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The consequences of selection bias in analysis of pre-mRNA splicing

ABSTRACT: The consequences of selection bias in analysis of pre-mRNA splicing

PROVIDER: PRJNA671694 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12889359_1.fastq.gz	Fastqsanger.gz
	SRR12889359_2.fastq.gz	Fastqsanger.gz
	SRR12889360_1.fastq.gz	Fastqsanger.gz
	SRR12889360_2.fastq.gz	Fastqsanger.gz
	SRR12889361_1.fastq.gz	Fastqsanger.gz

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The consequences of selection bias in analysis of pre-mRNA splicing

Project description:Investigating the consequences of selection bias in analysis of pre-mRNA splicing

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Splicing factors and chromatin organization enhance exon recognition by alleviating constraints generated by gene nucleotide composition bias

Project description:To characterize the rules governing exon recognition during splicing, we analyzed RNA-seq datasets and identified ~4,000 GC-rich and ~5,000 AT-rich exons, labelled GC-exons and AT-exons, respectively whose inclusion depends on different sets of splicing factors. We show that a high GC-load is associated with predicted RNA secondary structures at 5'ss and that GC-exons are dependent on U1 snRNP-associated proteins. Meanwhile, a high AT-load is associated with a large number of decoy splicing-related signals upstream exons such as the number of branchpoints and SF1- or U2AF65-binding sites and AT-exons are dependent on U2 snRNP-associated proteins. Nucleotide composition bias also influences local chromatin organization. Since the GC content of exons correlates with that of their hosting-genes, -isochores and – topologically-associated domains, we propose that regional nucleotide composition bias leaves a footprint locally, at the exon level, inducing, during splicing, constraints that are alleviated by the local chromatin organization and specific splicing factors.

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Competition between pre-mRNAs for a limiting splicing machinery drives global changes in splicing

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