Next Generation Sequencing-based analysis of RNA polymerase functions

Methods

Volumn 86, Issue , 2015, Pages 37-44

  Heyduk, Tomasz ^a   Heyduk, Ewa ^a  

^a SAINT LOUIS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Next Generation Sequencing; RNA polymerase; Sequence dependence; Transcription

Indexed keywords

BACTERIAL RNA; DNA; DOUBLE STRANDED DNA; MESSENGER RNA; NUCLEIC ACID; RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE;

BINDING AFFINITY; DNA SEQUENCE; DNA TEMPLATE; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; HUMAN; IN VITRO STUDY; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; RNA ANALYSIS; RNA SEQUENCE; RNA SYNTHESIS; BACTERIAL GENOME; CHEMISTRY; GENETIC TRANSCRIPTION; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; PROTEIN SYNTHESIS; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA; DNA-DIRECTED RNA POLYMERASES; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC; PROTEIN BIOSYNTHESIS; TRANSCRIPTION, GENETIC;

EID: 84941745399     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2015.04.030     Document Type: Review

References (38)

1. Voelkerding K.V., Dames S.A., Durtschi J.D. Clin. Chem. 2009, 55(4):641-658.
2. Niedringhaus T.P., et al. Anal. Chem. 2011, 83(12):4327-4341.
3. Metzker M.L. Nat. Rev. Genet. 2010, 11(1):31-46.
4. Meyer M., Kircher M. Cold Spring Harb. Protoc. 2010, 2010(6). pdb prot5448.
5. van Dijk E.L., et al. Trends Genet. 2014, 30(9):418-426.
6. Buermans H.P., den Dunnen J.T. Biochim. Biophys. Acta 2014, 1842(10):1932-1941.
7. Wang Z., Gerstein M., Snyder M. Nat. Rev. Genet. 2009, 10(1):57-63.
8. Barski A., et al. Cell 2007, 129(4):823-837.
9. Johnson D.S., et al. Science 2007, 316(5830):1497-1502.
10. Robertson G., et al. Nat. Methods 2007, 4(8):651-657.
11. Heyduk E., Heyduk T. Biochemistry 2014, 53(2):282-292.
12. RNA Polymerases as Molecular Motors 2009, Royal Society of Chemistry. H.B. Strick (Ed.).
13. Record M.T., R.W.S., Craig M.L., McQuade K.L., Schlax P.J. Escherichia coli and Salmonella: Cellular and Molecular Biology 1996, 792-820. ASM Press, Washington, DC. F.C. Neidhardt, R. Curtis III, J.L. Ingraham, E.C.C. Lin, K.R. Low, B. Magasanik, W.S. Reznikoff, M. Riley, M. Schaechter, H.E. Umbarger (Eds.).
14. Pribnow D. Proc. Natl. Acad. Sci. U.S.A. 1975, 72(3):784-788.
15. Shultzaberger R.K., et al. Nucleic Acids Res. 2007, 35(3):771-788.
16. Saecker R.M., Record M.T., Dehaseth P.L. J. Mol. Biol. 2011, 412(5):754-771.
17. Savinkova L.K., et al. Mol. Biol. (Mosk.) 1988, 22(3):807-812.
18. Marr M.T., Roberts J.W. Science 1997, 276(5316):1258-1260.
19. Roberts C.W., Roberts J.W. Cell 1996, 86(3):495-501.
20. Callaci S., Heyduk T. Biochemistry 1998, 37(10):3312-3320.
21. Ring B.Z., Yarnell W.S., Roberts J.W. Cell 1996, 86(3):485-493.
22. Matlock D.L., Heyduk T. Biochemistry 2000, 39(40):12274-12283.
23. Tsujikawa L., et al. Biochemistry 2002, 41(51):15334-15341.
24. Heyduk E., et al. J. Biol. Chem. 2006, 281(18):12362-12369.
25. Schroeder L.A., et al. J. Mol. Biol. 2009, 385(2):339-349.
26. Schroeder L.A. J. Mol. Biol. 2008, 376(1):153-165.
27. Feklistov A., Darst S.A. Cell 2011, 147(6):1257-1269.
28. Ko J., Heyduk T. Biochem. J. 2014, 463(1):135-144.
29. Chan C.L., Gross C.A. J. Biol. Chem. 2001, 276(41):38201-38209.
30. Hsu L.M., et al. Biochemistry 2003, 42(13):3777-3786.
31. Vo N.V., et al. Biochemistry 2003, 42(13):3798-3811.
32. Vo N.V., et al. Biochemistry 2003, 42(13):3787-3797.
33. Hsu L.M. Methods 2009, 47(1):25-36.
34. Aird D., et al. Genome Biol. 2011, 12(2):R18.
35. Friedl J. Mastering Regular Expressions 2002, O'Reilly.
36. Heyduk E., Heyduk T. Anal. Biochem. 2014, 464C:73-82.
37. Schneider T.D., Stephens R.M. Nucleic Acids Res. 1990, 18(20):6097-6100.
38. Crooks G.E., et al. Genome Res. 2004, 14(6):1188-1190.