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U2AF35(S34F) Promotes Transformation by Directing Aberrant ATG7 Pre-mRNA 3’ End Formation

ABSTRACT: We sequenced mRNA from Ba/F3 cells with U2AF35(S34F) expressing or parental Ba/F3

ORGANISM(S): Mus musculus

PROVIDER: GSE63404 | GEO | 2016/05/01

SECONDARY ACCESSION(S): PRJNA267679

REPOSITORIES: GEO

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U2AF35(S34F) Promotes Transformation by Directing Aberrant ATG7 Pre-mRNA 3' End Formation.

Project description: Not available

| S-EPMC5012111 | biostudies-literature

Expression analysis of mutant U2AF35 transduced cells

Project description:In this study, to obtain the biological impact of the mutated U2AF35, HeLa and TF-1 cells were retrovirally transduced with either mock, wild-type or S34F mutant of U2AF35, and Expression array was performed. Expression analysis was performed for mock, wild-type U2AF35 or S34F mutant transduced HeLa and MDS-derived TF-1 cell line in triplicate.

2011-09-11 | E-GEOD-31172 | biostudies-arrayexpress

Exon level expression profiling of mutant U2AF35 transduced HeLa cells

Project description:In this study, to obtain the biological impact of the mutated U2AF35, HeLa cells were retrovirally transduced with either mock, wild-type or S34F mutant of U2AF35, and Exon array was performed. Exon level analysis was performed for mock, wild-type U2AF35 or S34F mutant transduced HeLa in triplicate.

2011-09-11 | E-GEOD-31171 | biostudies-arrayexpress

Expression analysis of mutant U2AF35 transduced cells

2011-09-12 | GSE31172 | GEO

Exon level expression profiling of mutant U2AF35 transduced HeLa cells

2011-09-12 | GSE31171 | GEO

Expression profile of mutant U2AF35 transduced cells

Project description:This SuperSeries is composed of the following subset Series: GSE31171: Exon level expression profiling of mutant U2AF35 transduced HeLa cells GSE31172: Expression analysis of mutant U2AF35 transduced cells Refer to individual Series

2012-04-09 | E-GEOD-31173 | biostudies-arrayexpress

Identification of differentially spliced genes by wild type or S34F mutation of U2AF1

Project description:Identification of differentially spliced genes by wild type or S34F mutation of U2AF1 Examination of effects on splicing events by overexpressing wipdtype or S34F mutation of two U2AF1 isoforms in A549 cells. All experimental conditions are performed in duplicate.

2015-11-01 | E-GEOD-66553 | biostudies-arrayexpress

Murine Ba/F3 Cells: Ba/F3 cells expressing wild type JAK2 (WT cells) vs. Ba/F3 cells expressing JAK2 V617F mutant (VF cells)

Project description:Transcriptional profiling of transformed Ba/F3 cells by myeloproliferative neoplasm-associated JAK2 V617F mutant comparing control Ba/F3 cells expressing wild type JAK2.

2013-10-31 | GSE34239 | GEO

RNA sequencing of common myeloid progenitors following short term induction of mutant U2AF1(S34F) expression in transgenic mice

Project description:Mutations in the splicing factor gene U2AF1 have been found in the bone marrow of patients with myelodysplastic syndrome and acute myeloid leukemia, as well as in other cancers. To study the effects of mutant U2AF1(S34F) expression on hematopoiesis and pre-mRNA splicing in hematopoietic cells, we generated two inducible transgenic mouse lines expressing either mutant U2AF1(S34F) or U2AF1(wildtype, WT) as control. We performed strand-specific transcriptome sequencing on bone marrow common myeloid progenitor cells from U2AF1(S34F) and U2AF1(WT)-expressing mice to examine the pre-mRNA splicing changes associated with expression of mutant U2AF1(S34F). Donor-derived common myeloid progenitor cells from mice transplanted with U2AF1(S34F)/rtTA or U2AF1(WT)/rtTA bone marrow were sorted by flow cytometry, and RNA was extracted for transcriptome analysis. Ribosomal RNA was depleted prior to strand-specific RNA sequencing (TruSeq stranded library production, followed by 2 x 100bp paired-end sequencing performed on the HiSeq2000 platform from Illumina). Three samples were sequenced per genotype (n=3), and each sample was composed of bone marrow from 4-5 mice pooled. Reads were aligned to the mouse mm9 reference genome using TopHat (version 2.0.8), and we performed all subsequent analyses in R.

2015-05-11 | E-GEOD-66793 | biostudies-arrayexpress

Nanopore sequencing reveals isoform-specific alterations in human bronchial epithelial cells with U2AF1 S34F mutations

Project description:U2AF1 S34F is one of the most recurrent splicing factor mutations in lung adenocarcinoma (ADC) and has been shown to cause transcriptome-wide pre-mRNA splicing alterations. While U2AF1 S34F-associated splicing alterations have been described, the fate of affected mRNA isoforms remains largely unexplored. To better understand the impact U2AF1 S34F has on isoform fate and function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells with and without U2AF1 S34F mutation. We find that nearly 75% (49,366) of our long-read constructed multi-exon isoforms do not overlap GENCODE or short-read assembled isoforms, a large proportion of which (12,397) are due to novel junction connectivity rather than novel splice site usage. We find 198 transcript isoforms with significant expression and usage changes relative to wild-type, some of which were not assembled by short-reads. We find an enrichment of isoforms from immune related genes are down regulated in the presence of U2Af1 S34F, none of which are observed to have splicing changes detected from long-read data. Finally, we reveal that isoforms likely targeted by nonsense-mediated decay are largely downregulated in U2AF1 S34F cells, suggesting that the impact of observed isoform changes may alter the translational output of affected genes. Altogether, our data builds on previous work by providing a higher resolution transcriptome snapshot of full-length isoform alterations associated with U2AF1 S34F in HBEC3kt cells.

2022-06-30 | GSE140734 | GEO

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