1711-1719. (PMID: 35811283) Nature. 2020 Aug;584(7819):142-147. (PMID: 32612238) Genes Immun. 2023 Feb;24(1):21-31. (PMID: 36539592) Cell. 2024 Feb 29;187(5):1024-1037. (PMID: 38290514) Genomics. 1994 Jul 1;22(1):189-97. (PMID: 7959766) Nature. 2009 Feb 12;457(7231):877-81. (PMID: 19212409) Nat Rev Genet. 2023 Sep;24(9):627-641. (PMID: 37161088) Am J Hum Genet. 2023 Feb 2;110(2):195-214. (PMID: 36736292) Am J Hum Genet. 2024 Jan 4;111(1):11-23. (PMID: 38181729) J Immunol. 2016 May 15;196(10):4358-66. (PMID: 27053761) |
| معلومات مُعتمدة: | R24 AI138963 United States AI NIAID NIH HHS; R24AI138963 HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) |
| المشرفين على المادة: | 0 (Immunoglobulin Heavy Chains) |
| تواريخ الأحداث: | Date Created: 20240715 Date Completed: 20240819 Latest Revision: 20240821 |
| رمز التحديث: | 20240821 |
| مُعرف محوري في PubMed: | PMC11333172 |
| DOI: | 10.4049/jimmunol.2400131 |
| PMID: | 39007649 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1550-6606 |
|---|---|
| DOI: | 10.4049/jimmunol.2400131 |