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Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [Tra2bKO]

ABSTRACT: Analysis of transcript changes with enough depth for evaluation of splicing changes between naïve, scrambled control CD8+ T or Tra2bKO CD8+ T cells from mice

ORGANISM(S): Mus musculus

PROVIDER: GSE267603 | GEO | 2024/06/01

REPOSITORIES: GEO

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Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [PEKOSeq]

Project description:Analysis of transcript changes with enough depth for evaluation of splicing changes between scrambled control CD8+ T or Tra2b-PE KO CD8+ T cells from mice

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Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [ASO_RNASeq]

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Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [N4T4Seq]

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Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [CLIP-seq]

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Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate

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RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons.

Project description:While RNA-seq has enabled comprehensive quantification of alternative splicing, no correspondingly high-throughput assay exists for functionally interrogating individual isoforms. We describe pgFARM (paired guide RNAs for alternative exon removal), a CRISPR-Cas9-based method to manipulate isoforms independent of gene inactivation. This approach enabled rapid suppression of exon recognition in polyclonal settings to identify functional roles for individual exons, such as an SMNDC1 cassette exon that regulates pan-cancer intron retention. We generalized this method to a pooled screen to measure the functional relevance of 'poison' cassette exons, which disrupt their host genes' reading frames yet are frequently ultraconserved. Many poison exons were essential for the growth of both cultured cells and lung adenocarcinoma xenografts, while a subset had clinically relevant tumor-suppressor activity. The essentiality and cancer relevance of poison exons are likely to contribute to their unusually high conservation and contrast with the dispensability of other ultraconserved elements for viability.

| S-EPMC6962552 | biostudies-literature

RNA isoform screens reveal the essentiality and tumor suppressor activity of ultraconserved poison exons

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ER stress increases alternative splicing of SRFS3âs poison exon.

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