Deciphering the code for retroviral integration target site selection (Q33760990)

29 July 2017

title

Deciphering the code for retroviral integration target site selection (English)

1 reference

29 July 2017

Jeremy Luban

3

0 references

author name string

Federico Andrea Santoni

series ordinal

1

1 reference

29 July 2017

Oliver Hartley

series ordinal

2

1 reference

29 July 2017

publication date

24 November 2010

1 reference

PLOS Computational Biology

29 July 2017

published in

1 reference

29 July 2017

volume

6

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29 July 2017

issue

11

1 reference

29 July 2017

page(s)

e1001008

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Creative Commons Attribution 4.0 International

29 July 2017

copyright license

start time

24 November 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Identification of a high incidence region for retroviral vector integration near exon 1 of the LMO2 locus

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Murine leukemias with retroviral insertions at Lmo2 are predictive of the leukemias induced in SCID-X1 patients following retroviral gene therapy

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21 June 2018

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Methods for integration site distribution analyses in animal cell genomes

21 June 2018

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Genome areas with high gene density and CpG island neighborhood strongly attract porcine endogenous retrovirus for integration and favor the formation of hot spots.

21 June 2018

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Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition

21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients

21 June 2018

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Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1

21 June 2018

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Integration site preference of xenotropic murine leukemia virus-related virus, a new human retrovirus associated with prostate cancer

21 June 2018

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A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

21 June 2018

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Host proteins interacting with the Moloney murine leukemia virus integrase: multiple transcriptional regulators and chromatin binding factors

21 June 2018

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Combinatorial patterns of histone acetylations and methylations in the human genome

21 June 2018

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DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer

21 June 2018

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Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting

21 June 2018

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Evidence for direct involvement of the capsid protein in HIV infection of nondividing cells

21 June 2018

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Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy

21 June 2018

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LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

A chromatin landmark and transcription initiation at most promoters in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

High-resolution profiling of histone methylations in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Hot spots of retroviral integration in human CD34+ hematopoietic cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Human T-cell leukemia virus type 1 integration target sites in the human genome: comparison with those of other retroviruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Chromatin modifications and their function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T cell populations during effective highly active antiretroviral therapy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Selection of target sites for mobile DNA integration in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

An essential role for LEDGF/p75 in HIV integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Regulation of MLL1 H3K4 methyltransferase activity by its core components

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Retroviral DNA integration: viral and cellular determinants of target-site selection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Methylation of histone H3 mediates the association of the NuA3 histone acetyltransferase with chromatin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Retroviral DNA integration: reaction pathway and critical intermediates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Retroviral vector integration deregulates gene expression but has no consequence on the biology and function of transplanted T cells.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Foamy virus vector integration sites in normal human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Cellular co-factors of HIV-1 integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Interaction of moloney murine leukemia virus capsid with Ubc9 and PIASy mediates SUMO-1 addition required early in infection.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

A role for LEDGF/p75 in targeting HIV DNA integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Retroviral insertional mutagenesis: past, present and future

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

The cell cycle independence of HIV infections is not determined by known karyophilic viral elements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

The role of LMO2 in development and in T cell leukemia after chromosomal translocation or retroviral insertion

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Acetylation of HIV-1 integrase by p300 regulates viral integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

TRIM5alpha selectively binds a restriction-sensitive retroviral capsid

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Retroviral DNA integration and the DNA damage response

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Genome-wide analyses of avian sarcoma virus integration sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Human cell proteins and human immunodeficiency virus DNA integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Transcription start regions in the human genome are favored targets for MLV integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

HIV-1 integrase forms stable tetramers and associates with LEDGF/p75 protein in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Active genes are tri-methylated at K4 of histone H3

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

IFN-Stimulated transcription through a TBP-free acetyltransferase complex escapes viral shutoff

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Physical association between the histone acetyl transferase CBP and a histone methyl transferase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Initial sequencing and analysis of the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Repair of gaps in retroviral DNA integration intermediates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

A role for DNA-PK in retroviral DNA integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Exon shuffling by L1 retrotransposition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

The paleontology of intergene retrotransposons of maize

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Two contact regions between Stat1 and CBP/p300 in interferon gamma signaling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Concerted integration of linear retroviral DNA by the avian sarcoma virus integrase in vitro: dependence on both long terminal repeat termini

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Human immunodeficiency virus type 1 Gag protein binds to cyclophilins A and B

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Integration of murine leukemia virus DNA depends on mitosis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Use of a selectable marker regulated by alpha interferon to obtain mutations in the signaling pathway

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Productive human immunodeficiency virus type 1 (HIV-1) infection of nonproliferating human monocytes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Site-specific hydrolysis and alcoholysis of human immunodeficiency virus DNa termini mediated by the viral integrase protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Human immunodeficiency virus infection of cells arrested in the cell cycle

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Nonrandom integration of retroviral DNA in vitro: effect of CpG methylation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Retroviral integration into minichromosomes in vitro

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2991247

Integrase mutants defective for interaction with LEDGF/p75 are impaired in chromosome tethering and HIV-1 replication

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001008

Comparative experiments on learning information extractors for proteins and their interactions.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001008

Prediction of protein functional residues from sequence by probability density estimation

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001008

Cyclin D2 dysregulation by chromosomal translocations to TCR loci in T-cell acute lymphoblastic leukemias

21 January 2018

1 reference

12 December 2020

Retrotransposons as epigenetic mediators of phenotypic variation in mammals

1 reference

12 December 2020

The influence of DNA and nucleosome structure on integration events directed by HIV integrase

1 reference

12 December 2020

Immune response in Stat2 knockout mice

1 reference

12 December 2020

Distribution of targets for avian retrovirus DNA integration in vivo

1 reference

12 December 2020

Structure of the termini of DNA intermediates in the integration of retroviral DNA: dependence on IN function and terminal DNA sequence

1 reference

12 December 2020

HIV-1 DNA integration: Mechanism of viral DNA cleavage and DNA strand transfer

1 reference

12 December 2020

Random Forests

1 reference

Astrophysics Data System

15 December 2022

https://ui.adsabs.harvard.edu/abs/2001MachL..45....5B/citations

Identifiers

DOI

10.1371/JOURNAL.PCBI.1001008

1 reference

journals/ploscb/SantoniHL10

29 July 2017

0 references

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

29 July 2017

1 reference