ArticleGenome biology2019
Characterizing the interplay between gene nucleotide composition bias and splicing.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 23 citations in OpenAlex.
- Detection of a sequence feature for recursive splicing.bioRxiv : the preprint server for biology · 2026Article
- Association of hybridization and genome doubling with codon usage landscapes in the subgenomes of bread wheat.Frontiers in plant science · 2026Article
- Population genetic structure of Uroteuthis edulis in the East China Sea based on the COI gene.Molecular biology reports · 2025Article
- Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing.Life science alliance · 2024Article
- Genetic Diversity in Bronchial Asthma Susceptibility: Exploring the Role of Vitamin D Receptor Gene Polymorphisms in Varied Geographic Contexts.International journal of molecular sciences · 2024Article
- SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors.Database : the journal of biological databases and curation · 2023Article
- Article
- Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing.Molecular cell · 2022Article
- False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.Genome biology · 2022Article
- EWS splicing regulation contributes to balancing Foxp1 isoforms required for neuronal differentiation.Nucleic acids research · 2022Article
- The endogenous HBZ interactome in ATL leukemic cells reveals an unprecedented complexity of host interacting partners involved in RNA splicing.Frontiers in immunology · 2022Article
- The oncogenic kinase NEK2 regulates an RBFOX2-dependent pro-mesenchymal splicing program in triple-negative breast cancer cells.Journal of experimental & clinical cancer research : CR · 2021Article
- Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.PLoS computational biology · 2021Article
- Article
- Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control.International journal of molecular sciences · 2020Review
- An Intergenic rs9275596 Polymorphism on Chr. 6p21 Is Associated with Multiple Sclerosis in Latvians.Medicina (Kaunas, Lithuania) · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNucleotide composition bias plays an important role in the 1D and 3D organization of the human genome. Here, we investigate the potential interplay between nucleotide composition bias and the regulation of exon recognition during splicing.
resultsBy analyzing dozens of RNA-seq datasets, we identify two groups of splicing factors that activate either about 3200 GC-rich exons or about 4000 AT-rich exons. We show that splicing factor-dependent GC-rich exons have predicted RNA secondary structures at 5' ss and are dependent on U1 snRNP-associated proteins. In contrast, splicing factor-dependent AT-rich exons have a large number of decoy branch points, SF1- or U2AF2-binding sites and are dependent on U2 snRNP-associated proteins. Nucleotide composition bias also influences local chromatin organization, with consequences for exon recognition during splicing. Interestingly, the GC content of exons correlates with that of their hosting genes, isochores, and topologically associated domains.
conclusionsWe propose that regional nucleotide composition bias over several dozens of kilobase pairs leaves a local footprint at the exon level and induces constraints during splicing that can be alleviated by local chromatin organization at the DNA level and recruitment of specific splicing factors at the RNA level. Therefore, nucleotide composition bias establishes a direct link between genome organization and local regulatory processes, like alternative splicing.
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