The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor Abundance
Open accessAbstract
SUMMARY LIN28 is a conserved RNA binding protein implicated in pluripotency, reprogramming and oncogenesis. Previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) targets. Through cross-linking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in human embryonic stem cells and somatic cells expressing exogenous LIN28, we have defined discrete LIN28 binding sites in a quarter of human transcripts. These sites revealed that LIN28 binds to GGAGA sequences enriched within loop structures in mRNAs, reminiscent of its interaction with let-7 miRNA precursors. Among LIN28 mRNA targets, we found evidence for LIN28 autoregulation and also direct but differing effects on the protein abundance of splicing regulators in somatic and pluripotent stem cells. Splicing-sensitive microarrays demonstrated that exogenous LIN28 expression causes widespread downstream alternative splicing changes. These findings identify important regulatory functions of LIN28 via direct mRNA interactions.
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Cites
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells
Yu, J., Vodyanik, M. A., Smuga-Otto, K., Antosiewicz-Bourget, J., Frane, J. L., Tian, S., Nie, J., Jonsdottir, G. A., Ruotti, V., Stewart, R., et al. (2007) · Science · doi:10.1126/science.1151526 · Cited by 10,310
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara, A., & Griffiths-Jones, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1027 · Cited by 3,634
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352 · cited 1×
“To generate a LIN28 protein-RNA interaction map, we used UV crosslinking and immunoprecipitation followed by highthroughput sequencing (CLIP-seq) (Licatalosi et al., 2008; Sanford et al., 2008; Yeo et al., 2009), which resulted in the discovery of LIN28-binding sites in over 6,000 gene targets.”
MethodLong pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43
Polymenidou, M., Lagier-Tourenne, C., Hutt, K. R., Huelga, S. C., Moran, J., Liang, T. Y., Ling, S.-C., Sun, E., Wancewicz, E., Mazur, C., et al. (2011) · Nature Neuroscience · doi:10.1038/nn.2779 · Cited by 1,335
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
Self-citationLin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells
Hagan, J. P., Piskounova, E., & Gregory, R. I. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1676 · Cited by 491
Xue, Y., Zhou, Y., Wu, T., Zhu, T., Ji, X., Kwon, Y.-S., Zhang, C., Yeo, G., Black, D. L., Sun, H., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.12.003 · Cited by 469
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Cited by
A census of human RNA-binding proteins
Gerstberger, S., Hafner, M., & Tuschl, T. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3813 · Cited by 2,032
Context-dependent control of alternative splicing by RNA-binding proteins
Fu, X.-D., & Ares, M. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3778 · Cited by 1,044
Landscape and variation of RNA secondary structure across the human transcriptome
Wan, Y., Qu, K., Zhang, Q. C., Flynn, R. A., Manor, O., Ouyang, Z., Zhang, J., Spitale, R. C., Snyder, M. P., Segal, E., et al. (2014) · Nature · doi:10.1038/nature12946 · Cited by 555
Lin28: Primal Regulator of Growth and Metabolism in Stem Cells
Shyh-Chang, N., & Daley, G. Q. (2013) · Cell Stem Cell · doi:10.1016/j.stem.2013.03.005 · Cited by 458
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges
Lovci, M. T., Ghanem, D., Marr, H., Arnold, J., Gee, S., Parra, M., Liang, T. Y., Stark, T. J., Gehman, L. T., Hoon, S., et al. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2699 · Cited by 385
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Metadata
- Authors
- Wilbert, M. L., Huelga, S. C., Kapeli, K., Stark, T. J., Liang, T. Y., Chen, S. X., Yan, B. Y., Nathanson, J. L., Hutt, K. R., Lovci, M. T., Kazan, H., Vu, A. Q., Massirer, K. B., Morris, Q., Hoon, S., & Yeo, G. W.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2012-10
- Volume
- 48
- Issue
- 2
- Pages
- 195-206
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2072470582
- Cited by
- 267
- References
- 9
- FWCI
- 9.76
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Wilbert, M. L., Huelga, S. C., Kapeli, K., Stark, T. J., Liang, T. Y., Chen, S. X., Yan, B. Y., Nathanson, J. L., Hutt, K. R., Lovci, M. T., Kazan, H., Vu, A. Q., Massirer, K. B., Morris, Q., Hoon, S., & Yeo, G. W. (2012). LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor Abundance. Molecular Cell. https://doi.org/10.1016/j.molcel.2012.08.004
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