Genome-wide Analysis of Alternative Pre-mRNA Splicing and RNA-Binding Specificities of the Drosophila hnRNP A/B Family Members
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Heterogeneous nuclear ribonucleoproteins (hnRNPs) have been traditionally seen as proteins packaging RNA nonspecifically into ribonucleoprotein particles (RNPs), but evidence suggests specific cellular functions on discrete target pre-mRNAs. Here we report genome-wide analysis of alternative splicing patterns regulated by four Drosophila homologs of the mammalian hnRNP A/B family (hrp36, hrp38, hrp40, and hrp48). Analysis of the global RNA-binding distributions of each protein revealed both small and extensively bound regions on target transcripts. A significant subset of RNAs were bound and regulated by more than one hnRNP protein, revealing a combinatorial network of interactions. In vitro RNA-binding site selection experiments (SELEX) identified distinct binding motif specificities for each protein, which were overrepresented in their respective regulated and bound transcripts. These results indicate that individual heterogeneous ribonucleoproteins have specific affinities for overlapping, but distinct, populations of target pre-mRNAs controlling their patterns of RNA processing.
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Very different motifs have been previously described for different HNRNPA family members from human and Drosophila, whereas RNAcompete motifs for the same proteins are closely related.
“very different motifs have been previously described for different HNRNPA family members from human and Drosophila19–22, whereas the RNAcompete motifs for the same proteins are closely related”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [21]
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- Authors
- Blanchette, M., Green, R. E., MacArthur, S., Brooks, A. N., Brenner, S. E., Eisen, M. B., & Rio, D. C.
- Affiliations
- University of California, Berkeley (US)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Blanchette, Marco
- Rio, Donald C.
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2009-02
- Volume
- 33
- Issue
- 4
- Pages
- 438-449
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC2674966
- OpenAlex
- W2103823160
- Cited by
- 86
- References
- 54
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 5 · 2023: 2 · 2022: 3 · 2021: 1 · 2020: 1 · 2019: 3 · 2018: 5 · 2017: 6 · 2016: 5 · 2015: 7 · 2014: 7 · 2013: 7 · 2012: 9
- FWCI
- 4.29
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- National Human Genome Research Institute (U01HG004271)
- National Institute of General Medical Sciences (R01GM061987, R01 GM61987, R01GM071655)
- 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
- hnRNP A/B, alternative splicing, RNA-binding proteins, Drosophila, SELEX, RNA-binding motif, ribonucleoprotein particles
- MeSH terms
- Animals, Base Sequence, Binding Sites, Cells, Cultured, Drosophila, Molecular Sequence Data, RNA Precursors, RNA, Messenger, Alternative Splicing, Heterogeneous-Nuclear Ribonucleoprotein Group A-B, Genome, Insect
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