Transcriptome-scale RNase-footprinting of RNA-protein complexes

Nature Biotechnology

Volumn 34, Issue 4, 2016, Pages 410-413

  Ji, Zhe ^a,b   Song, Ruisheng ^a   Huang, Hailiang ^b,c   Regev, Aviv ^b,d,e   Struhl, Kevin ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MACROMOLECULES; PROTEINS; RNA;

BIOLOGICAL FUNCTIONS; FOOTPRINTING; HUMAN CELLS; MICRORNAS; NUCLEOLAR RNA; RNA-PROTEIN COMPLEXES; TRANSCRIPTOMES; UNTRANSLATED REGIONS;

NUCLEIC ACIDS;

DNA; LONG UNTRANSLATED RNA; MICRORNA; MULTIPROTEIN COMPLEX; RIBONUCLEASE; RNA; SMALL NUCLEOLAR RNA; TRANSCRIPTOME; TRANSFER RNA; RNA BINDING PROTEIN;

3' UNTRANSLATED REGION; ARTICLE; BIOLOGICAL FUNCTIONS; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CHROMOSOME 1; CHROMOSOME 12; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN RNA BINDING; RNA ANALYSIS; RNA METHYLATION; RNA SEQUENCE; RNA SPLICING; BIOLOGY; CHEMISTRY; GENETICS; HUMAN; METABOLISM; PROCEDURES; SEQUENCE ANALYSIS; TUMOR CELL LINE;

CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; HUMANS; RIBONUCLEASES; RNA; RNA-BINDING PROTEINS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84963542142     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3441     Document Type: Article

References (25)

1. Zhang, C. & Darnell, R. B. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotechnol. 29, 607-614 (2011)
2. Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129-141 (2010)
3. Baltz, A. G. et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell 46, 674-690 (2012)
4. Freeberg, M. A. et al. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biol. 14, R13 (2013)
5. Silverman, I. M. et al. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biol. 15, R3 (2014)
6. Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218-223 (2009)
7. Ji, Z., Song, R., Huang, H., Regev, A. & Struhl, K. Many lincRNAs are translated and some are likely to express functional proteins. eLife 08890, doi:10. 7554/eLife. 08890 (19 December 2015)
8. Hirsch, H. A. et al. A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases. Cancer Cell 17, 348-361 (2010)
9. Matera, A. G., Terns, R. M. & Terns, M. P. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat. Rev. Mol. Cell Biol. 8, 209-220 (2007)
10. Kiss-László, Z., Henry, Y. & Kiss, T. Sequence and structural elements of methylation guide snoRNAs essential for site-specific ribose methylation of pre-rRNA. EMBO J. 17, 797-807 (1998)
11. Will, C. L. & Lührmann, R. Spliceosome structure and function. Cold Spring Harb. Perspect. Biol. 3, a003707 (2011)
12. Russell, A. G., Charette, J. M., Spencer, D. F. & Gray, M. W. An early evolutionary origin for the minor spliceosome. Nature 443, 863-866 (2006)
13. Hendrickson, T. L. Recognizing the D-loop of transfer RNAs. Proc. Natl. Acad. Sci. USA 98, 13473-13475 (2001)
14. Peattie, D. A. & Herr, W. Chemical probing of the tRNA-ribosome complex. Proc. Natl. Acad. Sci. USA 78, 2273-2277 (1981)
15. Batista, P. J. & Chang, H. Y. Long noncoding RNAs: cellular address codes in development and disease. Cell 152, 1298-1307 (2013)
16. Rinn, J. L. & Chang, H. Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145-166 (2012)
17. Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005)
18. Eichhorn, S. W. et al. mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol. Cell 56, 104-115 (2014)
19. Diaz-Muñoz, M. D. et al. The RNA-binding protein HuR is essential for the B cell antibody response. Nat. Immunol. 16, 415-425 (2015)
20. Hahn, W. C. et al. Creation of human tumour cells with defined genetic elements. Nature 400, 464-468 (1999)
21. Iliopoulos, D., Hirsch, H. A. & Struhl, K. An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell 139, 693-706 (2009)
22. Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534-1550 (2012)
23. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009)
24. Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760-1774 (2012)
25. Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).