Long non-coding RNAs and latent HIV – A search for novel targets for latency reversal

Long noncoding RNA MALAT1 releases epigenetic silencing of HIV-1 replication by displacing the polycomb repressive complex 2 from binding to the LTR promoter

(2019) Di Qu et al.   NUCLEIC ACIDS RESEARCH

Histone deacetylase inhibitors induce complex host responses that contribute to differential potencies of these compounds in HIV reactivation

(2019) Nadejda Beliakova-Bethell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Influence of biological sex, age and HIV status in an in vitro primary cell model of HIV latency using a CXCR4 tropic virus

(2018) Amanda B Macedo et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Long non-coding RNA PVT1 promotes cell proliferation and invasion through regulating miR-133a in ovarian cancer

(2018) Qi Yang et al.   BIOMEDICINE & PHARMACOTHERAPY

Long noncoding RNA PVT1 modulates hepatocellular carcinoma cell proliferation and apoptosis by recruiting EZH2

(2018) Jianping Guo et al.   Cancer Cell International

Long noncoding RNA PVT1 promotes EMT via mediating microRNA-186 targeting of Twist1 in prostate cancer

(2018) Zhongwen Chang et al.   GENE

Long Noncoding RNA uc002yug.2 Activates HIV-1 Latency through Regulation of mRNA Levels of Various RUNX1 Isoforms and Increased Tat Expression

(2018) Chen Huan et al.   JOURNAL OF VIROLOGY

LncRNA PVT1 triggers Cyto-protective autophagy and promotes pancreatic ductal adenocarcinoma development via the miR-20a-5p/ULK1 Axis

(2018) Fengting Huang et al.   Molecular Cancer

HIV-1 replication in CD4 + T cells exploits the down-regulation of antiviral NEAT1 long non-coding RNAs following T cell activation

(2018) Hongbing Liu et al.   VIROLOGY

Barriers for HIV Cure: The Latent Reservoir

(2018) Sergio Castro-Gonzalez et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

decodeRNA— predicting non-coding RNA functions using guilt-by-association

(2017) Steve Lefever et al.   Database-The Journal of Biological Databases and Curation

Modeling HIV-1 Latency in Primary T Cells Using a Replication-Competent Virus

(2016) Laura J. Martins et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Control of HIV-1 gene expression by SR proteins

(2016) Charlotte Mahiet et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The mTOR Complex Controls HIV Latency

(2016) Emilie Besnard et al.   Cell Host & Microbe

A Positive Feedback Loop of lncRNA- PVT1 and FOXM1 Facilitates Gastric Cancer Growth and Invasion

(2016) Mi-die Xu et al.   CLINICAL CANCER RESEARCH

Modulation of the splicing regulatory function of SRSF10 by a novel compound that impairs HIV-1 replication

(2016) Lulzim Shkreta et al.   NUCLEIC ACIDS RESEARCH

A negative regulation loop of long noncoding RNA HOTAIR and p53 in non-small-cell lung cancer

(2016) Fuquan Gao et al.   OncoTargets and Therapy

Long noncoding RNA NRON contributes to HIV-1 latency by specifically inducing tat protein degradation

(2016) Jun Li et al.   Nature Communications

Shocking HIV out of hiding

(2016) Thomas A. Rasmussen et al.   Current Opinion in HIV and AIDS

A long noncoding RNA positively regulates CD56 in human natural killer cells

(2016) Ruya Zhang et al.   Oncotarget

Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model

(2016) Cory H. White et al.   PLoS Pathogens

RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities

(2016) Richa Rai et al.   PLoS One

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay

(2016) Wim Trypsteen et al.   Scientific Reports

Select host restriction factors are associated with HIV persistence during antiretroviral therapy

(2015) Mohamed Abdel-Mohsen et al.   AIDS

Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency

(2015) Cory H. White et al.   ANTIVIRAL RESEARCH

Blimp-1, an Intrinsic Factor that Represses HIV-1 Proviral Transcription in Memory CD4+T Cells

(2015) Katarzyna Kaczmarek Michaels et al.   JOURNAL OF IMMUNOLOGY

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

Balanced splicing at the Tat-specific HIV-1 3′ss A3 is critical for HIV-1 replication

(2015) Steffen Erkelenz et al.   Retrovirology

The lncRNA NRON modulates HIV-1 replication in a NFAT-dependent manner and is differentially regulated by early and late viral proteins

(2015) Hasan Imam et al.   Scientific Reports

Genome-wide analysis of histone modifications in latently HIV-1 infected T cells

(2014) Jihwan Park et al.   AIDS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Deep Sequencing of HIV-Infected Cells: Insights into Nascent Transcription and Host-Directed Therapy

(2014) X. Peng et al.   JOURNAL OF VIROLOGY

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

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

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

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

(2013) Ya-Chi Ho et al.   CELL

The effect of cell subset isolation method on gene expression in leukocytes

(2013) Nadejda Beliakova-Bethell et al.   CYTOMETRY PART A

Proteasome inhibitors act as bifunctional antagonists of human immunodeficiency virus type 1 latency and replication

(2013) Leia K Miller et al.   Retrovirology

IFI16 DNA Sensor Is Required for Death of Lymphoid CD4 T Cells Abortively Infected with HIV

(2013) K. M. Monroe et al.   SCIENCE

NEAT1 Long Noncoding RNA and Paraspeckle Bodies Modulate HIV-1 Posttranscriptional Expression

(2013) Q. Zhang et al.   mBio

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

An In-Depth Comparison of Latent HIV-1 Reactivation in Multiple Cell Model Systems and Resting CD4+ T Cells from Aviremic Patients

(2013) Celsa A. Spina et al.   PLoS Pathogens

Suberoylanilide hydroxamic acid induces limited changes in the transcriptome of primary CD4+ T cells

(2012) Nadejda Beliakova-Bethell et al.   AIDS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Human Immunodeficiency Virus Type 1 (HIV-1) Transactivator of Transcription through Its Intact Core and Cysteine-Rich Domains Inhibits Wnt/ -Catenin Signaling in Astrocytes: Relevance to HIV Neuropathogenesis

(2012) L. J. Henderson et al.   JOURNAL OF NEUROSCIENCE

CD4+ T cells from elite controllers resist HIV-1 infection by selective upregulation of p21

(2011) Huabiao Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Membrane Perturbation Elicits an IRF3-Dependent, Interferon-Independent Antiviral Response

(2011) R. S. Noyce et al.   JOURNAL OF VIROLOGY

Inhibition of splicing by serine-arginine rich protein 55 (SRp55) causes the appearance of partially spliced HIV-1 mRNAs in the cytoplasm

(2011) Anna Tranell et al.   VIRUS RESEARCH

Interferon-stimulated genes and their antiviral effector functions

(2011) John W Schoggins et al.   Current Opinion in Virology

Homeostatic Proliferation Fails to Efficiently Reactivate HIV-1 Latently Infected Central Memory CD4+ T Cells

(2011) Alberto Bosque et al.   PLoS Pathogens

Vorinostat interferes with the signaling transduction pathway of T-cell receptor and synergizes with phosphoinositide-3 kinase inhibitors in cutaneous T-cell lymphoma

(2010) M. B. Wozniak et al.   HAEMATOLOGICA

Serine- and Arginine-rich Proteins 55 and 75 (SRp55 and SRp75) Induce Production of HIV-1 vpr mRNA by Inhibiting the 5′-Splice Site of Exon 3

(2010) Anna Tranell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

DNA microarray profiling of genes differentially regulated by the histone deacetylase inhibitors vorinostat and LBH589 in colon cancer cell lines

(2009) Melissa J LaBonte et al.   BMC Medical Genomics

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

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

(2009) Nicolas Chomont et al.   NATURE MEDICINE

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Challenge of Finding a Cure for HIV Infection

(2009) D. D. Richman et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Induction of HIV-1 latency and reactivation in primary memory CD4+ T cells

(2008) A. Bosque et al.   BLOOD