ArticleNucleic acids research2024
NELF focuses sites of initiation and maintains promoter architecture.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 13 citations in OpenAlex.
- Article
- The nascent transcriptome delineates the regulatory landscape in human health and disease.bioRxiv : the preprint server for biology · 2026Article
- A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation.bioRxiv : the preprint server for biology · 2026Article
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- NELF prevents transcriptional readthrough into DNA replication zones in cancer cells.EMBO reports · 2026Article
- Transcription quality control at the promoter-proximal checkpoint.Genes & development · 2025Review
- A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes.Nucleic acids research · 2025Article
- Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome.Science advances · 2025Article
- Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription.Nucleic acids research · 2025Article
- RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease.Journal of molecular biology · 2025Review
- Toward structural understanding of eukaryotic transcription elongation.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2025Review
- DFF-ChIP: a method to detect and quantify complex interactions between RNA polymerase II, transcription factors, and chromatin.Nucleic acids research · 2024Article
- Multiple direct and indirect roles of the Paf1 complex in transcription elongation, splicing, and histone modifications.Cell reports · 2024Article
- The Wild West of spike-in normalization.Nature biotechnology · 2024Article
- Multiple direct and indirect roles of Paf1C in elongation, splicing, and histone post-translational modifications.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Many factors control the elongation phase of transcription by RNA polymerase II (Pol II), a process that plays an essential role in regulating gene expression. We utilized cells expressing degradation tagged subunits of NELFB, PAF1 and RTF1 to probe the effects of depletion of the factors on nascent transcripts using PRO-Seq and on chromatin architecture using DFF-ChIP. Although NELF is involved in promoter proximal pausing, depletion of NELFB had only a minimal effect on the level of paused transcripts and almost no effect on control of productive elongation. Instead, NELF depletion increased the utilization of downstream transcription start sites and caused a dramatic, genome-wide loss of H3K4me3 marked nucleosomes. Depletion of PAF1 and RTF1 both had major effects on productive transcript elongation in gene bodies and also caused initiation site changes like those seen with NELFB depletion. Our study confirmed that the first nucleosome encountered during initiation and early elongation is highly positioned with respect to the major TSS. In contrast, the positions of H3K4me3 marked nucleosomes in promoter regions are heterogeneous and are influenced by transcription. We propose a model defining NELF function and a general role of the H3K4me3 modification in blocking transcription initiation.
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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.