Spatial and Genomic Correlates of HIV-1 Integration Site Targeting

rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

(2021) Gregory J Bedwell et al.   NUCLEIC ACIDS RESEARCH

HIV-1 uncoats in the nucleus near sites of integration

(2020) Ryan C. Burdick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The chromatin landscape at the HIV-1 provirus integration site determines viral expression

(2020) Gerlinde Vansant et al.   NUCLEIC ACIDS RESEARCH

HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains

(2020) Ashwanth C. Francis et al.   Nature Communications

CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration

(2020) Wen Li et al.   mBio

Factors that mold the nuclear landscape of HIV-1 integration

(2020) Gregory J Bedwell et al.   NUCLEIC ACIDS RESEARCH

HIV-1 nuclear import in macrophages is regulated by CPSF6-capsid interactions at the Nuclear Pore Complex

(2019) David Alejandro Bejarano et al.   eLife

Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans

(2019) Andrea L. Ferris et al.   PLoS Pathogens

Dominant negative MA-CA fusion protein is incorporated into HIV-1 cores and inhibits nuclear entry of viral preintegration complexes

(2019) Jordan Anderson-Daniels et al.   JOURNAL OF VIROLOGY

Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration

(2019) Bojana Lucic et al.   Nature Communications

LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription in differentiated cells

(2019) Gary LeRoy et al.   Science Advances

Single HIV-1 Imaging Reveals Progression of Infection through CA-Dependent Steps of Docking at the Nuclear Pore, Uncoating, and Nuclear Transport

(2018) Ashwanth C. Francis et al.   Cell Host & Microbe

Capsid-CPSF6 Interaction Licenses Nuclear HIV-1 Trafficking to Sites of Viral DNA Integration

(2018) Vasudevan Achuthan et al.   Cell Host & Microbe

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

(2018) Benjamin J. Schmiedel et al.   CELL

Capsid-CPSF6 Interaction Is Dispensable for HIV-1 Replication in Primary Cells but Is Selected during Virus PassageIn Vivo

(2016) Akatsuki Saito et al.   JOURNAL OF VIROLOGY

A critical role for alternative polyadenylation factor CPSF6 in targeting HIV-1 integration to transcriptionally active chromatin

(2016) Gregory A. Sowd et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

(2016) Erik Serrao et al.   Jove-Journal of Visualized Experiments

LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes

(2015) Parmit Kumar Singh et al.   GENES & DEVELOPMENT

Nuclear architecture dictates HIV-1 integration site selection

(2015) Bruna Marini et al.   NATURE

Direct Visualization of HIV-1 Replication Intermediates Shows that Capsid and CPSF6 Modulate HIV-1 Intra-nuclear Invasion and Integration

(2015) Christopher R. Chin et al.   Cell Reports

Gene density and chromosome territory shape

(2014) Nitasha Sehgal et al.   CHROMOSOMA

Molecular mechanisms of retroviral integration site selection

(2014) Mamuka Kvaratskhelia et al.   NUCLEIC ACIDS RESEARCH

Host and viral determinants for MxB restriction of HIV-1 infection

(2014) Kenneth A Matreyek et al.   Retrovirology

Specific HIV integration sites are linked to clonal expansion and persistence of infected cells

(2014) F. Maldarelli et al.   SCIENCE

Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes

(2013) Jocelyn O. Eidahl et al.   NUCLEIC ACIDS RESEARCH

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells

(2012) Rik Schrijvers et al.   Retrovirology

Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing

(2012) Madapura M. Pradeepa et al.   PLoS Genetics

LEDGF/p75-Independent HIV-1 Replication Demonstrates a Role for HRP-2 and Remains Sensitive to Inhibition by LEDGINs

(2012) Rik Schrijvers et al.   PLoS Pathogens

Gammaretroviral Integration into Nucleosomal Target DNA In Vivo

(2011) S. L. Roth et al.   JOURNAL OF VIROLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Flexible Use of Nuclear Import Pathways by HIV-1

(2010) KyeongEun Lee et al.   Cell Host & Microbe

Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration

(2010) A. L. Ferris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Novel Co-Crystal Structure Affords the Design of Gain-of-Function Lentiviral Integrase Mutants in the Presence of Modified PSIP1/LEDGF/p75

(2009) Stephen Hare et al.   PLoS Pathogens

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY