Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.
Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, we used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Motif analysis revealed that SRSF10 binding to cassette exons was associated with exon inclusion, whereas the binding of SRSF10 within downstream constitutive exons was associated with exon exclusion. This positional effect was further demonstrated by the mutagenesis of potential SRSF10 binding motifs in two minigene constructs. Functionally, many of SRSF10-verified alternative exons are linked to pathways of stress and apoptosis. Consistent with this observation, cells depleted of SRSF10 expression were far more susceptible to endoplasmic reticulum stress-induced apoptosis than control cells. Importantly, reconstituted SRSF10 in knockout cells recovered wild-type splicing patterns and considerably rescued the stress-related defects. Together, our results provide mechanistic insight into SRSF10-regulated alternative splicing events in vivo and demonstrate that SRSF10 plays a crucial role in cell survival under stress conditions.
Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China, Novel Bioinformatics Co., Ltd, Shanghai, China, Department of Biological Sciences, Columbia University, New York, NY 10027, USA and Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China.
Xuexia
X
Zhou
Wenwu
W
Wu
Huang
H
Li
Yuanming
Y
Cheng
Ning
N
Wei
Jie
J
Zong
Xiaoyan
X
Feng
Zhiqin
Z
Xie
Dai
D
Chen
James L
JL
Manley
Hui
H
Wang
Ying
Y
Feng
D017398:Alternative Splicing; D000818:Animals; D017209:Apoptosis; D002460:Cell Line; D002645:Chickens; D059865:Endoplasmic Reticulum Stress; D005091:Exons; D020869:Gene Expression Profiling; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D000068103:Serine-Arginine Splicing Factors
D009687:Nuclear Proteins; D016601:RNA-Binding Proteins; D000068103:Serine-Arginine Splicing Factors; D012313:RNA