ArticleNucleic acids research2003
Integrated functional and bioinformatics approach for the identification and experimental verification of RNA signals: application to HIV-1 INS.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 29 citations in OpenAlex.
- Translation initiation of the HIV-1 mRNA.Translation (Austin, Tex.) · 2014Review
- Heterogenous nuclear ribonucleoprotein Q increases protein expression from HIV-1 Rev-dependent transcripts.Virology journal · 2013Article
- A cis-acting element present within the Gag open reading frame negatively impacts on the activity of the HIV-1 IRES.PloS one · 2013Article
- HIV-1 suppressive sequences are modulated by Rev transport of unspliced RNA and are required for efficient HIV-1 production.PloS one · 2012Article
- A suicide gene approach using the human pro-apoptotic protein tBid inhibits HIV-1 replication.BMC biotechnology · 2011Article
- EASY-HIT: HIV full-replication technology for broad discovery of multiple classes of HIV inhibitors.Antimicrobial agents and chemotherapy · 2010Article
- High natural permissivity of primary rabbit cells for HIV-1, with a virion infectivity defect in macrophages as the final replication barrier.Journal of virology · 2010Article
- Functional nuclear topography of transcriptionally inducible extra-chromosomal transgene clusters.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2010Article
- Identification of a heterogeneous nuclear ribonucleoprotein-recognition region in the HIV Rev protein.The Journal of biological chemistry · 2009Article
- Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences.Virology journal · 2008Review
- The secondary structure of the human immunodeficiency virus type 1 transcript modulates viral splicing and infectivity.Journal of virology · 2008Article
- A scoring matrix approach to detecting miRNA target sites.Algorithms for molecular biology : AMB · 2008Article
- Identification of a novel Rev-interacting cellular protein.BMC cell biology · 2005Article
- Linking disease-associated genes to regulatory networks via promoter organization.Nucleic acids research · 2005Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Regulation of gene expression involves sequence elements in nucleic acids. In promoters, multiple sequence elements cooperate as functional modules, which in combination determine overall promoter activity. We previously developed computational tools based on this hierarchical structure for in silico promoter analysis. Here we address the functional organization of post-transcriptional control elements, using the HIV-1 genome as a model. Numerous mutagenesis studies demonstrate that expression of HIV structural proteins is restricted by inhibitory sequences (INS) in HIV mRNAs in the absence of the HIV-1 Rev protein. However, previous attempts to detect conserved sequence patterns of HIV-1 INS have failed. We defined four distinct sequence patterns for inhibitory motifs (weight matrices), which identified 22 out of the 25 known INS as well as several new candidate INS regions contained in numerous HIV-1 strains. The conservation of INS motifs within the HIV genome was not due to overall sequence conservation. The functionality of two candidate INS regions was analyzed with a new assay that measures the effect of non-coding mRNA sequences on production of red fluorescent reporter protein. Both new INS regions showed inhibitory activity in sense but not in antisense orientation. Inhibitory activity increased by combining both INS regions in the same mRNA. Inhibitory activity of known and new INS regions was overcome by co-expression of the HIV-1 Rev protein.
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