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Genomic profiling of HIV-1 integration in microglia links viral insertions to TAD organization
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide
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Expression profiling suggests microglial impairment in human immunodeficiency virus neuropathogenesis
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Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method
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HIV-1 target cells in the CNS
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Immortalization of primary microglia: a new platform to study HIV regulation in the central nervous system
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Limited correlation between systemic biomarkers and neurocognitive performance before and during HIV treatment
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Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability
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Brain Cell Reservoirs of Latent Virus in Presymptomatic HIV-Infected Individuals
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Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
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Super-Enhancers in the Control of Cell Identity and Disease
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A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia
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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
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HIV-1 Integration Landscape during Latent and Active Infection
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Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
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Multiscale 3D Genome Rewiring during Mouse Neural Development
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A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
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IRF1 governs the differential interferon-stimulated gene responses in human monocytes and macrophages by regulating chromatin accessibility
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Capsid-CPSF6 Interaction Licenses Nuclear HIV-1 Trafficking to Sites of Viral DNA Integration
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LEDGIN-mediated Inhibition of Integrase–LEDGF/p75 Interaction Reduces Reactivation of Residual Latent HIV
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Targeting the Latent Reservoir for HIV-1
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Transcription-Dependent Gene Looping of the HIV-1 Provirus Is Dictated by Recognition of Pre-mRNA Processing Signals
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
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Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains
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Chromatin Domains: The Unit of Chromosome Organization
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An Activity-Mediated Transition in Transcription in Early Postnatal Neurons
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HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots
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NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis
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Spatial partitioning of the regulatory landscape of the X-inactivation centre
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Topological domains in mammalian genomes identified by analysis of chromatin interactions
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An integrated encyclopedia of DNA elements in the human genome
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HIV-infected T cells are migratory vehicles for viral dissemination
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An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma
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Molecular control of activation and priming in macrophages
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A role for LEDGF/p75 in targeting HIV DNA integration
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ChromHMM: automating chromatin-state discovery and characterization
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Chromatin-state discovery and genome annotation with ChromHMM
inferredcites →https://doi.org/10.1038/nrmicro.2015.5openalex-snapshot
HIV reservoirs: what, where and how to target them
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Nuclear landscape of HIV-1 infection and integration
inferredcites →https://doi.org/10.1038/nsmb.3328openalex-snapshot
Position effects influence HIV latency reversal
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Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands
inferredcites →https://doi.org/10.1038/s41467-019-12046-3openalex-snapshot
Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration
inferredcites →https://doi.org/10.1038/s41467-020-17256-8openalex-snapshot
HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains
inferredcites →https://doi.org/10.1038/s41467-020-18035-1openalex-snapshot
ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
inferredcites →https://doi.org/10.1038/s41467-021-24243-0openalex-snapshot
Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders
inferredcites →https://doi.org/10.1038/s41586-020-2651-8openalex-snapshot
Distinct viral reservoirs in individuals with spontaneous control of HIV-1
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A map of transcriptional heterogeneity and regulatory variation in human microglia
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Super enhancers define regulatory subtypes and cell identity in neuroblastoma
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Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4+ T cells
inferredcites →https://doi.org/10.1073/pnas.1524213113openalex-snapshot
A critical role for alternative polyadenylation factor CPSF6 in targeting HIV-1 integration to transcriptionally active chromatin
inferredcites →https://doi.org/10.1074/jbc.m209278200openalex-snapshot
HIV-1 Integrase Forms Stable Tetramers and Associates with LEDGF/p75 Protein in Human Cells
inferredcites →https://doi.org/10.1080/13550280600748946openalex-snapshot
Use of laser capture microdissection to detect integrated HIV-1 DNA in macrophages and astrocytes from autopsy brain tissues
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Recurrent HIV‐1 Integration at theBACH2Locus in Resting CD4+T Cell Populations during Effective Highly Active Antiretroviral Therapy
inferredcites →https://doi.org/10.1089/omi.2011.0118openalex-snapshot
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
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BEDTools: a flexible suite of utilities for comparing genomic features
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Complex heatmaps reveal patterns and correlations in multidimensional genomic data
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ShinyButchR: Interactive NMF-based decomposition workflow of genome-scale datasets
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Human Immunodeficiency Virus Type 1 RNA Detected in the Central Nervous System (CNS) After Years of Suppressive Antiretroviral Therapy Can Originate from a Replicating CNS Reservoir or Clonally Expanded Cells
inferredcites →https://doi.org/10.1093/infdis/jiw505openalex-snapshot
Prevalence and Correlates of Persistent HIV-1 RNA in Cerebrospinal Fluid During Antiretroviral Therapy
inferredcites →https://doi.org/10.1093/nar/gkaa516openalex-snapshot
A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase
inferredcites →https://doi.org/10.1093/nar/gkaa536openalex-snapshot
The chromatin landscape at the HIV-1 provirus integration site determines viral expression
inferredcites →https://doi.org/10.1093/nar/gkab514openalex-snapshot
rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo
inferredcites →https://doi.org/10.1093/nar/gkq1313openalex-snapshot
Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis
inferredcites →https://doi.org/10.1093/nar/gkt074openalex-snapshot
Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes
inferredcites →https://doi.org/10.1093/nar/gkw257openalex-snapshot
deepTools2: a next generation web server for deep-sequencing data analysis
inferredcites →https://doi.org/10.1093/nar/gkx1081openalex-snapshot
The Encyclopedia of DNA elements (ENCODE): data portal update
inferredcites →https://doi.org/10.1097/qad.0b013e32832caf28openalex-snapshot
HIV integration site distributions in resting and activated CD4 + T cells infected in culture
inferredcites →https://doi.org/10.1101/gad.1565107openalex-snapshot
LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration
inferredcites →https://doi.org/10.1101/gr.082800.108openalex-snapshot
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1101/gr.6286907openalex-snapshot
HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications
inferredcites →https://doi.org/10.1126/science.1076469openalex-snapshot
Corepressor-Dependent Silencing of Chromosomal Regions Encoding Neuronal Genes
inferredcites →https://doi.org/10.1126/science.1132319openalex-snapshot
An Essential Role for LEDGF/p75 in HIV Integration
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.1254194openalex-snapshot
Specific HIV integration sites are linked to clonal expansion and persistence of infected cells
inferredcites →https://doi.org/10.1126/science.1256304openalex-snapshot
Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection
inferredcites →https://doi.org/10.1126/science.1262088openalex-snapshot
CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation
inferredcites →https://doi.org/10.1126/science.aal3222openalex-snapshot
An environment-dependent transcriptional network specifies human microglia identity
inferredcites →https://doi.org/10.1126/science.aay0793openalex-snapshot
Brain cell type–specific enhancer–promoter interactome maps and disease - risk association
inferredcites →https://doi.org/10.1128/jvi.00463-17openalex-snapshot
Effects of Inner Nuclear Membrane Proteins SUN1/UNC-84A and SUN2/UNC-84B on the Early Steps of HIV-1 Infection
inferredcites →https://doi.org/10.1128/jvi.80.4.1939-1948.2006openalex-snapshot
Human Immunodeficiency Virus Type 1 Incorporated with Fusion Proteins Consisting of Integrase and the Designed Polydactyl Zinc Finger Protein E2C Can Bias Integration of Viral DNA into a Predetermined Chromosomal Region in Human Cells
inferredcites →https://doi.org/10.1128/mbio.01186-17openalex-snapshot
Brain Macrophages in Simian Immunodeficiency Virus-Infected, Antiretroviral-Suppressed Macaques: a Functional Latent Reservoir
inferredcites →https://doi.org/10.1128/mbio.01280-17openalex-snapshot
Mechanisms of CNS Viral Seeding by HIV + CD14 + CD16 + Monocytes: Establishment and Reseeding of Viral Reservoirs Contributing to HIV-Associated Neurocognitive Disorders
inferredcites →https://doi.org/10.1128/mbio.02254-20openalex-snapshot
CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
inferredcites →https://doi.org/10.1172/jci.insight.121718openalex-snapshot
Single-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV
inferredcites →https://doi.org/10.1172/jci124291openalex-snapshot
Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy
inferredcites →https://doi.org/10.1172/jci127413openalex-snapshot
Persistent HIV-infected cells in cerebrospinal fluid are associated with poorer neurocognitive performance
inferredcites →https://doi.org/10.1182/blood.2020005780openalex-snapshot
Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis
inferredcites →https://doi.org/10.1186/1471-2105-11-237openalex-snapshot
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
inferredcites →https://doi.org/10.1186/1742-4690-10-67openalex-snapshot
HIV-1 transcription and latency: an update
inferredcites →https://doi.org/10.1186/1742-4690-10-90openalex-snapshot
HIV latency and integration site placement in five cell-based models
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/s13059-018-1519-9openalex-snapshot
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions
inferredcites →https://doi.org/10.1186/s13059-020-02108-xopenalex-snapshot
Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries
inferredcites →https://doi.org/10.1212/wnl.0000000000002485openalex-snapshot
Neuroinflammation in treated HIV-positive individuals
inferredcites →https://doi.org/10.1371/journal.pgen.1002717openalex-snapshot
Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing
inferredcites →https://doi.org/10.1371/journal.ppat.1009141openalex-snapshot
Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy
inferredcites →https://doi.org/10.1371/journal.ppat.1009346openalex-snapshot
Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.15252/embj.2019102209openalex-snapshot
Alterations of redox and iron metabolism accompany the development of HIV latency
inferredcites →https://doi.org/10.18637/jss.v028.i05openalex-snapshot
Building Predictive Models in R Using the caret Package
inferredcites →https://doi.org/10.3389/fcimb.2019.00362openalex-snapshot
Microglial Cells: The Main HIV-1 Reservoir in the Brain
inferredcites →https://doi.org/10.3389/fimmu.2021.633762openalex-snapshot
Utilization of Host Cell Chromosome Conformation by Viral Pathogens: Knowing When to Hold and When to Fold
inferredcites →https://doi.org/10.3791/53840openalex-snapshot
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
inferredcites →https://doi.org/10.7554/elife.34655openalex-snapshot
Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4+ T cells
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/j.molcel.2022.11.016openalex-snapshot
HIV integration in the human brain is linked to microglial activation and 3D genome remodeling
inferred← citeshttps://doi.org/10.4014/jmb.2208.08020openalex-snapshot
Dynamics of Viral and Host 3D Genome Structure upon Infection
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