Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2
Open accessAbstract
The precise regulation of many alternative splicing (AS) events by specific splicing factors is essential to determine tissue types and developmental stages. However, the molecular basis of tissue-specific AS regulation and the properties of splicing regulatory networks (SRNs) are poorly understood. Here we comprehensively predict the targets of the brain- and muscle-specific splicing factor Fox-1 (A2BP1) and its paralog Fox-2 (RBM9) and systematically define the corresponding SRNs genome-wide. Fox-1/2 are conserved from worm to human, and specifically recognize the RNA element UGCAUG. We integrate Fox-1/2-binding specificity with phylogenetic conservation, splicing microarray data, and additional computational and experimental characterization. We predict thousands of Fox-1/2 targets with conserved binding sites, at a false discovery rate (FDR) of ∼24%, including many validated experimentally, suggesting a surprisingly extensive SRN. The preferred position of the binding sites differs according to AS pattern, and determines either activation or repression of exon recognition by Fox-1/2. Many predicted targets are important for neuromuscular functions, and have been implicated in several genetic diseases. We also identified instances of binding site creation or loss in different vertebrate lineages and human populations, which likely reflect fine-tuning of gene expression regulation during evolution.
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Among the 212 significant alternative splicing events, 36 had been defined by Zhang et al. as predicted targets of A2BP1/2, representing a highly significant overlap (p=2.2E-16).
“Among these, 36 had been defined by Zhang et al. 19 as predicted targets of A2BP1/2 , which represents a highly significant overlap (p=2.2E-16).”
From Transcriptomic Analysis of Autistic Brain Reveals Convergent Molecular Pathology (2011) · cites this paper as [19]
Known splicing regulators, including RBFOX and PTB family members, were associated with preferential exon inclusion or exclusion in a manner correlated with the expression and binding location of the RBP.
“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 [35]
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Orchestration of Neurodevelopmental Programs by RBFOX1
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- Authors
- Zhang, C., Zhang, Z., Castle, J., Sun, S., Johnson, J., Krainer, A. R., & Zhang, M. Q.
- Affiliations
- Cold Spring Harbor Laboratory (US)
- Merck & Co., Inc., Rahway, NJ, USA (United States) (US)
- State University of New York (US)
- ORCID
- Venue
- Genes & Development
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-09-15
- Volume
- 22
- Issue
- 18
- Pages
- 2550-2563
- ISSN
- 0890-9369 (ISSN-L)
- 1549-5477
- PMC
- PMC2546699
- OpenAlex
- W2124182320
- Cited by
- 300
- References
- 63
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 12 · 2023: 10 · 2022: 16 · 2021: 9 · 2020: 9 · 2019: 7 · 2018: 12 · 2017: 16 · 2016: 11 · 2015: 18 · 2014: 32 · 2013: 27 · 2012: 27
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genes & Development (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (GM74688, R01GM074688)
- 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
- A2BP1, alternative splicing, splicing regulatory network, tissue-specific splicing, binding site prediction, exon recognition, binding site evolution, phylogenetic conservation
- MeSH terms
- RNA Splicing Factors, Binding Sites, Gene Expression Regulation, HeLa Cells, Humans, Repressor Proteins, RNA-Binding Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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