Journal article
A compendium of RNA-binding motifs for decoding gene regulation
Nature (London), Vol.499(7457), pp.172-177
07/11/2013
Handle:
https://hdl.handle.net/2376/109800
PMCID: PMC3929597
PMID: 23846655
Abstract
RNA-binding proteins are key regulators of gene expression, yet only a small fraction have been functionally characterized. Here we report a systematic analysis of the RNA motifs recognized by RNA-binding proteins, encompassing 205 distinct genes from 24 diverse eukaryotes. The sequence specificities of RNA-binding proteins display deep evolutionary conservation, and the recognition preferences for a large fraction of metazoan RNA-binding proteins can thus be inferred from their RNA-binding domain sequence. The motifs that we identify
in vitro
correlate well with
in vivo
RNA-binding data. Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA-binding proteins both in normal physiology and in human disease. These data provide an unprecedented overview of RNA-binding proteins and their targets, and constitute an invaluable resource for determining post-transcriptional regulatory mechanisms in eukaryotes.
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Details
- Title
- A compendium of RNA-binding motifs for decoding gene regulation
- Creators
- Debashish Ray - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaHilal Kazan - Department of Computer Science, University of Toronto, Toronto M5S 2E4, CanadaKate B Cook - Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, CanadaMatthew T Weirauch - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaHamed S Najafabadi - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaXiao Li - Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, CanadaSerge Gueroussov - Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, CanadaMihai Albu - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaHong Zheng - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaAlly Yang - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaHong Na - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaManuel Irimia - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaLeah H Matzat - Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USARyan K Dale - Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USASarah A Smith - Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USAChristopher A Yarosh - Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USASeth M Kelly - Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USABehnam Nabet - Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USADesirea Mecenas - Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003, USAWeimin Li - Molecular and Cellular Pharmacology Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USARakesh S Laishram - Molecular and Cellular Pharmacology Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USAMei Qiao - Children’s Cancer Research Institute, UTHSCSA, San Antonio, Texas 78229, USAHoward D Lipshitz - Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, CanadaFabio Piano - Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003, USAAnita H Corbett - Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USARuss P Carstens - Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USABrendan J Frey - Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4, CanadaRichard A Anderson - Molecular and Cellular Pharmacology Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USAKristen W Lynch - Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USALuiz O. F Penalva - Children’s Cancer Research Institute, UTHSCSA, San Antonio, Texas 78229, USAElissa P Lei - Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USAAndrew G Fraser - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaBenjamin J Blencowe - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaQuaid D Morris - Donnelly Centre, University of Toronto, Toronto M5S 3E1, CanadaTimothy R Hughes - Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
- Publication Details
- Nature (London), Vol.499(7457), pp.172-177
- Academic Unit
- Department of Biomedical Sciences
- Publisher
- Springer Nature
- Number of pages
- 6
- Grant note
- R01 GM084034 || GM / National Institute of General Medical Sciences : NIGMS R01 GM051968 || GM / National Institute of General Medical Sciences : NIGMS R01 HG005700 || HG / National Human Genome Research Institute : NHGRI
- Identifiers
- 99900547055701842
- Language
- English
- Resource Type
- Journal article