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

[1]  H. Wu,et al.  Detection of the long noncoding RNAs nuclear‐enriched autosomal transcript 1 (NEAT1) and metastasis associated lung adenocarcinoma transcript 1 in the peripheral blood of HIV‐1‐infected patients , 2016, HIV medicine.

[2]  Xia Li,et al.  Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data , 2015, Database J. Biol. Databases Curation.

[3]  Vladimir B. Bajic,et al.  DENdb: database of integrated human enhancers , 2015, Database J. Biol. Databases Curation.

[4]  Charles M. Rice,et al.  Corrigendum: A diverse range of gene products are effectors of the type I interferon antiviral response , 2015, Nature.

[5]  O. Thas,et al.  Robust regression methods for real-time polymerase chain reaction. , 2015, Analytical biochemistry.

[6]  Marcus C. Chibucos,et al.  The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations , 2015, Database J. Biol. Databases Curation.

[7]  M. Mhlanga,et al.  Non-coding RNAs and HIV: viral manipulation of host dark matter to shape the cellular environment , 2015, Front. Genet..

[8]  S. Jameel,et al.  The lncRNA NRON modulates HIV-1 replication in a NFAT-dependent manner and is differentially regulated by early and late viral proteins , 2015, Scientific Reports.

[9]  V. Villegas,et al.  Neighboring Gene Regulation by Antisense Long Non-Coding RNAs , 2015, International journal of molecular sciences.

[10]  J. Weinberg,et al.  The immunoproteasome and viral infection: a complex regulator of inflammation , 2015, Front. Microbiol..

[11]  G. Braus,et al.  One Juliet and four Romeos: VeA and its methyltransferases , 2015, Front. Microbiol..

[12]  J. van Helden,et al.  Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape , 2014, Nucleic acids research.

[13]  Guangfeng Song,et al.  HIV-1, human interaction database: current status and new features , 2014, Nucleic Acids Res..

[14]  Marcel E. Dinger,et al.  lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs , 2014, Nucleic Acids Res..

[15]  John A. Young,et al.  CHD1 and CHD2 are positive regulators of HIV-1 gene expression , 2014, Virology Journal.

[16]  M. Askarian-Amiri,et al.  Emerging Role of Long Non-Coding RNA SOX2OT in SOX2 Regulation in Breast Cancer , 2014, PloS one.

[17]  Alberto Bosque,et al.  An HIV-encoded antisense long noncoding RNA epigenetically regulates viral transcription. , 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

[18]  O. Fardel,et al.  Nrf2 expression and activity in human T lymphocytes: stimulation by T cell receptor activation and priming by inorganic arsenic and tert-butylhydroquinone. , 2014, Free radical biology & medicine.

[19]  Jun Wang,et al.  Deep Sequencing of HIV-Infected Cells: Insights into Nascent Transcription and Host-Directed Therapy , 2014, Journal of Virology.

[20]  K. Morris,et al.  The rise of regulatory RNA , 2014, Nature Reviews Genetics.

[21]  Gokul Swaminathan,et al.  MicroRNAs and HIV-1 infection: antiviral activities and beyond. , 2014, Journal of molecular biology.

[22]  L. Bekker,et al.  CD4+ T cells in HIV infection show increased levels of expression of a receptor for vasoactive intestinal peptide, VPAC2 , 2014, Immunologic research.

[23]  Hanfei Sun,et al.  Target analysis by integration of transcriptome and ChIP-seq data with BETA , 2013, Nature Protocols.

[24]  Y. Ron,et al.  Proteasome inhibitors act as bifunctional antagonists of human immunodeficiency virus type 1 latency and replication , 2013, Retrovirology.

[25]  G. Silvestri,et al.  Host-pathogen interaction in HIV infection. , 2013, Current opinion in immunology.

[26]  R. Wu,et al.  Characterization of a novel long noncoding RNA, SCAL1, induced by cigarette smoke and elevated in lung cancer cell lines. , 2013, American journal of respiratory cell and molecular biology.

[27]  S. Lewin,et al.  Altering cell death pathways as an approach to cure HIV infection , 2013, Cell Death and Disease.

[28]  Kevin V. Morris,et al.  Chromatin, Non-Coding RNAs, and the Expression of HIV , 2013, Viruses.

[29]  Amit Kumar,et al.  HIV-1 Nef Interacts with HCV Core, Recruits TRAF2, TRAF5 and TRAF6, and Stimulates HIV-1 Replication in Macrophages , 2013, Journal of Innate Immunity.

[30]  Anders F. Andersson,et al.  Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria , 2013, mBio.

[31]  J. Mattick,et al.  Structure and function of long noncoding RNAs in epigenetic regulation , 2013, Nature Structural &Molecular Biology.

[32]  K. Jeang,et al.  NEAT1 Long Noncoding RNA and Paraspeckle Bodies Modulate HIV-1 Posttranscriptional Expression , 2013, mBio.

[33]  A. Telenti,et al.  24 Hours in the Life of HIV-1 in a T Cell Line , 2013, PLoS pathogens.

[34]  Lennart Martens,et al.  LNCipedia: a database for annotated human lncRNA transcript sequences and structures , 2012, Nucleic Acids Res..

[35]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[36]  D. Schriemer,et al.  Characterization of Staufen1 Ribonucleoproteins by Mass Spectrometry and Biochemical Analyses Reveal the Presence of Diverse Host Proteins Associated with Human Immunodeficiency Virus Type 1 , 2012, Front. Microbio..

[37]  David G. Knowles,et al.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.

[38]  J. Mattick,et al.  Genome-wide analysis of long noncoding RNA stability , 2012, Genome research.

[39]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[40]  Andrej Sali,et al.  Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection , 2011, Nature.

[41]  K. Nakano,et al.  HIV-1-encoded antisense RNA suppresses viral replication for a prolonged period , 2012, Retrovirology.

[42]  Howard Y. Chang,et al.  Molecular mechanisms of long noncoding RNAs. , 2011, Molecular cell.

[43]  Damian Smedley,et al.  BioMart Central Portal: an open database network for the biological community , 2011, Database J. Biol. Databases Curation.

[44]  Filip Pattyn,et al.  The microRNA body map: dissecting microRNA function through integrative genomics , 2011, Nucleic acids research.

[45]  Howard Y. Chang,et al.  Long noncoding RNAs and human disease. , 2011, Trends in cell biology.

[46]  D. Reinberg,et al.  The Polycomb complex PRC2 and its mark in life , 2011, Nature.

[47]  John S. Mattick,et al.  lncRNAdb: a reference database for long noncoding RNAs , 2010, Nucleic Acids Res..

[48]  U. Sandhu,et al.  Strict control of transgene expression in a mouse model for sensitive biological applications based on RMCE compatible ES cells , 2010, Nucleic Acids Res..

[49]  Tae-Young Roh,et al.  Gene silencing in HIV-1 latency by polycomb repressive group , 2011, Virology Journal.

[50]  Steven L Salzberg,et al.  Between a chicken and a grape: estimating the number of human genes , 2010, Genome Biology.

[51]  M. Salto‐Tellez,et al.  Elucidating the molecular physiopathology of acute respiratory distress syndrome in severe acute respiratory syndrome patients , 2009, Virus Research.

[52]  A. Moses,et al.  Vpu Directs the Degradation of the Human Immunodeficiency Virus Restriction Factor BST-2/Tetherin via a βTrCP-Dependent Mechanism , 2009, Journal of Virology.

[53]  Kuan-Teh Jeang,et al.  A Genome-wide Short Hairpin RNA Screening of Jurkat T-cells for Human Proteins Contributing to Productive HIV-1 Replication* , 2009, The Journal of Biological Chemistry.

[54]  S. Goff,et al.  Somatic cell genetic analyses to identify HIV-1 host restriction factors. , 2009, Methods in molecular biology.

[55]  D. Avramopoulos,et al.  Orientation, distance, regulation and function of neighbouring genes , 2009, Human Genomics.

[56]  Amy S. Espeseth,et al.  Genome-scale RNAi screen for host factors required for HIV replication. , 2008, Cell host & microbe.

[57]  J. Church Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen , 2008, Pediatrics.

[58]  R. König,et al.  Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication , 2008, Cell.

[59]  Kazuyoshi Ikuta,et al.  The RING finger ubiquitin ligase RNF125/TRAC-1 down-modulates HIV-1 replication in primary human peripheral blood mononuclear cells. , 2007, Virology.

[60]  Derin Tugal,et al.  The role of the proteasome–ubiquitin pathway in regulation of the IFN-γ mediated anti-VSV response in neurons , 2006, Journal of Neuroimmunology.

[61]  Eric Verdin,et al.  The SWI/SNF Chromatin-remodeling Complex Is a Cofactor for Tat Transactivation of the HIV Promoter* , 2006, Journal of Biological Chemistry.

[62]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[63]  Crafford A. Harris,et al.  HIV-1 Nef-induced FasL induction and bystander killing requires p38 MAPK activation. , 2005, Blood.

[64]  R. Reeves,et al.  Recruitment of SWI/SNF to the Human Immunodeficiency Virus Type 1 Promoter , 2004, Molecular and Cellular Biology.

[65]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[66]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[67]  George Karypis,et al.  CLUTO - A Clustering Toolkit , 2002 .

[68]  W. Greene,et al.  HIV-1 Nef inhibits ASK1-dependent death signalling providing a potential mechanism for protecting the infected host cell , 2001, Nature.

[69]  R. Shoeman,et al.  Amino-terminal polypeptides of vimentin are responsible for the changes in nuclear architecture associated with human immunodeficiency virus type 1 protease activity in tissue culture cells. , 2001, Molecular biology of the cell.

[70]  Bertrand Friguet,et al.  Antiviral Activity of the Proteasome on Incoming Human Immunodeficiency Virus Type 1 , 1998, Journal of Virology.

[71]  A. Evstafieva,et al.  HsN3 proteasomal subunit as a target for human immunodeficiency virus type 1 Nef protein. , 1997, Virology.

[72]  J. Silver,et al.  Rapid degradation of CD4 in cells expressing human immunodeficiency virus type 1 Env and Vpu is blocked by proteasome inhibitors. , 1997, The Journal of general virology.

[73]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[74]  F. Kashanchi,et al.  Direct interaction of human TFIID with the HIV-1 transactivator Tat , 1994, Nature.