ArticleMolecular and cellular biology2010
Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription.
Article in Molecular and cellular biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
53 citing papers in PubMed, 76 citations in OpenAlex.
- Functional analysis and transcriptional profiling of non-coding RNAs in yeast.The Biochemical journal · 2025Review
- Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages.International journal of molecular sciences · 2023Article
- Nucleosome-directed replication origin licensing independent of a consensus DNA sequence.Nature communications · 2022Article
- Bidirectional promoters: an enigmatic genome architecture and their roles in cancers.Molecular biology reports · 2021Review
- Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer.International journal of molecular sciences · 2021Review
- Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.PLoS computational biology · 2021Article
- A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning.Applied microbiology and biotechnology · 2020Article
- Opposing chromatin remodelers control transcription initiation frequency and start site selection.Nature structural & molecular biology · 2019Article
- Multiple Negative Regulators Restrict Recruitment of the SWI/SNF Chromatin Remodeler to theGenetics · 2019Article
- Nucleosome remodeling at origins of global genome-nucleotide excision repair occurs at the boundaries of higher-order chromatin structure.Genome research · 2019Article
- Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis.Blood · 2017Review
- Sequence-specific targeting of chromatin remodelers organizes precisely positioned nucleosomes throughout the genome.BioEssays : news and reviews in molecular, cellular and developmental biology · 2017Review
- R-loop: an emerging regulator of chromatin dynamics.Acta biochimica et biophysica Sinica · 2016Review
- The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast.Genome biology and evolution · 2016Article
- Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler.Genome research · 2016Article
- Systematic approaches to identify functional lncRNAs.Current opinion in genetics & development · 2016Review
- A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis.Developmental biology · 2016Article
- Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects.PLoS genetics · 2016Article
- Nucleosome architecture throughout the cell cycle.Scientific reports · 2016Article
- Intrauterine growth restriction perturbs nucleosome depletion at a growth hormone-responsive element in the mouse IGF-1 gene.Physiological genomics · 2015Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Nucleosome-free regions (NFRs) at the 5' and 3' ends of genes are general sites of transcription initiation for mRNA and noncoding RNA (ncRNA). The presence of NFRs within transcriptional regulatory regions and the conserved location of transcription start sites at NFRs strongly suggest that the regulation of NFRs profoundly affects transcription initiation. To date, multiple factors are known to facilitate transcription initiation by positively regulating the formation and/or size of NFRs in vivo. However, mechanisms to repress transcription by negatively regulating the size of NFRs have not been identified. We identified four distinct classes of NFRs located at the 5' and 3' ends of genes, within open reading frames (ORFs), and far from ORFs. The ATP-dependent chromatin-remodeling enzyme Isw2 was found enriched at all classes of NFRs. Analysis of RNA levels also demonstrated Isw2 is required to repress ncRNA transcription from many of these NFRs. Thus, by the systematic annotation of NFRs across the yeast genome and analysis of ncRNA transcription, we established, for the first time, a mechanism by which NFR size is negatively regulated to repress ncRNA transcription from NFRs. Finally, we provide evidence suggesting that one biological consequence of repression of ncRNA, by Isw2 or by the exosome, is prevention of transcriptional interference of mRNA.
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Registered trials
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.