ArticlePLoS genetics2014
Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 63 citations in OpenAlex.
- Identification of proteins in semen-derived extracellular vesicles that bind to Tat and NF-κB and that may impair HIV replication.Science signaling · 2025Article
- Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome.Science advances · 2025Article
- The HIV-1 Transcriptional Program: From Initiation to Elongation Control.Journal of molecular biology · 2025Review
- Toward structural understanding of eukaryotic transcription elongation.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2025Review
- Transcriptional elongation control in developmental gene expression, aging, and disease.Molecular cell · 2023Review
- Epigenetic Regulation of HIV-1 Sense and Antisense Transcription in Response to Latency-Reversing Agents.Non-coding RNA · 2023Article
- Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures.Trends in genetics : TIG · 2022Review
- How to Shut Down Transcription in Archaea during Virus Infection.Microorganisms · 2022Review
- Review
- Structural advances in transcription elongation.Current opinion in structural biology · 2022Review
- Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.Nature communications · 2022Article
- High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers.International journal of molecular sciences · 2021Review
- Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans.Journal of molecular biology · 2021Review
- CDK9 keeps RNA polymerase II on track.Cellular and molecular life sciences : CMLS · 2021Review
- Review
- Multiple competing RNA structures dynamically control alternative splicing in the human ATE1 gene.Nucleic acids research · 2021Article
- Review
- RNA aptamer capture of macromolecular complexes for mass spectrometry analysis.Nucleic acids research · 2020Article
- INTS10-INTS13-INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module.Nature communications · 2020Article
- HIV-1 Proviral Transcription and Latency in the New Era.Viruses · 2020Review
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
The four-subunit Negative Elongation Factor (NELF) is a major regulator of RNA Polymerase II (Pol II) pausing. The subunit NELF-E contains a conserved RNA Recognition Motif (RRM) and is proposed to facilitate Poll II pausing through its association with nascent transcribed RNA. However, conflicting ideas have emerged for the function of its RNA binding activity. Here, we use in vitro selection strategies and quantitative biochemistry to identify and characterize the consensus NELF-E binding element (NBE) that is required for sequence specific RNA recognition (NBE: CUGAGGA(U) for Drosophila). An NBE-like element is present within the loop region of the transactivation-response element (TAR) of HIV-1 RNA, a known regulatory target of human NELF-E. The NBE is required for high affinity binding, as opposed to the lower stem of TAR, as previously claimed. We also identify a non-conserved region within the RRM that contributes to the RNA recognition of Drosophila NELF-E. To understand the broader functional relevance of NBEs, we analyzed promoter-proximal regions genome-wide in Drosophila and show that the NBE is enriched +20 to +30 nucleotides downstream of the transcription start site. Consistent with the role of NELF in pausing, we observe a significant increase in NBEs among paused genes compared to non-paused genes. In addition to these observations, SELEX with nuclear run-on RNA enrich for NBE-like sequences. Together, these results describe the RNA binding behavior of NELF-E and supports a biological role for NELF-E in promoter-proximal pausing of both HIV-1 and cellular genes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.