ArticleRNA (New York, N.Y.)2015
Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 47 citations in OpenAlex.
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
- Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.Genome biology · 2026Article
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Alternative splicing is coupled to gene expression in a subset of variably expressed genes.NPJ genomic medicine · 2024Article
- Unveil Intrahepatic Cholangiocarcinoma Heterogeneity through the Lens of Omics and Multi-Omics Approaches.Cancers · 2024Review
- Alternative splicing is coupled to gene expression in a subset of variably expressed genes.bioRxiv : the preprint server for biology · 2023Article
- Histone Marks-Dependent Effect on Alternative Splicing: New Perspectives for Targeted Splicing Modulation in Cancer?International journal of molecular sciences · 2022Review
- GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency inGenome research · 2022Article
- Progesterone receptor antagonists reverse stem cell expansion and the paracrine effectors of progesterone action in the mouse mammary gland.Breast cancer research : BCR · 2021Article
- Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition.Nature communications · 2021Article
- dSreg: a Bayesian model to integrate changes in splicing and RNA-binding protein activity.Bioinformatics (Oxford, England) · 2020Article
- The changing paradigm of intron retention: regulation, ramifications and recipes.Nucleic acids research · 2019Review
- Review
- ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development.Nucleic acids research · 2019Article
- Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing.Journal of molecular biology · 2016Review
- Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast.G3 (Bethesda, Md.) · 2016Article
- Chromatin structure and pre-mRNA processing work together.Transcription · 2016Article
- A deformation energy-based model for predicting nucleosome dyads and occupancy.Scientific reports · 2016Article
- Connecting the dots: chromatin and alternative splicing in EMT.Biochemistry and cell biology = Biochimie et biologie cellulaire · 2016Review
- Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Splicing of mRNA precursors can occur cotranscriptionally and it has been proposed that chromatin structure influences splice site recognition and regulation. Here we have systematically explored potential links between nucleosome positioning and alternative splicing regulation upon progesterone stimulation of breast cancer cells. We confirm preferential nucleosome positioning in exons and report four distinct profiles of nucleosome density around alternatively spliced exons, with RNA polymerase II accumulation closely following nucleosome positioning. Hormone stimulation induces switches between profile classes, correlating with a subset of alternative splicing changes. Hormone-induced exon inclusion often correlates with higher nucleosome occupancy at the exon or the preceding intronic region and with higher RNA polymerase II accumulation. In contrast, exons skipped upon hormone stimulation display low nucleosome densities even before hormone treatment, suggesting that chromatin structure primes alternative splicing regulation. Skipped exons frequently harbor binding sites for hnRNP AB, a hormone-induced splicing regulator whose knock down prevents some hormone-induced skipping events. Collectively, our results argue that a variety of chromatin architecture mechanisms can influence alternative splicing decisions.
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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.