Literature DB >> 15802467

Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites.

Alexander G Holman1, John M Coffin.   

Abstract

To investigate retroviral integration targeting on a nucleotide scale, we examined the base frequencies directly surrounding cloned in vivo HIV-1, murine leukemia virus, and avian sarcoma/leukosis virus integrations. Base preferences of up to 2-fold the expected frequencies were found for three viruses, representing P values down to <10(-100) and defining what appear to be preferred integration sequences. Offset symmetry reflecting the topology of the integration reaction was found for HIV-1 and avian sarcoma/leukosis virus but not murine leukemia virus, suggesting fundamental differences in the way different retroviral integration complexes interact with host-cell DNA.

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Year:  2005        PMID： 15802467      PMCID： PMC1087937          DOI： 10.1073/pnas.0501646102

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


  12 in total

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Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

2.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

3.  The UCSC Genome Browser Database.

Authors:  D Karolchik; R Baertsch; M Diekhans; T S Furey; A Hinrichs; Y T Lu; K M Roskin; M Schwartz; C W Sugnet; D J Thomas; R J Weber; D Haussler; W J Kent
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  HIV-1 integration in the human genome favors active genes and local hotspots.

Authors:  Astrid R W Schröder; Paul Shinn; Huaming Chen; Charles Berry; Joseph R Ecker; Frederic Bushman
Journal:  Cell       Date:  2002-08-23       Impact factor: 41.582

5.  Relationship between retroviral DNA-integration-site selection and host cell transcription.

Authors:  Lori F Maxfield; Camilla D Fraize; John M Coffin
Journal:  Proc Natl Acad Sci U S A       Date:  2005-01-19       Impact factor: 11.205

6.  Chromosome structure and human immunodeficiency virus type 1 cDNA integration: centromeric alphoid repeats are a disfavored target.

Authors:  S Carteau; C Hoffmann; F Bushman
Journal:  J Virol       Date:  1998-05       Impact factor: 5.103

7.  Genome-wide analyses of avian sarcoma virus integration sites.

Authors:  Anna Narezkina; Konstantin D Taganov; Samuel Litwin; Radka Stoyanova; Junpei Hayashi; Christoph Seeger; Anna Marie Skalka; Richard A Katz
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Journal:  J Virol       Date:  1995-10       Impact factor: 5.103

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Authors:  Xiaolin Wu; Yuan Li; Bruce Crise; Shawn M Burgess
Journal:  Science       Date:  2003-06-13       Impact factor: 47.728

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Authors:  Rick S Mitchell; Brett F Beitzel; Astrid R W Schroder; Paul Shinn; Huaming Chen; Charles C Berry; Joseph R Ecker; Frederic D Bushman
Journal:  PLoS Biol       Date:  2004-08-17       Impact factor: 8.029
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  102 in total

Review 1.  HIV DNA integration.

Authors:  Robert Craigie; Frederic D Bushman
Journal:  Cold Spring Harb Perspect Med       Date:  2012-07       Impact factor: 6.915

2.  DNA pattern recognition using canonical correlation algorithm.

Authors:  B K Sarkar; Chiranjib Chakraborty
Journal:  J Biosci       Date:  2015-10       Impact factor: 1.826

3.  A high-throughput method for cloning and sequencing human immunodeficiency virus type 1 integration sites.

Authors:  Sanggu Kim; Yein Kim; Teresa Liang; Janet S Sinsheimer; Samson A Chow
Journal:  J Virol       Date:  2006-09-13       Impact factor: 5.103

4.  Symmetrical recognition of cellular DNA target sequences during retroviral integration.

Authors:  Duane P Grandgenett
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-19       Impact factor: 11.205

5.  HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications.

Authors:  Gary P Wang; Angela Ciuffi; Jeremy Leipzig; Charles C Berry; Frederic D Bushman
Journal:  Genome Res       Date:  2007-06-01       Impact factor: 9.043

Review 6.  Integrase, LEDGF/p75 and HIV replication.

Authors:  E M Poeschla
Journal:  Cell Mol Life Sci       Date:  2008-05       Impact factor: 9.261

7.  Biochemical and biophysical analyses of concerted (U5/U3) integration.

Authors:  Duane P Grandgenett; Sibes Bera; Krishan K Pandey; Ajaykumar C Vora; Jacob Zahm; Sapna Sinha
Journal:  Methods       Date:  2008-11-29       Impact factor: 3.608

8.  Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells.

Authors:  Gary P Wang; Bruce L Levine; Gwendolyn K Binder; Charles C Berry; Nirav Malani; Gary McGarrity; Pablo Tebas; Carl H June; Frederic D Bushman
Journal:  Mol Ther       Date:  2009-03-03       Impact factor: 11.454

9.  Differential effects of human immunodeficiency virus type 1 capsid and cellular factors nucleoporin 153 and LEDGF/p75 on the efficiency and specificity of viral DNA integration.

Authors:  Yasuhiro Koh; Xiaolin Wu; Andrea L Ferris; Kenneth A Matreyek; Steven J Smith; KyeongEun Lee; Vineet N KewalRamani; Stephen H Hughes; Alan Engelman
Journal:  J Virol       Date:  2012-10-24       Impact factor: 5.103

10.  Bromo- and extraterminal domain chromatin regulators serve as cofactors for murine leukemia virus integration.

Authors:  Saumya Shree Gupta; Tobias Maetzig; Goedele N Maertens; Azar Sharif; Michael Rothe; Magdalena Weidner-Glunde; Melanie Galla; Axel Schambach; Peter Cherepanov; Thomas F Schulz
Journal:  J Virol       Date:  2013-09-18       Impact factor: 5.103
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