Literature DB >> 22308462

Nonimmunoglobulin target loci of activation-induced cytidine deaminase (AID) share unique features with immunoglobulin genes.

Lucia Kato1, Nasim A Begum, A Maxwell Burroughs, Tomomitsu Doi, Jun Kawai, Carsten O Daub, Takahisa Kawaguchi, Fumihiko Matsuda, Yoshihide Hayashizaki, Tasuku Honjo.   

Abstract

Activation-induced cytidine deaminase (AID) is required for both somatic hypermutation and class-switch recombination in activated B cells. AID is also known to target nonimmunoglobulin genes and introduce mutations or chromosomal translocations, eventually causing tumors. To identify as-yet-unknown AID targets, we screened early AID-induced DNA breaks by using two independent genome-wide approaches. Along with known AID targets, this screen identified a set of unique genes (SNHG3, MALAT1, BCL7A, and CUX1) and confirmed that these loci accumulated mutations as frequently as Ig locus after AID activation. Moreover, these genes share three important characteristics with the Ig gene: translocations in tumors, repetitive sequences, and the epigenetic modification of chromatin by H3K4 trimethylation in the vicinity of cleavage sites.

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Year:  2012        PMID： 22308462      PMCID： PMC3289292          DOI： 10.1073/pnas.1120791109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  61 in total

1.  A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription.

Authors:  Bong-Gun Ju; Victoria V Lunyak; Valentina Perissi; Ivan Garcia-Bassets; David W Rose; Christopher K Glass; Michael G Rosenfeld
Journal:  Science       Date:  2006-06-23       Impact factor: 47.728

2.  The host gene for intronic U17 small nucleolar RNAs in mammals has no protein-coding potential and is a member of the 5'-terminal oligopyrimidine gene family.

Authors:  P Pelczar; W Filipowicz
Journal:  Mol Cell Biol       Date:  1998-08       Impact factor: 4.272

3.  Infection of human B cells with Epstein-Barr virus results in the expression of somatic hypermutation-inducing molecules and in the accrual of oncogene mutations.

Authors:  Marta Epeldegui; Yee Ping Hung; Amy McQuay; Richard F Ambinder; Otoniel Martínez-Maza
Journal:  Mol Immunol       Date:  2006-05-26       Impact factor: 4.407

4.  A target selection of somatic hypermutations is regulated similarly between T and B cells upon activation-induced cytidine deaminase expression.

Authors:  Ai Kotani; Il-Mi Okazaki; Masamichi Muramatsu; Kazuo Kinoshita; Nasim A Begum; Toshiharu Nakajima; Hirohisa Saito; Tasuku Honjo
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-14       Impact factor: 11.205

5.  Helicobacter pylori infection triggers aberrant expression of activation-induced cytidine deaminase in gastric epithelium.

Authors:  Yuko Matsumoto; Hiroyuki Marusawa; Kazuo Kinoshita; Yoko Endo; Tadayuki Kou; Toshiyuki Morisawa; Takeshi Azuma; Il-Mi Okazaki; Tasuku Honjo; Tsutomu Chiba
Journal:  Nat Med       Date:  2007-04-01       Impact factor: 53.440

6.  DNA sequence of the translocation breakpoints in undifferentiated embryonal sarcoma arising in mesenchymal hamartoma of the liver harboring the t(11;19)(q11;q13.4) translocation.

Authors:  Veena Rajaram; Stevan Knezevich; Kevin E Bove; Arie Perry; John D Pfeifer
Journal:  Genes Chromosomes Cancer       Date:  2007-05       Impact factor: 5.006

7.  Histone modifications associated with somatic hypermutation.

Authors:  Valerie H Odegard; Sean T Kim; Shannon M Anderson; Mark J Shlomchik; David G Schatz
Journal:  Immunity       Date:  2005-07       Impact factor: 31.745

8.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

9.  Expression of the AID protein in normal and neoplastic B cells.

Authors:  Laura Pasqualucci; Roberta Guglielmino; Jane Houldsworth; Jessica Mohr; Said Aoufouchi; Roberto Polakiewicz; R S K Chaganti; Riccardo Dalla-Favera
Journal:  Blood       Date:  2004-08-10       Impact factor: 22.113

10.  Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells.

Authors:  Niklas Feldhahn; Nadine Henke; Kai Melchior; Cihangir Duy; Bonaventure Ndikung Soh; Florian Klein; Gregor von Levetzow; Bernd Giebel; Aihong Li; Wolf-Karsten Hofmann; Hassan Jumaa; Markus Müschen
Journal:  J Exp Med       Date:  2007-05-07       Impact factor: 14.307
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  34 in total

1.  Collateral DNA damage produced by genome-editing drones: exception or rule?

Authors:  Andres Canela; Andre Stanlie; André Nussenzweig
Journal:  Mol Cell       Date:  2015-05-21       Impact factor: 17.970

2.  Accumulation of the FACT complex, as well as histone H3.3, serves as a target marker for somatic hypermutation.

Authors:  Masatoshi Aida; Nesreen Hamad; Andre Stanlie; Nasim A Begum; Tasuku Honjo
Journal:  Proc Natl Acad Sci U S A       Date:  2013-04-22       Impact factor: 11.205

3.  Identification of DNA cleavage- and recombination-specific hnRNP cofactors for activation-induced cytidine deaminase.

Authors:  Wenjun Hu; Nasim A Begum; Samiran Mondal; Andre Stanlie; Tasuku Honjo
Journal:  Proc Natl Acad Sci U S A       Date:  2015-04-20       Impact factor: 11.205

4.  AID-associated DNA repair pathways regulate malignant transformation in a murine model of BCL6-driven diffuse large B-cell lymphoma.

Authors:  Xiwen Gu; Carmen J Booth; Zongzhi Liu; Matthew P Strout
Journal:  Blood       Date:  2015-09-18       Impact factor: 22.113

Review 5.  The cellular etiology of chromosome translocations.

Authors:  Vassilis Roukos; Bharat Burman; Tom Misteli
Journal:  Curr Opin Cell Biol       Date:  2013-03-14       Impact factor: 8.382

6.  The Transcription Factor AP4 Mediates Resolution of Chronic Viral Infection through Amplification of Germinal Center B Cell Responses.

Authors:  Chun Chou; Daniel J Verbaro; Elena Tonc; Melanie Holmgren; Marina Cella; Marco Colonna; Deepta Bhattacharya; Takeshi Egawa
Journal:  Immunity       Date:  2016-08-23       Impact factor: 31.745

7.  The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult.

Authors:  Bin Zhang; Gayatri Arun; Yuntao S Mao; Zsolt Lazar; Gene Hung; Gourab Bhattacharjee; Xiaokun Xiao; Carmen J Booth; Jie Wu; Chaolin Zhang; David L Spector
Journal:  Cell Rep       Date:  2012-06-28       Impact factor: 9.423

8.  The histone chaperone Spt6 is required for activation-induced cytidine deaminase target determination through H3K4me3 regulation.

Authors:  Nasim A Begum; Andre Stanlie; Mikiyo Nakata; Hideo Akiyama; Tasuku Honjo
Journal:  J Biol Chem       Date:  2012-07-26       Impact factor: 5.157

9.  BCL6 breaks occur at different AID sequence motifs in Ig-BCL6 and non-Ig-BCL6 rearrangements.

Authors:  Zhengfei Lu; Albert G Tsai; Takashi Akasaka; Hitoshi Ohno; Yanwen Jiang; Ari M Melnick; Harvey A Greisman; Michael R Lieber
Journal:  Blood       Date:  2013-03-08       Impact factor: 22.113

Review 10.  The origin of recurrent translocations in recombining lymphocytes: a balance between break frequency and nuclear proximity.

Authors:  Pedro P Rocha; Jane A Skok
Journal:  Curr Opin Cell Biol       Date:  2013-03-13       Impact factor: 8.382
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