The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins
Open accessAbstract
Summary Specific protein-RNA interactions guide post-transcriptional gene regulation. Here we describe RNA Bind-n-Seq (RBNS), a method that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs), and its application to the developmental alternative splicing factors RBFOX2, CELF1/CUGBP1 and MBNL1. For each factor, we recovered both canonical motifs and additional near-optimal binding motifs. RNA secondary structure inhibits binding of RBFOX2 and CELF1, while MBNL1 favors unpaired Us but tolerates C/G pairing in motifs containing UGC and/or GCU. Dissociation constants calculated from RBNS data using a novel algorithm correlated highly with values measured by surface plasmon resonance. Motifs identified by RBNS were conserved, were bound and active in vivo, and distinguished the subset of motifs enriched by CLIP-Seq that had regulatory activity. Together, our data demonstrate that RBNS complements crosslinking-based methods and show that in vivo binding and activity of these splicing factors is driven largely by intrinsic RNA affinity.
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Cites
Most mammalian mRNAs are conserved targets of microRNAs
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Self-citationAlternative isoform regulation in human tissue transcriptomes
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Self-citationA compendium of RNA-binding motifs for decoding gene regulation
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“analysis, enabling high-throughput identification of RNA binding motifs (Ray et al., 2009; Ray et al., 2013).”
BackgroundMethodiCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
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CLIP Identifies Nova-Regulated RNA Networks in the Brain
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Streaming fragment assignment for real-time analysis of sequencing experiments
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Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues
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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
A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart
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Self-citationJin, Y., Suzuki, H., Maegawa, S., Endo, H., Sugano, S., Hashimoto, K., Yasuda, K., & Inoue, K. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg089 · Cited by 311
Cited by
Predicting effective microRNA target sites in mammalian mRNAs
Agarwal, V., Bell, G. W., Nam, J.-W., & Bartel, D. P. (2015) · eLife · doi:10.7554/elife.05005 · Cited by 7,318
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2493-4 · Cited by 2,378
Self-citationA brave new world of RNA-binding proteins
Hentze, M. W., Castello, A., Schwarzl, T., & Preiss, T. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.130 · Cited by 1,821
The biochemical basis of microRNA targeting efficacy
(2019) · doi:10.1126/science.aav1741 · Cited by 1,570
A large-scale binding and functional map of human RNA-binding proteins
Van Nostrand, E. L., Freese, P., Pratt, G. A., Wang, X., Wei, X., Xiao, R., Blue, S. M., Chen, J.-Y., Cody, N. A. L., Dominguez, D., et al. (2020) · Nature · doi:10.1038/s41586-020-2077-3 · Cited by 1,317
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Metadata
- Authors
- Lambert, N., Robertson, A., Jangi, M., McGeary, S., Sharp, P. A., & Burge, C. B.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2014-06
- Volume
- 54
- Issue
- 5
- Pages
- 887-900
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2081164083
- Cited by
- 400
- References
- 13
- FWCI
- 13.99
- Type
- journal article
- Language
- en
- Open access
- bronze
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