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

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

(2019) David Alejandro Bejarano et al.   eLife

Targeting the Latent Reservoir for HIV-1

(2018) Srona Sengupta et al.   IMMUNITY

BRD4 interacts with NIPBL and BRD4 is mutated in a Cornelia de Lange–like syndrome

(2018) Gabrielle Olley et al.   NATURE GENETICS

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

The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin-Remodeling Complexes

(2017) Ryan J. Conrad et al.   MOLECULAR CELL

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Capsid-Dependent Host Factors in HIV-1 Infection

(2017) Masahiro Yamashita et al.   TRENDS IN MICROBIOLOGY

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

What Integration Sites Tell Us about HIV Persistence

(2016) Stephen H. Hughes et al.   Cell Host & Microbe

Nucleoporin-mediated regulation of cell identity genes

(2016) Arkaitz Ibarra et al.   GENES & DEVELOPMENT

The Cleavage and Polyadenylation Specificity Factor 6 (CPSF6) Subunit of the Capsid-recruited Pre-messenger RNA Cleavage Factor I (CFIm) Complex Mediates HIV-1 Integration into Genes

(2016) Sheeba Rasheedi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Erratum: Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Nuclear landscape of HIV-1 infection and integration

(2016) Marina Lusic et al.   NATURE REVIEWS MICROBIOLOGY

Position effects influence HIV latency reversal

(2016) Heng-Chang Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes

(2016) Wei Shao et al.   Retrovirology

Position effects influence HIV latency reversal

(2016) Heng-Chang Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

LEDGIN-mediated Inhibition of Integrase–LEDGF/p75 Interaction Reduces Reactivation of Residual Latent HIV

(2016) Lenard S. Vranckx et al.   EBioMedicine

Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4+ T cells

(2016) Yik Lim Kok et al.   Scientific Reports

Understanding HIV Latency: The Road to an HIV Cure

(2015) Matthew S. Dahabieh et al.   Annual Review of Medicine

High-density P300 enhancers control cell state transitions

(2015) Steven Witte et al.   BMC GENOMICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2015) Suhas S.P. Rao et al.   CELL

A Hardwired HIV Latency Program

(2015) Brandon S. Razooky et al.   CELL

An Evolutionary Role for HIV Latency in Enhancing Viral Transmission

(2015) Igor M. Rouzine et al.   CELL

HIV-1 Integration Landscape during Latent and Active Infection

(2015) Lillian B. Cohn et al.   CELL

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

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

Regulation of HIV-1 Latency by Chromatin Structure and Nuclear Architecture

(2015) Marina Lusic et al.   JOURNAL OF MOLECULAR BIOLOGY

Super-enhancers delineate disease-associated regulatory nodes in T cells

(2015) Golnaz Vahedi et al.   NATURE

Nuclear architecture dictates HIV-1 integration site selection

(2015) Bruna Marini et al.   NATURE

HIV reservoirs: what, where and how to target them

(2015) Melissa J. Churchill et al.   NATURE REVIEWS MICROBIOLOGY

dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Super-enhancers: Asset management in immune cell genomes

(2015) Steven Witte et al.   TRENDS IN IMMUNOLOGY

Chromatin organization at the nuclear pore favours HIV replication

(2015) Mickaël Lelek et al.   Nature Communications

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Deep Imaging: the next frontier in microscopy

(2014) Vassilis Roukos et al.   HISTOCHEMISTRY AND CELL BIOLOGY

MLV integration site selection is driven by strong enhancers and active promoters

(2014) Matthew C. LaFave et al.   NUCLEIC ACIDS RESEARCH

Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection

(2014) T. A. Wagner et al.   SCIENCE

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

(2014) F. Maldarelli et al.   SCIENCE

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

BET bromodomain-targeting compounds reactivate HIV from latency via a Tat-independent mechanism

(2013) Daniela Boehm et al.   CELL CYCLE

BACH2 represses effector programs to stabilize Treg-mediated immune homeostasis

(2013) Rahul Roychoudhuri et al.   NATURE

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BET proteins promote efficient murine leukemia virus integration at transcription start sites

(2013) A. Sharma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bach2 maintains T cells in a naive state by suppressing effector memory-related genes

(2013) S.-i. Tsukumo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Imaging of HIV-1 Provirus (SCIP)

(2013) C. Di Primio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HIV restriction in quiescent CD4+ T cells

(2013) Jerome A Zack et al.   Retrovirology

Spatial Dynamics of Chromosome Translocations in Living Cells

(2013) V. Roukos et al.   SCIENCE

Nup153 and Nup98 bind the HIV-1 core and contribute to the early steps of HIV-1 replication

(2013) Francesca Di Nunzio et al.   VIROLOGY

The BET Family of Proteins Targets Moloney Murine Leukemia Virus Integration near Transcription Start Sites

(2013) Jan De Rijck et al.   Cell Reports

HIV DNA Integration

(2013) R. Craigie et al.   Cold Spring Harbor Perspectives in Medicine

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

(2012) Y. Koh et al.   JOURNAL OF VIROLOGY

Understanding the language of Lys36 methylation at histone H3

(2012) Eric J. Wagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The BET bromodomain inhibitor JQ1 activates HIV latency through antagonizing Brd4 inhibition of Tat-transactivation

(2012) Zichong Li et al.   NUCLEIC ACIDS RESEARCH

Directly Infected Resting CD4+T Cells Can Produce HIV Gag without Spreading Infection in a Model of HIV Latency

(2012) Matthew J. Pace et al.   PLoS Pathogens

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

HIV Integration Targeting: A Pathway Involving Transportin-3 and the Nuclear Pore Protein RanBP2

(2011) Karen E. Ocwieja et al.   PLoS Pathogens

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HIV integration site distributions in resting and activated CD4+ T cells infected in culture

(2009) Troy Brady et al.   AIDS

Integration target site selection by a resurrected human endogenous retrovirus

(2009) T. Brady et al.   GENES & DEVELOPMENT

Human Immunodeficiency Virus Integrates Directly into Naive Resting CD4+ T Cells but Enters Naive Cells Less Efficiently than Memory Cells

(2009) J. Dai et al.   JOURNAL OF VIROLOGY

The CXCR4-Tropic Human Immunodeficiency Virus Envelope Promotes More-Efficient Gene Delivery to Resting CD4+ T Cells than the Vesicular Stomatitis Virus Glycoprotein G Envelope

(2009) L. M. Agosto et al.   JOURNAL OF VIROLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation

(2009) Nicolas Chomont et al.   NATURE MEDICINE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE