FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing (original) (raw)
References
Gesteland, R., Cech, T. & Atkins, J. (eds). The RNA World 3rd edn. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2005).
Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature457, 1028–1032 (2009).
Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature458, 223–227 (2009). ArticleCAS Google Scholar
Ambros, V. microRNAs: tiny regulators with great potential. Cell107, 823–826 (2001). ArticleCAS Google Scholar
Kapranov, P. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science316, 1484–1488 (2007). ArticleCAS Google Scholar
Knapp, G. Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol.2, 192–212 (1989). Article Google Scholar
Machado-Lima, A., del Portillo, H.A. & Durham, A.M. Computational methods in noncoding RNA research. J. Math. Biol.56, 15–49 (2008). Article Google Scholar
Crawford, G.E. et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res.16, 123–131 (2006). ArticleCAS Google Scholar
Ying, Q.-L., Stavridis, M., Griffiths, D., Li, M. & Smith, A. Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture. Nat. Biotechnol.21, 183–186 (2003). ArticleCAS Google Scholar
Desai, N.A. & Shankar, V. Single-strand-specific nucleases. FEMS Microbiol. Rev.26, 457–491 (2003). ArticleCAS Google Scholar
Cameron, V. & Uhlenbeck, O.C. 3′-phosphatase activity in T4 polynucleotide kinase. Biochemistry16, 5120–5126 (1977). ArticleCAS Google Scholar
Romier, C., Dominguez, R., Lahm, A., Dahl, O. & Suck, D. Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs. Proteins32, 414–424 (1998). ArticleCAS Google Scholar
Naik, A.K. & Raghavan, S.C. P1 nuclease cleavage is dependent on length of the mismatches in DNA. DNA Repair (Amst.)7, 1384–1391 (2008). ArticleCAS Google Scholar
Parker, K.A. & Steitz, J.A. Structural analyses of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA. Mol. Cell. Biol.7, 2899–2913 (1987). ArticleCAS Google Scholar
Mougin, A., Gottschalk, A., Fabrizio, P., Lührmann, R. & Branlant, C. Direct probing of RNA structure and RNA-protein interactions in purified HeLa cell's and yeast spliceosomal U4/U6.U5 tri-snRNP particles. J. Mol. Biol.317, 631–649 (2002). ArticleCAS Google Scholar
Granneman, S. et al. Role of pre-rRNA base pairing and 80S complex formation in subnucleolar localization of the U3 snoRNP. Mol. Cell. Biol.24, 8600–8610 (2004). ArticleCAS Google Scholar
Kass, S., Tyc, K., Steitz, J.A. & Sollner-Webb, B. The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell60, 897–908 (1990). ArticleCAS Google Scholar
Peculis, B.A. & Steitz, J.A. Disruption of U8 nucleolar snRNA inhibits 5.8S and 28S rRNA processing in the Xenopus oocyte. Cell73, 1233–1245 (1993). ArticleCAS Google Scholar
Tycowski, K., Shu, M. & Steitz, J. Requirement for intron-encoded U22 small nucleolar RNA in 18S ribosomal RNA maturation. Science266, 1558–1561 (1994). ArticleCAS Google Scholar
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet.10, 57–63 (2009). ArticleCAS Google Scholar
Kertesz, M. et al. Genome-wide measurement of RNA secondary structure in yeast. Nature467, 103–107 (2010). ArticleCAS Google Scholar
Reuter, J.S. & Mathews, D.H. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics11, 129 (2010). Article Google Scholar
Mandal, M. & Breaker, R.R. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol.5, 451–463 (2004). ArticleCAS Google Scholar
Maroney, P., Romfo, C. & Nilsen, T. Nuclease protection of RNAs containing site-specific labels: a rapid method for mapping RNA-protein interactions. RNA6, 1905–1909 (2000). ArticleCAS Google Scholar
Kiss-László, Z., Henry, Y., Bachellerie, J.P., Caizergues-Ferrer, M. & Kiss, T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell85, 1077–1088 (1996). Article Google Scholar
Beard, C., Hochedlinger, K., Plath, K., Wutz, A. & Jaenisch, R. Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis44, 23–28 (2006). ArticleCAS Google Scholar
Skarnes, W.C. Gene trapping methods for the identification and functional analysis of cell surface proteins in mice. Methods Enzymol.328, 592–615 (2000). ArticleCAS Google Scholar
Sobczak, K., Michlewski, G., de Mezer, M., Krol, J. & Krzyzosiak, W.J. Trinucleotide repeat system for sequence specificity analysis of RNA structure probing reagents. Anal. Biochem.402, 40–46 (2010). ArticleCAS Google Scholar
Mortazavi, A., Williams, B.A., Mccue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods5, 621–628 (2008). ArticleCAS Google Scholar