Using RNase sequence specificity to refine the identification of RNA-protein binding regions

BMC Genomics

Volumn 9, Issue SUPPL. 1, 2008, Pages

  Wang, Xin ^a,b   Wang, Guohua ^a,c   Shen, Changyu ^a   Li, Lang ^a   Wang, Xinguo ^d   Mooney, Sean D ^a   Edenberg, Howard J ^a   Sanford, Jeremy R ^a   Liu, Yunlong ^a  

^a INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b HARBIN ENGINEERING UNIVERSITY   (China)

^c HARBIN INSTITUTE OF TECHNOLOGY   (China)

^d INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE DERIVATIVE; RIBONUCLEASE; DNA BINDING PROTEIN; RNA;

AMPLICON; ARTICLE; BINDING SITE; CONTROLLED STUDY; ENZYME ANALYSIS; ENZYME DEGRADATION; ENZYME SPECIFICITY; GENE MAPPING; GENOME ANALYSIS; PROTEIN LOCALIZATION; PROTEIN RNA BINDING; PYROSEQUENCING; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ANALYSIS; BIOLOGY; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; GENOMICS; IMMUNOPRECIPITATION; METABOLISM; METHODOLOGY; PROTEIN BINDING;

BINDING SITES; COMPUTATIONAL BIOLOGY; DNA-BINDING PROTEINS; GENOMICS; IMMUNOPRECIPITATION; PROTEIN BINDING; RIBONUCLEASES; RNA; SEQUENCE ANALYSIS, DNA; SUBSTRATE SPECIFICITY;

EID: 44449117557     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-S1-S17     Document Type: Article

References (13)

1. Sanford JR Caceres JF Pre-mRNA splicing: Life at the centre of the central dogma J Cell Sci 2004, 117:6261-3. 10.1242/jcs.01513 15591240
2. Sanchez-Diaz P Penalva LO Post-transcription meets post-genomic: The saga of RNA binding proteins in a new era RNA Biol 2006, 3:101-9. 17114948
3. Baralle D Baralle M Splicing in action: Assessing disease causing sequence changes J Med Genet 2005, 42:737-48. 10.1136/jmg.2004.029538 16199547
4. Cartegni L Krainer AR Correction of disease-associated exon skipping by synthetic exon-specific activators Nat Struct Biol 2003, 10:120-5. 10.1038/nsb887 12524529
5. Faustino NA Cooper TA Pre-mRNA splicing and human disease Genes Dev 2003, 17:419-37. 10.1101/gad.1048803 12600935
6. Valadkhan S snRNAs as the catalysts of pre-mRNA splicing Curr Opin Chem Biol 2005, 9:603-8. 10.1016/j.cbpa.2005.10.008 16242989
7. Ule J Jensen K Mele Aldo Darnell RB CLIP: A method for identifying protein-RNA interaction sites in living cells Methods 2005, 37:376-386. 10.1016/j.cell.2006.06.023 16839875
8. Ule J Jensen KB Ruggiu M Mele A Ule A Darnell RB CLIP identifies Nova-Regulated RNA Networks in the Brain Science 2003, 302:1212-1215. 10.1016/S0168-9525(00)02176-4 11173120
9. Goldberg SM Johnson J Busam D Feldblyum T Ferriera S Friedman R Halpern A Khouri H Kravitz SA Lauro FM Li K Rogers YH Strausberg R Sutton G Tallon L Thomas T Venter E Frazier M Venter JC A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes Proc Natl Acad Sci U S A 2006, 103:11240-5. 1544072 16840556 10.1073/pnas.0604351103
10. Margulies M Egholm M Altman WE Attiya S Bader JS Bemben LA Berka J Braverman MS Chen YJ Chen Z Dewell SB Du L Fierro JM Gomes XV Godwin BC He W Helgesen S Ho CH Irzyk GP Jando SC Alenquer ML Jarvie TP Jirage KB Kim JB Knight JR Lanza JR Leamon JH Lefkowitz SM Lei M Li J Lohman KL Lu H Makhijani VB McDade KE McKenna MP Myers EW Nickerson E Nobile JR Plant R Puc BP Ronan MT Roth GT Sarkis GJ Simons JF Simpson JW Srinivasan M Tartaro KR Tomasz A Vogt KA Volkmer GA Wang SH Wang Y Weiner MP Yu P Begley RF Rothberg JM Genome sequencing in microfabricated high-density picolitre reactors Nature 2005, 437:376-80. 1464427 16056220
11. Bainbridge MN Warren RL Hirst M Romanuik T Zeng T Go A Delaney A Griffith M Hickenbotham M Magrini V Mardis ER Sadar MD Siddiqui AS Marra MA Jones SJ Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach BMC Genomics 2006, 7:246. 1592491 17010196 10.1186/1471-2164-7-246
12. Tock MR Walsh AP Carroll G McDowall KJ The CafA protein required for the 5′-maturation of 16 S rRNA is a 5′-end-dependent ribonuclease that has context-dependent broad sequence specificity J Biol Chem 2000, 275:8726-32. 10.1074/jbc.275.12.8726 10722715
13. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215:403-10. 2231712