The DOI matches its Crossref record; 41 of the 43 references it cites were found in a registry or an index.
Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping
Open accessAbstract
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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“known splicing regulators, including RBFOX and PTB family members4, were associated with preferential exon inclusion or exclusion in a manner that correlated with the expression and binding location of the RBP”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [34]
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Alternative isoform regulation in human tissue transcriptomes
Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181
The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth
Christofk, H. R., Vander Heiden, M. G., Harris, M. H., Ramanathan, A., Gerszten, R. E., Wei, R., Fleming, M. D., Schreiber, S. L., & Cantley, L. C. (2008) · Nature · doi:10.1038/nature06734 · Cited by 2,820
Mechanisms of Alternative Pre-Messenger RNA Splicing
Black, D. L. (2003) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.72.121801.161720 · Cited by 2,704
Self-citationThe UCSC Genome Browser Database
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg129 · Cited by 1,890
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352 · cited 9×
“However, splicing regulators can often affect alternative splicing in a position-dependent manner, as has recently emerged from genomewide analysis of RNA-binding splicing regulators (Licatalosi et al., 2008; Yeo et al., 2009).”
InfluentialAlternative pre-mRNA splicing and proteome expansion in metazoans
Maniatis, T., & Tasic, B. (2002) · Nature · doi:10.1038/418236a · Cited by 774
Systematic Identification and Analysis of Exonic Splicing Silencers
Wang, Z., Rolish, M. E., Yeo, G. W.-M., Tung, V., Mawson, M., & Burge, C. B. (2004) · Cell · doi:10.1016/j.cell.2004.11.010 · Cited by 678
Self-citationBoutz, P. L., Stoilov, P., Li, Q., Lin, C.-H., Chawla, G., Ostrow, K., Shiue, L., Ares, M., & Black, D. L. (2007) · Genes & Development · doi:10.1101/gad.1558107 · Cited by 577
Self-citationYeo, G. W., Coufal, N. G., Liang, T. Y., Peng, G. E., Fu, X.-D., & Gage, F. H. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1545 · Cited by 572
Self-citationSingh, R., Valcárcel, J., & Green, M. R. (1995) · Science · doi:10.1126/science.7761834 · Cited by 539
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2 of the 43 references couldn’t be matched to a known paper.
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Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Alipanahi, B., Delong, A., Weirauch, M. T., & Frey, B. J. (2015) · Nature Biotechnology · doi:10.1038/nbt.3300 · Cited by 2,873
A compendium of RNA-binding motifs for decoding gene regulation
Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., et al. (2013) · Nature · doi:10.1038/nature12311 · Cited by 1,480
Function of alternative splicing
Stamm, S., Ben‐Ari, S., Rafalska, I., Tang, Y., Zhang, Z., Toiber, D., Thanaraj, T. A., & Soreq, H. (2004) · Gene · doi:10.1016/j.gene.2004.10.022 · Cited by 1,398
Mechanisms and Regulation of Alternative Pre-mRNA Splicing
Lee, Y., & Rio, D. C. (2015) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060614-034316 · Cited by 1,291
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1838 · Cited by 1,126
Metadata
- 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
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2009-12
- Volume
- 36
- Issue
- 6
- Pages
- 996-1006
- ISSN
- 1097-2765 (ISSN-L)
- 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
- 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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