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

ABSTRACT: 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

ORGANISM(S): Mus musculus

PROVIDER: GSE267601 | GEO | 2024/06/01

REPOSITORIES: GEO

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

Project description:Analysis of transcript changes with enough depth for evaluation of splicing changes between CD8+ T cells from human donor PBMCs receiving no stimulation,CD3/CD28 stimulation plus scrambled ASO, or CD3/CD28 plus Tra2b-PE ASO

2024-06-01 | GSE267586 | GEO

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

Project description: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

2024-06-01 | GSE267603 | GEO

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

Project description:Analysis of Tra2b binding sites in Naïve and Effector CD8+ T cells from spleens and lymph nodes of OT-I mice unstimulated or stimulated with SIINFEKL peptide + anti-OX40/41BB for 4 days

2024-06-01 | GSE267587 | GEO

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

Project description:Analysis of transcript changes with enough depth for evaluation of splicing changes between CD8+ T cells from mice receiving no stimulation, N4 stimulation, or N4 stimulation after treatment with Torin inhibitor

2024-06-01 | GSE267608 | GEO

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

Project description:Analysis of transcript changes with enough depth for evaluation of splicing changes between CD8+ T cells from mice receiving high affinity SIINFEKL (N4) and moderate affinity SIITFEKL (T4) peptide + anti-OX40/anti-41BB costimulation

2024-06-01 | GSE267588 | GEO

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-06-01 | GSE267609 | GEO

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

Project description:Paired gRNA/Cas9 delivery facilitates the removal of alternative exons and reveals splicing dependent phenotypes.

2019-11-19 | GSE120703 | GEO

Neuronal-specific Deficiency of the Splicing Factor Tra2b Causes p21-mediated Apoptosis in Neurogenic Areas of the Developing Mouse Brain

Project description:Alternative splicing (AS) increases the informational content of the genome and is more prevalent in the brain than in any other tissue. The splicing factor Tra2b (Sfrs10) can modulate splicing inclusion of exons by specifically detecting GAA-rich binding motifs and its absence causes early embryonic lethality in mice. TRA2B has been shown to be involved in splicing processes of Nasp (nuclear autoantigenic sperm protein), MAPT (microtubule associated protein tau) and SMN (survival motor neuron), and is therefore implicated in spermatogenesis and neurological diseases like AlzheimerM-^Rs disease, dementia, ParkinsonM-^Rs disease and spinal muscular atrophy. Here we generated a neuronal-specific Tra2b knock-out mouse that lacks Tra2b expression in neuronal and glial precursor cells by using the Nestin-Cre. Neuronal-specific Tra2b knock-out mice die immediately after birth and show severe abnormalities in cortical development, which are caused by massive apoptotic events in the ventricular layers of the cortex, demonstrating a pivotal role of Tra2b for the developing central nervous system. Using whole brain RNA on exon arrays we identified differentially expressed alternative exons of Tubulin?1 and Shugoshin like2 as in vivo targets of Tra2b. Most interestingly, we found increased expression of the cyclin dependent kinase inhibitor 1a (p21) which we could functionally link to neuronal precursor cells in the affected brain regions. We provide further evidence that the absence of Tra2b causes p21 upregulation and ultimately cell death in NSC34 neuronal-like cells. These findings demonstrate that Tra2b regulates splicing events essential for maintaining neuronal viability during development. Apoptotic events triggered via p21 might not be restricted to the developing brain but could possibly be generalized to the whole organism and explain early embryonic lethality in Tra2b-depleted mice.

2013-12-16 | E-MTAB-2157 | biostudies-arrayexpress

scRNAseq in Pten enhancer wild-type or deleted thymocytes, enriched for immature thymocyte stages (CD4-CD3-)

Project description:Single cell suspensions of total thymocytes were obtained from Pten enhancer (PE) wild-type or knockout mice. This single-cell suspension was enriched in CD4-CD3- immature thymocyte progenitor cells. CD4-CD3- enriched thymocytes were then mixed 1:1 with single-cell suspensions from total unenriched thymocytes and subsequntly loaded in a 10x Chromium instrument for single-cell RNAseq analyses. Our results revealed Pten levels are signifcantly decreased in CD4-CD8- double negative (DN) thymocytes, CD8+ intermediate single positive (ISP) thymocytes and CD4+CD8+ double positive (DP) thymocytes in PE knockout mice, compared to PE wild-type mice.

2020-12-17 | GSE156070 | GEO

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