DGCR8 HITS-CLIP reveals novel functions for the Microprocessor (original) (raw)
References
Bartel, D.P. MicroRNAs: target recognition and regulatory functions. Cell136, 215–233 (2009). ArticleCAS Google Scholar
Han, J. et al. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev.18, 3016–3027 (2004). ArticleCAS Google Scholar
Zeng, Y., Yi, R. & Cullen, B.R. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J.24, 138–148 (2005). ArticleCAS Google Scholar
Morlando, M. et al. Primary microRNA transcripts are processed co-transcriptionally. Nat. Struct. Mol. Biol.15, 902–909 (2008). ArticleCAS Google Scholar
Pawlicki, J.M. & Steitz, J.A. Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production. J. Cell Biol.182, 61–76 (2008). ArticleCAS Google Scholar
Yi, R., Qin, Y., Macara, I.G. & Cullen, B.R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev.17, 3011–3016 (2003). ArticleCAS Google Scholar
Lund, E., Guttinger, S., Calado, A., Dahlberg, J.E. & Kutay, U. Nuclear export of microRNA precursors. Science303, 95–98 (2004). ArticleCAS Google Scholar
Bohnsack, M.T., Czaplinski, K. & Gorlich, D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA10, 185–191 (2004). ArticleCAS Google Scholar
Bernstein, E., Caudy, A.A., Hammond, S.M. & Hannon, G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature409, 363–366 (2001). ArticleCAS Google Scholar
Hutvagner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science293, 834–838 (2001). ArticleCAS Google Scholar
Shiohama, A., Sasaki, T., Noda, S., Minoshima, S. & Shimizu, N. Molecular cloning and expression analysis of a novel gene DGCR8 located in the DiGeorge syndrome chromosomal region. Biochem. Biophys. Res. Commun.304, 184–190 (2003). ArticleCAS Google Scholar
Landthaler, M., Yalcin, A. & Tuschl, T. The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol.14, 2162–2167 (2004). ArticleCAS Google Scholar
Denli, A.M., Tops, B.B., Plasterk, R.H., Ketting, R.F. & Hannon, G.J. Processing of primary microRNAs by the Microprocessor complex. Nature432, 231–235 (2004). ArticleCAS Google Scholar
Gregory, R.I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature432, 235–240 (2004). ArticleCAS Google Scholar
Davis, B.N. & Hata, A. Regulation of microRNA biogenesis: a miRiad of mechanisms. Cell Commun. Signal.7, 18 (2009). Article Google Scholar
Winter, J., Jung, S., Keller, S., Gregory, R.I. & Diederichs, S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat. Cell Biol.11, 228–234 (2009). ArticleCAS Google Scholar
Krol, J., Loedige, I. & Filipowicz, W. The widespread regulation of microRNA biogenesis, function and decay. Nat. Rev. Genet.11, 597–610 (2010). ArticleCAS Google Scholar
Han, J. et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell125, 887–901 (2006). ArticleCAS Google Scholar
Faller, M., Matsunaga, M., Yin, S., Loo, J.A. & Guo, F. Heme is involved in microRNA processing. Nat. Struct. Mol. Biol.14, 23–29 (2007). ArticleCAS Google Scholar
Faller, M. et al. DGCR8 recognizes primary transcripts of microRNAs through highly cooperative binding and formation of higher-order structures. RNA16, 1570–1583 (2010). ArticleCAS Google Scholar
Licatalosi, D.D. et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature456, 464–469 (2008). ArticleCAS Google Scholar
Sanford, J.R. et al. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res.19, 381–394 (2009). ArticleCAS Google Scholar
Zisoulis, D.G. et al. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat. Struct. Mol. Biol.17, 173–179 (2010). ArticleCAS Google Scholar
Konig, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol.17, 909–915 (2010). Article Google Scholar
Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell141, 129–141 (2010). ArticleCAS Google Scholar
Han, J. et al. Posttranscriptional crossregulation between Drosha and DGCR8. Cell136, 75–84 (2009). ArticleCAS Google Scholar
Kadener, S. et al. Genome-wide identification of targets of the drosha-pasha/DGCR8 complex. RNA15, 537–545 (2009). ArticleCAS Google Scholar
Triboulet, R., Chang, H.M., LaPierre, R.J. & Gregory, R.I. Post-transcriptional control of DGCR8 expression by the Microprocessor. RNA15, 1005–1011 (2009). ArticleCAS Google Scholar
Ule, J., Jensen, K., Mele, A. & Darnell, R.B. CLIP: A method for identifying protein-RNA interaction sites in living cells. Methods37, 376–386 (2005). ArticleCAS Google Scholar
Licatalosi, D.D. & Darnell, R.B. RNA processing and its regulation: global insights into biological networks. Nat. Rev. Genet.11, 75–87 (2010). ArticleCAS Google Scholar
Karginov, F.V. et al. Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol. Cell38, 781–788 (2010). ArticleCAS Google Scholar
Ji, P. et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene22, 8031–8041 (2003). Article Google Scholar
Tollervey, D. & Kiss, T. Function and synthesis of small nucleolar RNAs. Curr. Opin. Cell Biol.9, 337–342 (1997). ArticleCAS Google Scholar
Kiss, T. SnoRNP biogenesis meets pre-mRNA splicing. Mol. Cell23, 775–776 (2006). ArticleCAS Google Scholar
Taft, R.J. et al. Small RNAs derived from snoRNAs. RNA15, 1233–1240 (2009). ArticleCAS Google Scholar
Ender, C. et al. A human snoRNA with microRNA-like functions. Mol. Cell32, 519–528 (2008). ArticleCAS Google Scholar
Bernstein, E. et al. Dicer is essential for mouse development. Nat. Genet.35, 215–217 (2003). ArticleCAS Google Scholar
Wang, Y., Medvid, R., Melton, C., Jaenisch, R. & Blelloch, R. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat. Genet.39, 380–385 (2007). ArticleCAS Google Scholar
Shenoy, A. & Blelloch, R. Genomic analysis suggests that mRNA destabilization by the microprocessor is specialized for the auto-regulation of Dgcr8. PLoS ONE4, e6971 (2009). Article Google Scholar
Chong, M.M. et al. Canonical and alternate functions of the microRNA biogenesis machinery. Genes Dev.24, 1951–1960 (2010). ArticleCAS Google Scholar
Lin, Y.T. & Sullivan, C.S. Expanding the role of Drosha to the regulation of viral gene expression. Proc. Natl. Acad. Sci. USA108, 11229–11234 (2011). ArticleCAS Google Scholar
Wu, H., Xu, H., Miraaglia, L.J. & Crooke, S.T. Human RNase III is a 160-kDa protein involved in preribosomal RNA processing. J. Biol. Chem.275, 36957–36965 (2000). ArticleCAS Google Scholar
Liang, T.J. & Qin, C.Y. The emerging role of microRNAs in immune cell development and differentiation. APMIS117, 635–643 (2009). ArticleCAS Google Scholar
Scott, M.S., Avolio, F., Ono, M., Lamond, A.I. & Barton, G.J. Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput. Biol.5, e1000507 (2009). Article Google Scholar
Shiohama, A., Sasaki, T., Noda, S., Minoshima, S. & Shimizu, N. Nucleolar localization of DGCR8 and identification of eleven DGCR8-associated proteins. Exp. Cell Res.313, 4196–4207 (2007). ArticleCAS Google Scholar
Stark, K.L. et al. Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model. Nat. Genet.40, 751–760 (2008). ArticleCAS Google Scholar
Fenelon, K. et al. Deficiency of Dgcr8, a gene disrupted by the 22q11.2 microdeletion, results in altered short-term plasticity in the prefrontal cortex. Proc. Natl. Acad. Sci. USA108, 4447–4452 (2011). ArticleCAS Google Scholar
Michlewski, G. & Caceres, J.F. Antagonistic role of hnRNP A1 and KSRP in the regulation of let-7a biogenesis. Nat. Struct. Mol. Biol.17, 1011–1018 (2010). ArticleCAS Google Scholar
Caceres, J.F., Misteli, T., Screaton, G.R., Spector, D.L. & Krainer, A.R. Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity. J. Cell Biol.138, 225–238 (1997). ArticleCAS Google Scholar
Guil, S. & Caceres, J.F. The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat. Struct. Mol. Biol.14, 591–596 (2007). ArticleCAS Google Scholar
Flicek, P. et al. Ensembl's 10th year. Nucleic Acids Res.38, D557–D562 (2010). ArticleCAS Google Scholar
Slater, G.S. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics6, 31 (2005). Article Google Scholar
Fujita, P.A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res.39, D876–D882 (2011). ArticleCAS Google Scholar