Cited by 469RNA Research and SplicingRNA regulation and diseaseRNA and protein synthesis mechanisms

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Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

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Xue, Yuanchao, Zhou, Yu, Wu, Tongbin, Zhu, Tuo, Ji, Xiong, Kwon, Young-Soo, Zhang, Chao, Yeo, Gene, Black, Douglas L., Sun, Hui, Fu, Xiang-Dong, Zhang, Yi·2009·Molecular Cell

DOI 10.1016/j.molcel.2009.12.003PMC PMC2807993

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Abstract

Recent transcriptome analysis indicates that > 90% of human genes undergo alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract-binding protein PTB is a well-characterized splicing repressor, but PTB knockdown causes both exon inclusion and skipping. Genome-wide mapping of PTB-RNA interactions and construction of a functional RNA map now reveal that dominant PTB binding near a competing constitutive splice site generally induces exon inclusion, whereas prevalent binding close to an alternative site often causes exon skipping. This positional effect was further demonstrated by disrupting or creating a PTB-binding site on minigene constructs and testing their responses to PTB knockdown or overexpression. These findings suggest a mechanism for PTB to modulate splice site competition to produce opposite functional consequences, which may be generally applicable to RNA-binding splicing factors to positively or negatively regulate alternative splicing in mammalian cells.

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Authors: Xue, Y., Zhou, Y., Wu, T., Zhu, T., Ji, X., Kwon, Y.-S., Zhang, C., Yeo, G., Black, D. L., Sun, H., Fu, X.-D., & Zhang, Y.
Affiliations: Wuhan University (CN)
University of California San Diego (US)
Howard Hughes Medical Institute (US)
Corresponding author: Fu, Xiang-Dong
Zhang, Yi
ORCID: Xue, Yuanchao
Zhou, Yu
Wu, Tongbin
Ji, Xiong
Kwon, Young-Soo
Yeo, Gene
Black, Douglas L.
Sun, Hui
Fu, Xiang-Dong
Zhang, Yi
Venue: Molecular Cell
Publisher: Elsevier BV
Published: 2009-12
Volume: 36
Issue: 6
Pages: 996-1006
ISSN: 1097-2765 (ISSN-L)
DOI: 10.1016/j.molcel.2009.12.003
PMC: PMC2807993
OpenAlex: W1974898488
Cited by: 469
References: 43
Citations by year: 2026: 14 · 2025: 17 · 2024: 23 · 2023: 28 · 2022: 25 · 2021: 19 · 2020: 22 · 2019: 15 · 2018: 35 · 2017: 24 · 2016: 25 · 2015: 34 · 2014: 44 · 2013: 35 · 2012: 43
FWCI: 14.24
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 1324 d)
Locations: Molecular Cell (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National High-tech Research and Development Program
National Key Research and Development Program of China
National Human Genome Research Institute (HG004659, R01HG004659)
National Institute of General Medical Sciences (R01GM084317, GM049369, R01GM049369, GM084317)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: polypyrimidine tract-binding protein, PTB, alternative splicing, exon skipping, exon inclusion, RNA-binding proteins, splicing repressor, minigene constructs, splice site selection
MeSH terms: Animals, Binding Sites, Exons, HeLa Cells, Humans, Molecular Sequence Data, Protein Binding, RNA, Genome, Human, Alternative Splicing, Gene Expression Profiling, Polypyrimidine Tract-Binding Protein

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Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

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