Landscape and variation of RNA secondary structure across the human transcriptome

Nature

Volumn 505, Issue 7485, 2014, Pages 706-709

  Wan, Yue ^a,b   Qu, Kun ^a   Zhang, Qiangfeng Cliff ^a   Flynn, Ryan A ^a   Manor, Ohad ^c   Ouyang, Zhengqing ^a,d   Zhang, Jiajing ^a   Spitale, Robert C ^a   Snyder, Michael P ^a   Segal, Eran ^c   Chang, Howard Y ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^d JACKSON LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84893358533     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature12946     Document Type: Article

References (26)

1. 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).
2. Kertesz, M. et al. Genome-widemeasurement ofRNA secondary structure in yeast. Nature 467, 103-107 (2010).
3. Li, F. et al. Global analysis of RNA secondary structure in two metazoans. Cell. Rep. 1, 69-82 (2012).
4. Shabalina, S. A., Ogurtsov, A. Y. & Spiridonov, N. A. A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res. 34, 2428-2437 (2006).
5. Barash, Y. et al. Deciphering the splicing code. Nature 465, 53-59 (2010).
6. Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233 (2009).
7. Skalsky, R. L. et al. The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathog. 8, e1002484 (2012).
8. Maŕn, R. M., Voellmy, F., von Erlach, T. & Vanicek, J. Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 39-end of the seed match. RNA 18, 1760-1770 (2012).
9. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91-105 (2007).
10. Ritz, J., Martin, J. S. & Laederach, A. Evaluating our ability to predict the structural disruption of RNA by SNPs. BMC Genomics 13, (Suppl. 4) S6, (2012).
11. Halvorsen, M., Martin, J. S., Broadaway, S. & Laederach, A. Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet. 6, e1001074 (2010).
12. Ouyang, Z., Snyder, M. P. & Chang, H. Y. SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Res. 377-387 (2013).
13. Salari, R., Kimchi-Sarfaty, C., Gottesman, M. M. & Przytycka, T. M. Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies.Nucleic Acids Res. 41, 44-53 (2013).
14. Katz, Y., Wang, E. T., Airoldi, E. M. & Burge, C. B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods 7, 1009-1015 (2010).
15. Barbosa-Morais, N. L. et al. The evolutionary landscape of alternative splicing in vertebrate species. Science 338, 1587-1593 (2012).
16. Spitale, R. C. et al. RNA SHAPE analysis in living cells. Nature Chem. Biol. 9, 18-20 (2013).
17. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357-359 (2012).
18. Wilkinson, K. A., Merino, E. J. & Weeks, K. M. Selective 29-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nature Protocols 1, 1610-1616 (2006).
19. Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of humangenes are microRNA targets. Cell 120, 15-20 (2005).
20. Chi, S. W., Zang, J. B., Mele, A. & Darnell, R. B. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460, 479-486 (2009).
21. König, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nature Struct. Mol. Biol. 17, 909-915 (2010).
22. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNAsequences to the humangenome. Genome Biol. 10, R25 (2009).
23. International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003).
24. Anders, G. et al. doRiNA: a database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res. 40, D180-D186 (2012).
25. Wilbert, M. L. et al. LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Mol. Cell 48, 195-206 (2012).
26. Macias, S. et al.DGCR8HITS-CLIPreveals novel functions for the Microprocessor. Nature Struct. Mol. Biol. 19, 760-766 (2012).