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

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

PROVIDER: PRJNA1022433 | ENA |

REPOSITORIES: ENA

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Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness

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

Project description:CRISPR-Cas technology has transformed functional genomics, yet understanding of how individual exons differentially shape cellular phenotypes remains limited. Here, we optimized and conducted massively parallel exon deletion and splice-site mutation screens in human cell lines to identify exons that regulate cellular fitness. Fitness-promoting exons are prevalent in essential and highly expressed genes and commonly overlap with protein domains and interaction interfaces. Conversely, fitness-suppressing exons are enriched in nonessential genes, exhibiting lower inclusion levels, and overlap with intrinsically disordered regions and disease-associated mutations. In-depth mechanistic investigation of the screen-hit TAF5 alternative exon-8 revealed that its inclusion is required for assembly of the TFIID general transcription initiation complex, thereby regulating global gene expression output. Collectively, our orthogonal exon perturbation screens established a comprehensive repository of phenotypically important exons and uncovered regulatory mechanisms governing cellular fitness and gene expression.

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

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

Project description:Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness [ChIP-seq]

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

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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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