Research

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Recent Alt Lab Publications

2016

Long neural genes harbor recurrent DNA break clusters in neural stem/progenitor cells.

Wei P-C, Chang AN, Kao J, Du Z, Meyers RM, Alt FW, Schwer B. Cell (2016) Feb 11;164(4):644-55. (PDF)


Sequential activation and distinct functions for distal and proximal modules within the IgH 3' regulatory region.

Garot A, Marquet M, Saintamand A, Bender S, Le Noir S, Rouaud P, Carrion C, Oruc Z, Bébin A-G, Moreau J, Lebrigand K, Denizot Y, Alt FW, Cogné M, Pinaud E. Proc Natl Acad Sci U S A. (2016) 113(6):1618-23. (PDF)

Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells.  

Schwer B, Wei P-C, Chang AN, Kao J, Du Z, Meyers RM, Alt FW. Proc. Natl. Acad. Sci. USA  (2016) 113(8):2258-63. (PDF)

Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing.

Hu J, Meyers RM, Dong J, Panchakshari RA, Alt FW, Frock RL. Nat Protoc. (2016) 11(5):853-71. (PDF)


NEHJ and other repair factors in V(D)J recombination.

Kumar V, Alt FW. In: Ratcliffe MJH. Editor in Chief, Encyclopedia of Immunobiology, Vol. 2, Oxford: Academic Press, pp. 107–14. (PDF)


2015


The Mechanism of IgH Class Switch Recombination. 

Meng F-L, Alt FW and Tian M , In: Alt FW, Honjo T, Radbruch A, Reth M editors.  San Diego: Academic Press: Molecular Biology of B Cells, (2015), Pages 345-356  (PDF)


Frock R L, Hu J, Meyers RM, HoY-J, Kii E Alt, FW.  Nature Biotechnology, (2015), Volume: 33, Pages: 179-186 (PDF)


Lin S G, Guo C, Su A, Zhang Y,  Alt FW.  PNAS (2015), Volume: 112, Pages: 1815-1820 (PDF)

Jiang W, Lee BJ, Chen L, Dubois RL, Gostissa M, Alt FW, Zha S.  Blood (2015), Volume: 125, Pages: 2665-2668 (PDF)

Zhang B, Calado D P, Wang Z, Fröhler S, Köchert K, Qian Y, Koralov SB, Schmidt-Supprian M, Sasaki Y, Unitt C, Rodig S, Chen W, Dalla-Favera R, Alt FW, Pasqualucci L, Rajewsky K. Cell Reports, (2015), Volume: 11, Pages: 715-726 (PDF)

Ba Z, Meng F-L, Gostissa M, Huang P-Y, Ke Q, Wang Z, Dao MN, Fuiwara Y, Rajewsky K, Zhang B,  Alt  FW.  Cancer Immunol. Res.(2015), Volume: 3, Pages: 641-649 (PDF)

Hwang J, Alt FW, Yeap, L-S.  Microbiology Spectrum, (2015), Volume: 3 (PDF)

Dong J, Panchakshari RA, Zhang T, Zhang Y, Hu J, Volpi SA, Meyers RM, Ho Y-J, Du Z, Robbiani DF, Meng F, Gostissa M, Nussenzweig  M C, Manis J P, Alt FW.  Nature, (2015), Volume: 525, Pages: 134-139  (PDF)

Sequence-intrinsic mechanisms that target AID mutational outcomes on antibody genes 

Yeap LS, Hwang JK, Du Z, Meyers RM, Meng F-L, Jakubauskaite A, Liu M, Mani V, Neuberg D, Kepler TB, Wang JH, Alt FW.  Cell, (2015), Volume: 163 Pages: 1124-1137 (PDF)

Chromosomal loop domains direct the recombination of antigen receptor genes 

Hu J, Zhang Y, Zhao L, Frock R L, Du Z, Meyers RM, Meng F-L, Schatz DG, Alt FW.  Cell, (2015), Volume: 163, Pages: 947-959.  

Mechanisms of recurrent chromosomal translocations 

Frock RL, Hu J, Alt F W, In: Rowley, J.D., Le Beau  M M, Rabbitts T H editors.  Chromosomal Translocations and Genome Rearrangements in Cancer, (2015) Pages: 27-51  (PDF)


2014

A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency.     

Lee YN, Frugoni F, Dobbs K, Walter JE, Giliani S, Gennery AR, Al-Herz W, Haddad E, LeDeist F, Bleesing JH, Henderson LA, Pai S-Y, Nelson RP, El-Ghoneimy DH, El-Feky RA, Reda SM, Hossny E, Soler-Palacin P, Fuleihan RL, Patel NC, Massaad MJ, Geha RS, Puck JM, Palma P, Cancrini C, Chen K, Vihinen M, Alt FW, Notarangelo LD   J. Allergy & Clinical Immunology (2014), Volume: 133,  Pages: 1099-1108 (PDF)

Precise and in situ genetic humanization of 6 Mb of mouse immunoglobulin genes.

Macdonald LE, Karow M, Stevens S, Auerbach W, Poueymirou WT, Yasenchak J, Frendewey D, Valenzuela DM, Giallourakis CC, Alt FW, Yancopoulos G D, Murphy AJ Proc. Natl. Acad. Sci. USA (2014), Volume 111, Pages: 5147-52  (PDF)

Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability.   

Meng F-L, Du Z, Federation A, Hu J, Wang Q, Kieffer-Kwon KR, Meyers RM, Amor C, Wasserman CR, Neuberg D, Casellas R, Nussenzweig MC, Bradner JE, Liu XS,  Alt FW  Cell (2014), Volume: 159, PagesL 1538-48 (PDF)

IgH class switching exploits a general property of two DNA breaks to be joined in cis over long chromosomal distances

Gostissa M, Schwer B, Chang A, Dong J, Meyers RM, Marecki GT, Choi VW, Chiarle R, Zarrin AA, Alt FW.
Proc Natl Acad Sci U S A. (2014), Volume: 111, Issue: 7, Pages: 2644-9 (PDF)

Kumar Vipul, Alt Frederick W, Oksenych Valentyn.
DNA Repair (2014), Volume: 16, Pages: 11-22 (PDF)

Hu J, Tepsuporn S, Meyers RM, Gostissa M, Alt FW.
PNAS (2014), Volume: 111, Issue: 28, Pages: 10269-74 (PDF)

Tepsuporn S, Hu J, Gostissa M, Alt FW

Cancer Immunol Res. (2014), Volume: 2, Issue: 9, Pages: 857-66 (PDF)


2013

Functional redundancy between the XLF and DNA-PKcs DNA repair factors in VDJ recombination and nonhomologous DNA end joining
Oksenych V, Kumar V, Liu X, Guo C, Schwer B, Zha S, Alt FW.
Proc Natl Acad Sci U S A. (2013), Volume: 110, Issue: 6, Pages: 2234-9 (PDF)


Mechanisms of programmed DNA lesions and genomic instability in the immune system
Alt FW, Zhang Y, Meng FL, Guo C, Schwer B
Cell (2013), Volume: 152, Issue: 3, Pages: 417-29 (PDF)

Conditional inactivation of p53 in mature B cells promotes generation of nongerminal center-derived B-cell lymphomas
Gostissa M, Bianco JM, Malkin DJ, Kutok JL, Rodig SJ, Morse HC 3rd, Bassing CH, Alt FW
Proc Natl Acad Sci U S A. (2013), Volume: 110, Issue: 8, Pages: 2934-9 (PDF)

Microbial colonization influences early B-lineage development in the gut lamina propria.
Wesemann DR, Portuguese AJ, Meyers RM, Gallagher MP, Cluff-Jones K, Magee JM, Panchakshari RA, Rodig SJ, Kepler TB, Alt FW
Nature (2013), Volume: 501, Issue: 7465, Pages: 112-5 (PDF)

Ataxia telangiectasia mutated (ATM) is dispensable for endonuclease I-SceI-induced homologous recombination in mouse embryonic stem cells
Rass E, Chandramouly G, Zha S, Alt FW, Xie A
J Biol Chem (2013), Volume: 288, Issue: 10, Pages: 7086-95

Localized DNA demethylation at recombination intermediates during immunoglobulin heavy chain gene assembly.
Selimyan R, Gerstein RM, Ivanova I, Precht P, Subrahmanyam R, Perlot T, Alt FW, Sen R. 
PLoS Biol (2013), Volume: 11, Issue: 1, Pages: :e1001475

Essential developmental, genomic stability, and tumour suppressor functions of the mouse orthologue of hSSB1/NABP2.
Shi W, Bain AL, Schwer B, Al-Ejeh F, Smith C, Wong L, Chai H, Miranda MS, Ho U, Kawaguchi M, Miura Y, Finnie JW, Wall M, Heierhorst J, Wicking C, Spring KJ, Alt FW, Khanna KK. 
PLoS Genet (2013), Volume: 9, Issue: 2, Pages: e1003298

53BP1 mediates productive and mutagenic DNA repair through distinct phosphoprotein interactions.
Callen E, Di Virgilio M, Kruhlak MJ, Nieto-Soler M, Wong N, Chen HT, Faryabi RB, Polato F, Santos M, Starnes LM, Wesemann DR, Lee JE, Tubbs A, Sleckman BP, Daniel JA, Ge K, Alt FW, Fernandez-Capetillo O, Nussenzweig MC, Nussenzweig A
Cell (2013), Volume: 153, Issue: 6, Pages: 1266--80

Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.
Medvedovic J, Ebert A, Tagoh H, Tamir IM, Schwickert TA, Novatchkova M, Sun Q, Huis In 't Veld PJ, Guo C, Yoon HS, Denizot Y, Holwerda SJ, de Laat W, Cogné M, Shi Y, Alt FW, Busslinger M
Immunity (2013), Volume: 39, Issue: 2, Pages: 229-44

Antigen-specific B-cell receptor sensitizes B cells to infection by influenza virus.
Dougan SK, Ashour J, Karssemeijer RA, Popp MW, Avalos AM, Barisa M, Altenburg AF, Ingram JR, Cragnolini JJ, Guo C, Alt FW, Jaenisch R, Ploegh HL
Nature (2013), Volume: 503, Issue: 7476, Pages: 406-9

SIRT7 represses Myc activity to suppress ER stress and prevent fatty liver disease.
Shin J, He M, Liu Y, Paredes S, Villanova L, Brown K, Qiu X, Nabavi N, Mohrin M, Wojnoonski K, Li P, Cheng HL, Murphy AJ, Valenzuela DM, Luo H, Kapahi P, Krauss R, Mostoslavsky R, Yancopoulos GD, Alt FW, Chua KF, Chen D
Cell Rep (2013), Volume: 5, Issue: 3, Pages: 654-65
 
A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency.
Lee YN, Frugoni F, Dobbs K, Walter JE, Giliani S, Gennery AR, Al-Herz W, Haddad E, Ledeist F, Bleesing JH, Henderson LA, Pai SY, Nelson RP, El-Ghoneimy DH, El-Feky RA, Reda SM, Hossny E, Soler-Palacin P, Fuleihan RL, Patel NC, Massaad MJ, Geha RS, Puck JM, Palma P, Cancrini C, Chen K, Vihinen M, Alt FW, Notarangelo LD
J Allergy Clin Immunol (2013), Volume: S0091-6749, Issue: 13, Pages: 01558-3

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