Home LiteratureArticle Details
PMID: 23008333 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

A role for the RNA pol II-associated PAF complex in AID-induced immune diversification.

The Journal of experimental medicine ·Vol. 209 ·No. 11 ·2012-10-22 ·Pages 2099-111

Willmann KL, Milosevic S, Pauklin S, Schmitz KM, Rangam G, Simon MT, Maslen S, Skehel M, Robert I, Heyer V, Schiavo E, Reina-San-Martin B, Petersen-Mahrt SK

Abstract

Antibody diversification requires the DNA deaminase AID to induce DNA instability at immunoglobulin (Ig) loci upon B cell stimulation. For efficient cytosine deamination, AID requires single-stranded DNA and needs to gain access to Ig loci, with RNA pol II transcription possibly providing both aspects. To understand these mechanisms, we isolated and characterized endogenous AID-containing protein complexes from the chromatin of diversifying B cells. The majority of proteins associated with AID belonged to RNA polymerase II elongation and chromatin modification complexes. Besides the two core polymerase subunits, members of the PAF complex, SUPT5H, SUPT6H, and FACT complex associated with AID. We show that AID associates with RNA polymerase-associated factor 1 (PAF1) through its N-terminal domain, that depletion of PAF complex members inhibits AID-induced immune diversification, and that the PAF complex can serve as a binding platform for AID on chromatin. A model is emerging of how RNA polymerase II elongation and pausing induce and resolve AID lesions.

MeSH Terms
Animals Antibody Diversity B-Lymphocytes/metabolism Blotting, Western Cell Line, Tumor Chromatin/genetics,metabolism Cytidine Deaminase/genetics,metabolism DNA-Binding Proteins/genetics,metabolism HEK293 Cells HeLa Cells High Mobility Group Proteins/genetics,metabolism Humans Immunoglobulin Class Switching Immunoglobulins/genetics Immunoprecipitation Nuclear Proteins/genetics,metabolism Protein Binding RNA Interference Transcription Factors/genetics,metabolism Transcriptional Elongation Factors/genetics,metabolism
Chemicals
Chromatin DNA-Binding Proteins High Mobility Group Proteins Immunoglobulins Nuclear Proteins PAF1 protein, human SSRP1 protein, human SUPT5H protein, human SUPT6H protein, human Transcription Factors Transcriptional Elongation Factors AICDA (activation-induced cytidine deaminase) Cytidine Deaminase
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Willmann Katharina L
DNA Editing Laboratory, London Research Institute, South Mimms EN6 3LD, England, UK.
Milosevic Sara
Pauklin Siim
Schmitz Kerstin-Maike
Rangam Gopinath
Simon Maria T
Maslen Sarah
Skehel Mark
Robert Isabelle
Heyer Vincent
Schiavo Ebe
Reina-San-Martin Bernardo
Petersen-Mahrt Svend K
References (47)
47 references, click to expand
  1. Transcript Elongation by RNA Polymerase II.
    Annu Rev Biochem. 2010;79:271-93 PMID: 20367031
  2. CTNNBL1 is a novel nuclear localization sequence-binding protein that recognizes RNA-splicing factors CDC5L and Prp31.
    J Biol Chem. 2011 May 13;286(19):17091-102 PMID: 21385873
  3. Specificity of immunoglobulin heavy chain switch correlates with activity of germline heavy chain genes prior to switching.
    EMBO J. 1986 Jan;5(1):95-102 PMID: 3007121
  4. Probability-based protein identification by searching sequence databases using mass spectrometry data.
    Electrophoresis. 1999 Dec;20(18):3551-67 PMID: 10612281
  5. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS.
    Cell. 2010 Feb 19;140(4):491-503 PMID: 20178742
  6. Activation-induced cytidine deaminase shuttles between nucleus and cytoplasm like apolipoprotein B mRNA editing catalytic polypeptide 1.
    Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1975-80 PMID: 14769937
  7. The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates.
    Cell. 2011 Feb 4;144(3):353-63 PMID: 21255825
  8. DNA deamination in immunity.
    Immunol Rev. 2005 Feb;203:80-97 PMID: 15661023
  9. A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse.
    Genes Dev. 2008 Aug 1;22(15):2048-61 PMID: 18676810
  10. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II.
    Cell. 2006 May 19;125(4):703-17 PMID: 16713563
  11. Histone chaperone Spt6 is required for class switch recombination but not somatic hypermutation.
    Proc Natl Acad Sci U S A. 2011 May 10;108(19):7920-5 PMID: 21518874
  12. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
    Anal Chem. 2002 Oct 15;74(20):5383-92 PMID: 12403597
  13. Transcription-targeted DNA deamination by the AID antibody diversification enzyme.
    Nature. 2003 Apr 17;422(6933):726-30 PMID: 12692563
  14. Parp1 facilitates alternative NHEJ, whereas Parp2 suppresses IgH/c-myc translocations during immunoglobulin class switch recombination.
    J Exp Med. 2009 May 11;206(5):1047-56 PMID: 19364882
  15. Estrogen directly activates AID transcription and function.
    J Exp Med. 2009 Jan 16;206(1):99-111 PMID: 19139166
  16. A RECQ5-RNA polymerase II association identified by targeted proteomic analysis of human chromatin.
    Proc Natl Acad Sci U S A. 2008 Jun 24;105(25):8580-4 PMID: 18562274
  17. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification.
    Nature. 2002 Jul 4;418(6893):99-103 PMID: 12097915
  18. Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase.
    Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4102-7 PMID: 12651944
  19. DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation.
    Genes Dev. 2009 Dec 1;23(23):2765-77 PMID: 19952111
  20. Clonal selection and learning in the antibody system.
    Nature. 1996 Jun 27;381(6585):751-8 PMID: 8657279
  21. The splicing regulator PTBP2 interacts with the cytidine deaminase AID and promotes binding of AID to switch-region DNA.
    Nat Immunol. 2011 Feb;12(2):160-6 PMID: 21186367
  22. AID is essential for immunoglobulin V gene conversion in a cultured B cell line.
    Curr Biol. 2002 Mar 5;12(5):435-8 PMID: 11882297
  23. Elements regulating somatic hypermutation of an immunoglobulin kappa gene: critical role for the intron enhancer/matrix attachment region.
    Cell. 1994 Apr 22;77(2):239-48 PMID: 8168132
  24. Epigenetic tethering of AID to the donor switch region during immunoglobulin class switch recombination.
    J Exp Med. 2011 Aug 1;208(8):1649-60 PMID: 21746811
  25. AID-GFP chimeric protein increases hypermutation of Ig genes with no evidence of nuclear localization.
    Proc Natl Acad Sci U S A. 2002 May 14;99(10):7003-8 PMID: 12011459
  26. Targeting of somatic hypermutation.
    Nat Rev Immunol. 2006 Aug;6(8):573-83 PMID: 16868548
  27. Somatic hypermutation is limited by CRM1-dependent nuclear export of activation-induced deaminase.
    J Exp Med. 2004 May 3;199(9):1235-44 PMID: 15117971
  28. C-terminal deletion of AID uncouples class switch recombination from somatic hypermutation and gene conversion.
    Mol Cell. 2003 Aug;12(2):501-8 PMID: 14536088
  29. Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes.
    Nat Immunol. 2011 Jan;12(1):62-9 PMID: 21113164
  30. The DSIF subunits Spt4 and Spt5 have distinct roles at various phases of immunoglobulin class switch recombination.
    PLoS Genet. 2012;8(4):e1002675 PMID: 22570620
  31. GANP-mediated recruitment of activation-induced cytidine deaminase to cell nuclei and to immunoglobulin variable region DNA.
    J Biol Chem. 2010 Jul 30;285(31):23945-53 PMID: 20507984
  32. Molecular mechanisms of antibody somatic hypermutation.
    Annu Rev Biochem. 2007;76:1-22 PMID: 17328676
  33. Activation-induced cytosine deaminase (AID) is actively exported out of the nucleus but retained by the induction of DNA breaks.
    J Biol Chem. 2004 Jun 18;279(25):26395-401 PMID: 15087440
  34. Transcription-coupled events associating with immunoglobulin switch region chromatin.
    Science. 2003 Dec 19;302(5653):2137-40 PMID: 14684824
  35. Somatic hypermutation of immunoglobulin genes is linked to transcription initiation.
    Immunity. 1996 Jan;4(1):57-65 PMID: 8574852
  36. Analysis of intergenic transcription and histone modification across the human immunoglobulin heavy-chain locus.
    Proc Natl Acad Sci U S A. 2008 Oct 14;105(41):15872-7 PMID: 18836073
  37. Histone3 lysine4 trimethylation regulated by the facilitates chromatin transcription complex is critical for DNA cleavage in class switch recombination.
    Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22190-5 PMID: 21139053
  38. The Paf1 complex: platform or player in RNA polymerase II transcription?
    Biochim Biophys Acta. 2010 May-Jun;1799(5-6):379-88 PMID: 20060942
  39. Interaction between antibody-diversification enzyme AID and spliceosome-associated factor CTNNBL1.
    Mol Cell. 2008 Aug 22;31(4):474-484 PMID: 18722174
  40. Active nuclear import and cytoplasmic retention of activation-induced deaminase.
    Nat Struct Mol Biol. 2009 May;16(5):517-27 PMID: 19412186
  41. S region sequence, RNA polymerase II, and histone modifications create chromatin accessibility during class switch recombination.
    J Exp Med. 2009 Aug 3;206(8):1817-30 PMID: 19596805
  42. Two levels of protection for the B cell genome during somatic hypermutation.
    Nature. 2008 Feb 14;451(7180):841-5 PMID: 18273020
  43. Mechanism and regulation of class switch recombination.
    Annu Rev Immunol. 2008;26:261-92 PMID: 18370922
  44. Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5.
    Cell. 2010 Oct 1;143(1):122-33 PMID: 20887897
  45. H2B ubiquitylation plays a role in nucleosome dynamics during transcription elongation.
    Mol Cell. 2008 Jul 11;31(1):57-66 PMID: 18614047
  46. H3 trimethyl K9 and H3 acetyl K9 chromatin modifications are associated with class switch recombination.
    Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5288-93 PMID: 19276123
  47. Genetic and in vitro assays of DNA deamination.
    Methods Enzymol. 2006;408:156-70 PMID: 16793368
Article Info
Journal
The Journal of experimental medicine
Abbr.
J Exp Med
ISSN
1540-9538
DOI
10.1084/jem.20112145
Published
2012-10-22
Epub
2012-00-24
Pages
2099-111
Language
English
Region
United States
NLM ID
2985109R
PMCID
PMC3478926
Subset
IM
External Links
PubMed source DOI: 10.1084/jem.20112145 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2