The DOI matches its Crossref record; 79 of the 79 references it cites were found in a registry or an index.
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
Open accessAbstract
Metazoan genes are encrypted with at least two superimposed codes: the genetic code to specify the primary structure of proteins and the splicing code to expand their proteomic output via alternative splicing. Here, we define the specificity of a central regulator of pre-mRNA splicing, the conserved, essential splicing factor SFRS1. Cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq) identified 23,632 binding sites for SFRS1 in the transcriptome of cultured human embryonic kidney cells. SFRS1 was found to engage many different classes of functionally distinct transcripts including mRNA, miRNA, snoRNAs, ncRNAs, and conserved intergenic transcripts of unknown function. The majority of these diverse transcripts share a purine-rich consensus motif corresponding to the canonical SFRS1 binding site. The consensus site was not only enriched in exons cross-linked to SFRS1 in vivo, but was also enriched in close proximity to splice sites. mRNAs encoding RNA processing factors were significantly overrepresented, suggesting that SFRS1 may broadly influence the post-transcriptional control of gene expression in vivo. Finally, a search for the SFRS1 consensus motif within the Human Gene Mutation Database identified 181 mutations in 82 different genes that disrupt predicted SFRS1 binding sites. This comprehensive analysis substantially expands the known roles of human SR proteins in the regulation of a diverse array of RNA transcripts.
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Tuerk, C., & Gold, L. (1990) · Science · doi:10.1126/science.2200121 · Cited by 10,405
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
ROCR: visualizing classifier performance in R
Sing, T., Sander, O., Beerenwinkel, N., & Lengauer, T. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti623 · Cited by 3,200
MEME: discovering and analyzing DNA and protein sequence motifs
Bailey, T. L., Williams, N., Misleh, C., & Li, W. W. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl198 · Cited by 2,670
Identifying biological themes within lists of genes with EASE
Hosack, D. A., Dennis, G., Sherman, B. T., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-10-r70 · Cited by 1,950
The UCSC Genome Browser Database
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg129 · Cited by 1,887
Human Gene Mutation Database (HGMD®): 2003 update: HGMD 2003 UPDATE
Stenson, P. D., Ball, E. V., Mort, M., Phillips, A. D., Shiel, J. A., Thomas, N. S. T., Abeysinghe, S., Krawczak, M., & Cooper, D. N. (2003) · Human Mutation · doi:10.1002/humu.10212 · Cited by 1,829
Self-citationUltraconserved Elements in the Human Genome
Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., & Haussler, D. (2004) · Science · doi:10.1126/science.1098119 · Cited by 1,732
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Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M., Jungkamp, A.-C., Munschauer, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.03.009 · Cited by 2,873
Ten years of next-generation sequencing technology
van Dijk, E. L., Auger, H., Jaszczyszyn, Y., & Thermes, C. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.07.001 · Cited by 1,622
Function of alternative splicing
Stamm, S., Ben-Ari, S., Rafalska, I., Tang, Y., Zhang, Z., Toiber, D., Thanaraj, T. A., & Soreq, H. (2005) · Gene · doi:10.1016/j.gene.2004.10.022 · Cited by 1,377
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
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Metadata
- Authors
- Sanford, J. R., Wang, X., Mort, M., VanDuyn, N., Cooper, D. N., Mooney, S. D., Edenberg, H. J., & Liu, Y.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-12-30
- Volume
- 19
- Issue
- 3
- Pages
- 381-394
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2106309105
- Cited by
- 313
- References
- 79
- Type
- posted content
- Language
- en
- Open access
- bronze
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