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Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness [GUIDE-seq]

ABSTRACT: Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness [GUIDE-seq]

PROVIDER: PRJNA1093482 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR28503230_1.fastq.gz	Fastqsanger.gz
	SRR28503230_2.fastq.gz	Fastqsanger.gz
	SRR28503231_1.fastq.gz	Fastqsanger.gz
	SRR28503231_2.fastq.gz	Fastqsanger.gz
	SRR28503232_1.fastq.gz	Fastqsanger.gz

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Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness [GUIDE-seq]

Project description:Although CRISPR-Cas technology has revolutionized functional genomics, the systematic exploration of the role of individual exons for critical cellular phenotypes is lagging, limiting our understanding of genome regulation. To overcome this constraint, we have optimized and applied massively parallel exon deletion and splice site mutation screens in human cell lines identifying thousands of exons required for cell fitness. Fitness-promoting exons are enriched in essential and highly expressed genes and frequently overlap protein domains and interaction interfaces. In contrast, fitness-suppressing exons that are enriched in low-expressed, non-essential genes and tend to overlap intrinsically disordered regions. In-depth mechanistic investigation of a screen hit, TAF5 alternative exon-8, reveals that its inclusion controls the assembly of the TFIID general transcription initiation complex regulating gene expression outputs. Collectively, by applying orthogonal exon perturbation screening strategies we have generated a resource of phenotypically important exons and uncovered mechanisms that control gene expression and cell fitness.

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Project description:Although CRISPR-Cas technology has revolutionized functional genomics, the systematic exploration of the role of individual exons for critical cellular phenotypes is lagging, limiting our understanding of genome regulation. To overcome this constraint, we have optimized and applied massively parallel exon deletion and splice site mutation screens in human cell lines identifying thousands of exons required for cell fitness. Fitness-promoting exons are enriched in essential and highly expressed genes and frequently overlap protein domains and interaction interfaces. This contrasts fitness-suppressing exons that are enriched in low-expressed, non-essential genes and tend to overlap intrinsically disordered regions. In-depth mechanistic investigation of a screen hit, the alternative exon-8 in TAF5, reveals that its inclusion controls the assembly of the TFIID general transcription initiation complex regulating gene expression outputs. Collectively, by applying orthogonal exon perturbation screening strategies we have interrogated phenotypically important exons at genome-scale and uncovered mechanisms that control gene expression and cell fitness.

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