Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors

Systemic HIV and SIV latency reversal via non-canonical NF-κB signalling in vivo

(2020) Christopher C. Nixon et al.   NATURE

Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels

(2020) Wenliang Wang 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

HUSH, a Link Between Intrinsic Immunity and HIV Latency

(2019) Ghina Chougui et al.   Frontiers in Microbiology

FOXO1 transcription factor plays a key role in T cell—HIV-1 interaction

(2019) Arthur Roux et al.   PLoS Pathogens

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

(2019) Anders S. Hansen et al.   MOLECULAR CELL

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

(2019) Ricardo Saldaña-Meyer et al.   MOLECULAR CELL

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

(2019) Bojana Lucic et al.   Nature Communications

TADs and Their Borders: Free Movement or Building a Wall?

(2019) Li-Hsin Chang et al.   JOURNAL OF MOLECULAR BIOLOGY

Optimized RNP transfection for highly efficient CRISPR/Cas9-mediated gene knockout in primary T cells

(2018) Akiko Seki et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Depletion of the Insulator Protein CTCF Results in Herpes Simplex Virus 1 Reactivation In Vivo

(2018) Shannan D. Washington et al.   JOURNAL OF VIROLOGY

Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency

(2018) Todd Bradley et al.   Cell Reports

Current status of HIV/AIDS in the ART era

(2017) Kazuhisa Yoshimura   JOURNAL OF INFECTION AND CHEMOTHERAPY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART

(2017) Ann Wiegand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of HIV persistence in HIV reservoirs

(2017) Mayibongwe L. Mzingwane et al.   REVIEWS IN MEDICAL VIROLOGY

FOXP1 is a regulator of quiescence in healthy human CD4+ T cells and is constitutively repressed in T cells from patients with lymphoproliferative disorders

(2016) Soizic Garaud et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

CTCF: making the right connections

(2016) Rodolfo Ghirlando et al.   GENES & DEVELOPMENT

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

(2016) Elisa Fiorito et al.   NUCLEIC ACIDS RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Diversity of HIV-1 reservoirs in CD4+ T-cell subpopulations

(2016) Guinevere Q. Lee et al.   Current Opinion in HIV and AIDS

Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells

(2016) Valentina Boeva   Frontiers in Genetics

A Hardwired HIV Latency Program

(2015) Brandon S. Razooky et al.   CELL

H3K27 Demethylation at the Proviral Promoter Sensitizes Latent HIV to the Effects of Vorinostat inEx VivoCultures of Resting CD4+T Cells

(2015) Manoj K. Tripathy et al.   JOURNAL OF VIROLOGY

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

The Depsipeptide Romidepsin Reverses HIV-1 Latency In Vivo

(2015) Ole S. Søgaard et al.   PLoS Pathogens

Quantitation of Replication-Competent HIV-1 in Populations of Resting CD4+ T Cells

(2014) N. Soriano-Sarabia et al.   JOURNAL OF VIROLOGY

Selective HDAC Inhibition for the Disruption of Latent HIV-1 Infection

(2014) Kirston M. Barton et al.   PLoS One

Direct non-productive HIV-1 infection in a T-cell line is driven by cellular activation state and NFκB

(2014) Matthew S Dahabieh et al.   Retrovirology

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

(2014) F. Maldarelli et al.   SCIENCE

HIV-Infected Individuals with Low CD4/CD8 Ratio despite Effective Antiretroviral Therapy Exhibit Altered T Cell Subsets, Heightened CD8+ T Cell Activation, and Increased Risk of Non-AIDS Morbidity and Mortality

(2014) Sergio Serrano-Villar et al.   PLoS Pathogens

How Might We Cure HIV?

(2014) David M. Margolis   Current Infectious Disease Reports

Replication-Competent Noninduced Proviruses in the Latent Reservoir Increase Barrier to HIV-1 Cure

(2013) Ya-Chi Ho et al.   CELL

Unique characteristics of histone deacetylase inhibitors in reactivation of latent HIV-1 in Bcl-2-transduced primary resting CD4+ T cells

(2013) Liang Shan et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

HIV Latency

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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

An AP-1 Binding Site in the Enhancer/Core Element of the HIV-1 Promoter Controls the Ability of HIV-1 To Establish Latent Infection

(2012) A. Duverger et al.   JOURNAL OF VIROLOGY

Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy

(2012) N. M. Archin et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Biomarkers of immune dysfunction following combination antiretroviral therapy for HIV infection

(2011) Gregor F Lichtfuss et al.   Biomarkers in Medicine

Immunologic Failure Despite Suppressive Antiretroviral Therapy Is Related to Activation and Turnover of Memory CD4 Cells

(2011) Michael M. Lederman et al.   JOURNAL OF INFECTIOUS DISEASES

T-Cell Receptor Signaling Enhances Transcriptional Elongation from Latent HIV Proviruses by Activating P-TEFb through an ERK-Dependent Pathway

(2011) Young Kyeung Kim et al.   JOURNAL OF MOLECULAR BIOLOGY

Epigenetic Silencing of HIV-1 by the Histone H3 Lysine 27 Methyltransferase Enhancer of Zeste 2

(2011) J. Friedman et al.   JOURNAL OF VIROLOGY

Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency

(2011) Haleh Rafati et al.   PLOS BIOLOGY

Establishment of HIV Latency in Primary CD4+ Cells Is due to Epigenetic Transcriptional Silencing and P-TEFb Restriction

(2010) M. Tyagi et al.   JOURNAL OF VIROLOGY

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

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Nicolas Chomont et al.   NATURE MEDICINE

Epigenetic Silencing of Human Immunodeficiency Virus (HIV) Transcription by Formation of Restrictive Chromatin Structures at the Viral Long Terminal Repeat Drives the Progressive Entry of HIV into Latency

(2008) R. Pearson et al.   JOURNAL OF VIROLOGY