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Transcriptome wide identification of retained introns upon depletion of the splicing factors SNW1 or PRPF8

ABSTRACT: We identified which mRNAs are dependent on the splicing factors SNW1 or PRPF8. These factors were depleted in HeLa cells by RNAi, and the levels of intronic reads in mRNAs was compared to control RNAi. Intronic reads from polyA containing RNAs from HeLa cells and mSnw1-LAP 'rescued' cells, both depleted for endogenous SNW1, were compared. Furthermore, intronic reads from polyA containing RNAs from HeLa cells depleted for SNW1 or PRPF8 were compared to control depleted HeLa cells.

ORGANISM(S): Homo sapiens

SUBMITTER: Roman Stocsits

PROVIDER: E-GEOD-61071 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome wide identification of retained introns upon depletion of the splicing factors SNW1 or PRPF8

Project description:We identified which mRNAs are dependent on the splicing factors SNW1 or PRPF8. These factors were depleted in HeLa cells by RNAi, and the levels of intronic reads in mRNAs was compared to control RNAi.

2014-09-04 | GSE61071 | GEO

PRPF8 iCLIP on HeLa cells in response to eIF4A3 Knockdown

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2018-10-14 | E-MTAB-7269 | biostudies-arrayexpress

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RNAseq of Trypanosoma brucei 427 bloodstream forms after depleting RBSR1 using RNAi.

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PRPF8 iCLIP on HeLa cells in response to eIF4A3 Knockdown

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PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5'-splice-site selection causing tissue-specific defects

Project description:The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity mechanism. We used patient induced pluripotent stem cells-derived cells, carrying the heterozygous PRPF8 c.6926A>C (p.H2309P) mutation to demonstrate retinal-specific endophenotypes comprising photoreceptor loss, apical-basal polarity and ciliary defects. Comprehensive molecular, transcriptomic, and proteomic analyses revealed a role of the PRPF8/Brr2 regulation in 5’-splice site (5’SS) selection by spliceosomes, for which disruption impaired alternative splicing and weak/suboptimal 5’SS selection, and enhanced cryptic splicing, predominantly in ciliary and retinal-specific transcripts. Altered splicing efficiency, nuclear speckles organisation, and PRPF8 interaction with U6 snRNA, caused accumulation of active spliceosomes and poly(A)+ mRNAs in unique splicing clusters located at the nuclear periphery of photoreceptors. Collectively these elucidate the role of PRPF8/Brr2 regulatory mechanisms in splicing and the molecular basis of retinal disease, informing therapeutic approaches.

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PRPF8 controls alternative splicing of PIRH2 to modulate the p53 pathway and survival of human embryonic stem cells

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