ArticleNucleic acids research2010
The organization of nucleosomes around splice sites.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 74 citations in OpenAlex.
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications.eLife · 2025Article
- Differences in alternative splicing and their potential underlying factors between animals and plants.Journal of advanced research · 2024Review
- Stochastic Variation in DNA Methylation Modulates Nucleosome Occupancy and Alternative Splicing inPlants (Basel, Switzerland) · 2022Article
- Histone H1.5 binds over splice sites in chromatin and regulates alternative splicing.Nucleic acids research · 2019Article
- Does co-transcriptional regulation of alternative splicing mediate plant stress responses?Nucleic acids research · 2019Review
- Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition.Bioinformatics (Oxford, England) · 2017Article
- A deformation energy-based model for predicting nucleosome dyads and occupancy.Scientific reports · 2016Article
- Diverse regulation of 3' splice site usage.Cellular and molecular life sciences : CMLS · 2015Review
- Splicing of many human genes involves sites embedded within introns.Nucleic acids research · 2015Article
- Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits.BioEssays : news and reviews in molecular, cellular and developmental biology · 2014Article
- Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2014Article
- DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure.Genome research · 2013Article
- Function of alternative splicing.Gene · 2013Review
- Detecting splicing variants in idiopathic pulmonary fibrosis from non-differentially expressed genes.PloS one · 2013Article
- The function of introns.Frontiers in genetics · 2012Article
- Nucleosome Positioning.ISRN molecular biology · 2012Review
- The genomic signature of splicing-coupled selection differs between long and short introns.Molecular biology and evolution · 2012Article
- Article
- How do RNA sequence, DNA sequence, and chromatin properties regulate splicing?F1000 biology reports · 2010Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The occupancy of nucleosomes along chromosome is a key factor for gene regulation. However, except promoter regions, genome-wide properties and functions of nucleosome organization remain unclear in mammalian genomes. Using the computational model of Increment of Diversity with Quadratic Discriminant (IDQD) trained from the microarray data, the nucleosome occupancy score (NOScore) was defined and applied to splice junction regions of constitutive, cassette exon, alternative 3' and 5' splicing events in the human genome. We found an interesting relation between NOScore and RNA splicing: exon regions have higher NOScores compared with their flanking intron sequences in both constitutive and alternative splicing events, indicating the stronger nucleosome occupation potential of exon regions. In addition, NOScore valleys present at approximately 25 bp upstream of the acceptor site in all splicing events. By defining folding diversity-to-energy ratio to describe RNA structural flexibility, we demonstrated that primary RNA transcripts from nucleosome occupancy regions are relatively rigid and those from nucleosome depleted regions are relatively flexible. The negative correlation between nucleosome occupation/depletion of DNA sequence and structural flexibility/rigidity of its primary transcript around splice junctions may provide clues to the deeper understanding of the unexpected role for nucleosome organization in the regulation of RNA splicing.
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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.