Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains

Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses

(2022) Kevin B. Einkauf et al.   CELL

Role of the cellular factor CTCF in the regulation of bovine leukemia virus latency and three-dimensional chromatin organization

(2022) Maxime Bellefroid et al.   NUCLEIC ACIDS RESEARCH

Recruitment of the CoREST transcription repressor complexes by Nerve Growth factor IB-like receptor (Nurr1/NR4A2) mediates silencing of HIV in microglial cells

(2022) Fengchun Ye et al.   PLoS Pathogens

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

(2021) Naoki Kubo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability

(2021) Evonne McArthur et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors

(2021) Stuart R. Jefferys et al.   PLoS Pathogens

Utilization of Host Cell Chromosome Conformation by Viral Pathogens: Knowing When to Hold and When to Fold

(2021) Kinjal Majumder et al.   Frontiers in Immunology

Glycolysis downregulation is a hallmark of HIV‐1 latency and sensitizes infected cells to oxidative stress

(2021) Iart Luca Shytaj et al.   EMBO Molecular Medicine

A map of transcriptional heterogeneity and regulatory variation in human microglia

(2021) Adam M. H. Young et al.   NATURE GENETICS

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

Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders

(2021) Benxia Hu et al.   Nature Communications

Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains

(2020) Amanda Khoury et al.   Nature Communications

An Activity-Mediated Transition in Transcription in Early Postnatal Neurons

(2020) Hume Stroud et al.   NEURON

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

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

(2020) Mette Bentsen et al.   Nature Communications

Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis

(2020) Qian Qi et al.   BLOOD

Comparative analysis of human microglial models for studies of HIV replication and pathogenesis

(2020) Mohammad A. Rai et al.   Retrovirology

Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands

(2019) Florian Haller et al.   Nature Communications

Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy

(2019) Kevin B. Einkauf et al.   JOURNAL OF CLINICAL INVESTIGATION

Persistent HIV-infected cells in cerebrospinal fluid are associated with poorer neurocognitive performance

(2019) Serena Spudich et al.   JOURNAL OF CLINICAL INVESTIGATION

Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks

(2019) Seyed Ali Madani Tonekaboni et al.   GENOME RESEARCH

Limited correlation between systemic biomarkers and neurocognitive performance before and during HIV treatment

(2019) Kevin Robertson et al.   JOURNAL OF NEUROVIROLOGY

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

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

(2019) Bojana Lucic et al.   Nature Communications

Microglial Cells: The Main HIV-1 Reservoir in the Brain

(2019) Clementine Wallet et al.   Frontiers in Cellular and Infection Microbiology

Cross-talk between microglia and neurons regulates HIV latency

(2019) David Alvarez-Carbonell et al.   PLoS Pathogens

Expression profiling suggests microglial impairment in human immunodeficiency virus neuropathogenesis

(2018) Stephen D. Ginsberg et al.   ANNALS OF NEUROLOGY

Targeting the Latent Reservoir for HIV-1

(2018) Srona Sengupta et al.   IMMUNITY

Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4+ T cells

(2018) Emilie Battivelli et al.   eLife

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

HIV-1 RNA Detected in the CNS after Years of Suppressive Antiretroviral Therapy Can Originate from a Replicating CNS Reservoir or Clonally Expanded Cells

(2018) Sarah B Joseph et al.   CLINICAL INFECTIOUS DISEASES

Detailed Characterization of Early HIV-1 Replication Dynamics in Primary Human Macrophages

(2018) David Bejarano et al.   Viruses-Basel

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

An environment-dependent transcriptional network specifies human microglia identity

(2017) David Gosselin et al.   SCIENCE

Brain Macrophages in Simian Immunodeficiency Virus-Infected, Antiretroviral-Suppressed Macaques: a Functional Latent Reservoir

(2017) Claudia R. Avalos et al.   mBio

Mechanisms of CNS Viral Seeding by HIV + CD14 + CD16 + Monocytes: Establishment and Reseeding of Viral Reservoirs Contributing to HIV-Associated Neurocognitive Disorders

(2017) Mike Veenstra et al.   mBio

Sensitive quantification of the HIV-1 reservoir in gut-associated lymphoid tissue

(2017) Sara Morón-López et al.   PLoS One

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Prevalence and Correlates of Persistent HIV-1 RNA in Cerebrospinal Fluid During Antiretroviral Therapy

(2016) Albert M. Anderson et al.   JOURNAL OF INFECTIOUS DISEASES

Immortalization of primary microglia: a new platform to study HIV regulation in the central nervous system

(2016) Yoelvis Garcia-Mesa et al.   JOURNAL OF NEUROVIROLOGY

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma

(2016) Yotam Drier et al.   NATURE GENETICS

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

Neuroinflammation in treated HIV-positive individuals

(2016) Jaime H. Vera et al.   NEUROLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome

(2016) Yorifumi Satou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Position effects influence HIV latency reversal

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

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

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

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

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

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

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

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

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

(2014) Suhas S.P. Rao et al.   CELL

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

HIV-1 target cells in the CNS

(2014) Sarah B. Joseph et al.   JOURNAL OF NEUROVIROLOGY

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

HIV-1 transcription and latency: an update

(2013) Carine Van Lint et al.   Retrovirology

HIV-infected T cells are migratory vehicles for viral dissemination

(2012) Thomas T. Murooka et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Brain Cell Reservoirs of Latent Virus in Presymptomatic HIV-Infected Individuals

(2011) Katherine A. Thompson et al.   AMERICAN JOURNAL OF PATHOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

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

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

(2009) Troy Brady et al.   AIDS

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH

Transcription-Dependent Gene Looping of the HIV-1 Provirus Is Dictated by Recognition of Pre-mRNA Processing Signals

(2008) Kelly J. Perkins et al.   MOLECULAR CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY