Systematic discovery of structural elements governing stability of mammalian messenger RNAs

Nature

Volumn 485, Issue 7397, 2012, Pages 264-268

  Goodarzi, Hani ^a,e   Najafabadi, Hamed S ^b,c,e   Oikonomou, Panos ^a,e   Greco, Todd M ^a   Fish, Lisa ^d   Salavati, Reza ^b,c   Cristea, Ileana M ^b   Tavazoie, Saeed ^a,e  

^a PRINCETON UNIVERSITY   (United States)

^b MCGILL UNIVERSITY   (Canada)

^c MCGILL UNIVERSITY   (Canada)

^d ROCKEFELLER UNIVERSITY   (United States)

^e Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A2 B1; MESSENGER RNA; REGULATOR PROTEIN; UNCLASSIFIED DRUG; HNRNP A2; SMALL INTERFERING RNA;

BIOCHEMISTRY; COMPUTER SIMULATION; GENE EXPRESSION; HETEROGENEITY; MAMMAL; MASS SPECTROMETRY; NUMERICAL MODEL; PROTEIN; RNA; STABILIZATION;

COMPUTER MODEL; CONTROLLED STUDY; GENE INTERACTION; GENE TARGETING; GENOME ANALYSIS; IN VIVO STUDY; MAMMAL; MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; REVIEW; RING FINGER MOTIF; RNA STABILITY; RNA STRUCTURE; RNA TRANSCRIPTION; TRANSCRIPTION REGULATION; 3' UNTRANSLATED REGION; ALGORITHM; ANIMAL; ARTICLE; BREAST TUMOR; CHEMISTRY; CONFORMATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE SILENCING; GENETIC TRANSCRIPTION; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; METABOLISM; MOUSE; NUCLEOTIDE MOTIF; PHYSIOLOGY; TIME; TUMOR CELL LINE;

MAMMALIA;

3' UNTRANSLATED REGIONS; ALGORITHMS; ANIMALS; BREAST NEOPLASMS; CELL LINE, TUMOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE KNOCKDOWN TECHNIQUES; GENOME, HUMAN; GENOMICS; HETEROGENEOUS-NUCLEAR RIBONUCLEOPROTEIN GROUP A-B; HUMANS; MICE; NUCLEIC ACID CONFORMATION; NUCLEOTIDE MOTIFS; RNA STABILITY; RNA, MESSENGER; RNA, SMALL INTERFERING; TIME FACTORS; TRANSCRIPTION, GENETIC;

EID: 84860765680     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature11013     Document Type: Article

References (26)

1. Dolken, L. etal. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14, 1959-1972 (2008).
2. Elemento, O., Slonim, N. & Tavazoie, S. A universal framework for regulatory element discovery across all genomes and data types. Mol. Cell 28, 337-350 (2007).
3. Rabani, M., Kertesz, M. & Segal, E. Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc. Natl Acad. Sci. USA 105, 14885-14890 (2008).
4. Barash, Y. etal. Deciphering the splicing code. Nature 465, 53-59 (2010).
5. Wan, Y., Kertesz, M., Spitale, R. C., Segal, E. & Chang, H. Y. Understanding the transcriptome through RNA structure. Nature Rev. Genet 12, 641-655 (2011).
6. Pavesi, G., Mauri, G., Stefani, M. & Pesole, G. RNAProfile: an algorithm forfinding conserved secondary structure motifs in unaligned RNA sequences. Nucleic Acids Res. 32, 3258-3269 (2004).
7. Searls, D. B. The language of genes. Nature 420, 211-217 (2002).
8. Hofacker, I. L., Fekete, M. & Stadler, P. F. Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319, 1059-1066 (2002).
9. Kertesz, M. etal. Genome-wide measurement of RNA secondary structure in yeast. Nature 467, 103-107 (2010).
10. Goodarzi, H., Elemento, O. & Tavazoie, S. Revealing global regulatory perturbations across human cancers. Mol. Cell 36, 900-911 (2009).
11. Schwanhausser, B. etal. Global quantification of mammalian gene expression control. Nature 473, 337-342 (2011).
12. Cutroneo, K. R. & Ehrlich, H. Silencing or knocking out eukaryotic gene expression by oligodeoxynucleotide decoys. Crit Rev. Eukaryot. Gene Expr. 16, 23-30 (2006).
13. Windbichler, N. & Schroeder, R. Isolation of specific RNA-blndlng proteins using the streptomycin-binding RNA aptamer. Nature Protocols 1, 637-640 (2006).
14. Biamonti, G., Ruggiu, M., Saccone, S., Della Valle, G. & Riva, S. Two homologous genes, originated by duplication, encode the human hnRNP proteins A2 and A1. Nucleic Acids Res. 22, 1996-2002 (1994).
15. Wilusz, C.J., Wormington, M. & Peltz, S. W. The cap-to-tail guide to mRNA turnover. Nature Rev. Mol. Cell Biol. 2, 237-246 (2001).
16. Michlewski, G. & Caceres, J. F. Antagonistic role of hnRNP A1 and KSRP in the regulation of let-7a biogenesis. Nature Struct Mol. Biol. 17, 1011-1018 (2010).
17. Ross, D.T. etal. Systematic variation in gene expression patterns in human cancer cell lines. Nature Genet 24, 227-235 (2000).
18. Jensen, K. B. & Darnell, R. B. CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins. Methods Mol. Biol. 488, 85-98 (2008).
19. Keene, J. D., Komisarow, J. M. & Friedersdorf, M. B. RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nature Protocols 1, 302-307 (2006).
20. Licatalosi, D. D. etal. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456, 464-469 (2008).
21. Giannopoulou, E. G. & Elemento, O. An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics 12, 277-294 (2011).
22. Beer, M. A. & Tavazoie, S. Predicting gene expression from sequence. Cell 117, 185-198 (2004).
23. Yang, Y. etal. RNAsecondary structure in mutually exclusive splicing. Nature Struct Mol. Biol. 18, 159-168 (2011).
24. Greco, T. M., Yu, F., Guise, A. J. & Cristea, I. M. Nuclear import of histonedeacetylase 5 by requisite nuclear localization signal phosphorylation. Mol. CellProteomics 10, M110.004317 (2011).
25. Wisniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nature Methods 6, 359-362 (2009).
26. Chi, S. W., Zang, J. B., Mele, A. & Darnell, R. B. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460, 479-486 (2009).