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Insplico: Effective computational tool for studying intron splicing order genome-wide with short and long RNA-seq reads

ABSTRACT: Insplico: Effective computational tool for studying intron splicing order genome-wide with short and long RNA-seq reads

PROVIDER: PRJNA855685 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19977700_1.fastq.gz	Fastqsanger.gz
	SRR19977700_2.fastq.gz	Fastqsanger.gz
	SRR19977701_1.fastq.gz	Fastqsanger.gz
	SRR19977701_2.fastq.gz	Fastqsanger.gz
	SRR19977702_1.fastq.gz	Fastqsanger.gz

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Insplico: Effective computational tool for studying intron splicing order genome-wide with short and long RNA-seq reads

Project description:Investigation of the intron splicing order in different tissues , cell lines and conditions

2023-06-14 | GSE207459 | GEO

Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads.

Project description:Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence whether or not an intron is spliced before its downstream neighbor, multiple questions related to adjacent introns' splicing order (AISO) remain unanswered. Here, we present Insplico, the first standalone software for quantifying AISO that works with both short and long read sequencing technologies. We first demonstrate its applicability and effectiveness using simulated reads and by recapitulating previously reported AISO patterns, which unveiled overlooked biases associated with long read sequencing. We next show that AISO around individual exons is remarkably constant across cell and tissue types and even upon major spliceosomal disruption, and it is evolutionarily conserved between human and mouse brains. We also establish a set of universal features associated with AISO patterns across various animal and plant species. Finally, we used Insplico to investigate AISO in the context of tissue-specific exons, particularly focusing on SRRM4-dependent microexons. We found that the majority of such microexons have non-canonical AISO, in which the downstream intron is spliced first, and we suggest two potential modes of SRRM4 regulation of microexons related to their AISO and various splicing-related features. Insplico is available on gitlab.com/aghr/insplico.

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RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants

Project description:RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants

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RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants

Project description:Single nucleotide variants (SNVs) in intronic regions have yet to be systematically investigated for their disease-causing potential. Using known pathogenic and neutral intronic SNVs (iSNVs) as training data, we develop the RegSNPs-intron algorithm based on a random forest classifier that integrates RNA splicing, protein structure and evolutionary conservation features. RegSNPs-intron shows excellent performance in evaluating the pathogenic impacts of iSNVs. Using a high-throughput functional reporter assay called ASSET-seq (ASsay for Splicing using ExonTrap and sequencing), we evaluate the impact of regSNPs-intron predictions on splicing outcome. Together, RegSNPs-intron and ASSET-seq enable effective prioritization of iSNVs for disease pathogenesis.

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pre-mRNA splicing order is defined and maintains splicing fidelity across multi-intronic transcripts [II]

Project description:Combinatorially, intron excision within a given nascent transcript could proceed down any of thousands of paths, each of which would expose different dynamic landscapes of cis-elements and contribute to alternative splicing. In this study, we found that post-transcriptional multi-intron splicing order in human cells is largely predetermined, with most genes spliced in one or a few predominant orders. Strikingly, these orders were conserved across cell types and stages of motor neuron differentiation. Introns flanking alternatively spliced exons were frequently excised last, after their neighboring introns. Perturbations to the spliceosomal U2 snRNA altered the preferred splicing order of many genes, and these alterations were associated with the retention of other introns in the same transcript. In one gene, early removal of specific introns was sufficient to induce delayed excision of three proximal introns, and this delay was caused by two distinct cis-regulatory mechanisms. Together, our results demonstrate that multi-intron splicing order in human cells is predetermined, is influenced by a component of the spliceosome and ensures splicing fidelity across long pre-mRNAs.

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