3S: Shotgun secondary structure determination of long non-coding RNAs

Methods

Volumn 63, Issue 2, 2013, Pages 170-177

  Novikova, Irina V ^a   Dharap, Ashutosh ^a   Hennelly, Scott P ^a   Sanbonmatsu, Karissa Y ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

LncRNA; LncRNA structure; Long non coding RNA; Long non coding RNA structure; Secondary structure; Steroid receptor RNA activator

Indexed keywords

LONG UNTRANSLATED RNA;

ARTICLE; PRIORITY JOURNAL; RNA ANALYSIS; RNA PROBE; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSCRIPTION;

LNCRNA; LNCRNA STRUCTURE; LONG NON-CODING RNA; LONG NON-CODING RNA STRUCTURE; SECONDARY STRUCTURE; STEROID RECEPTOR RNA ACTIVATOR;

BASE PAIRING; BASE SEQUENCE; DNA, COMPLEMENTARY; HUMANS; INVERTED REPEAT SEQUENCES; MOLECULAR SEQUENCE DATA; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, DOUBLE-STRANDED; RNA, LONG NONCODING;

EID: 84885127971     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.07.030     Document Type: Article

References (56)

1. Rinn J.L., Chang H.Y. Annual Review of Biochemistry 2012, 81:145-166.
2. Klattenhoff C.A., Scheuermann J.C., Surface L.E., Bradley R.K., Fields P.A., Steinhauser M.L., Ding H., Butty V.L., Torrey L., Haas S., Abo R., Tabebordbar M., Lee R.T., Burge C.B., Boyer L.A. Cell 2013, 152:570-583.
3. Swiezewski S., Liu F., Magusin A., Dean C. Nature 2009, 462:799-802.
4. Sun Q., Csorba T., Skourti-Stathaki K., Proudfoot N.J., Dean C. Science 2013, 340:619-621.
5. Dinger M.E., Amaral P.P., Mercer T.R., Pang K.C., Bruce S.J., Gardiner B.B., Askarian-Amiri M.E., Ru K., Solda G., Simons C., Sunkin S.M., Crowe M.L., Grimmond S.M., Perkins A.C., Mattick J.S. Genome Research 2008, 18:1433-1445.
6. Sone M., Hayashi T., Tarui H., Agata K., Takeichi M., Nakagawa S. Journal of Cell Science 2007, 120:2498-2506.
7. Mercer T.R., Dinger M.E., Sunkin S.M., Mehler M.F., Mattick J.S. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:716-721.
8. Bernard D., Prasanth K.V., Tripathi V., Colasse S., Nakamura T., Xuan Z., Zhang M.Q., Sedel F., Jourdren L., Coulpier F., Triller A., Spector D.L., Bessis A. The EMBO Journal 2010, 29:3082-3093.
9. Wilusz J.E., Freier S.M., Spector D.L. Cell 2008, 135:919-932.
10. Clemson C.M., Hutchinson J.N., Sara S.A., Ensminger A.W., Fox A.H., Chess A., Lawrence J.B. Molecular Cell 2009, 33:717-726.
11. Ietswaart R., Wu Z., Dean C. Trends in Genetics: TIG 2012, 28:445-453.
12. Cabianca D.S., Casa V., Bodega B., Xynos A., Ginelli E., Tanaka Y., Gabellini D. Cell 2012, 149:819-831.
13. Gupta R.A., Shah N., Wang K.C., Kim J., Horlings H.M., Wong D.J., Tsai M.C., Hung T., Argani P., Rinn J.L., Wang Y., Brzoska P., Kong B., Li R., West R.B., van de Vijver M.J., Sukumar S., Chang H.Y. Nature 2010, 464:1071-1076.
14. Tsai M.C., Spitale R.C., Chang H.Y. Cancer Research 2011, 71:3-7.
15. Gutschner T., Hammerle M., Eissmann M., Hsu J., Kim Y., Hung G., Revenko A.S., Arun G., Stentrup M., Gross M., Zornig M., Macleod A.R., Spector D.L., Diederichs S. Cancer Research 2012.
16. Banfai B., Jia H., Khatun J., Wood E., Risk B., Gundling W.E., Kundaje A., Gunawardena H.P., Yu Y., Xie L., Krajewski K., Strahl B.D., Chen X., Bickel P., Giddings M.C., Brown J.B., Lipovich L. Genome Research 2012, 22:1646-1657.
17. Korostowski L., Raval A., Breuer G., Engel N. Epigenetics & Chromatin 2011, 4:21.
18. Sleutels F., Zwart R., Barlow D.P. Nature 2002, 415:810-813.
19. Pandey R.R., Mondal T., Mohammad F., Enroth S., Redrup L., Komorowski J., Nagano T., Mancini-Dinardo D., Kanduri C. Molecular Cell 2008, 32:232-246.
20. Derrien T., Johnson R., Bussotti G., Tanzer A., Djebali S., Tilgner H., Guernec G., Martin D., Merkel A., Knowles D.G., Lagarde J., Veeravalli L., Ruan X., Ruan Y., Lassmann T., Carninci P., Brown J.B., Lipovich L., Gonzalez J.M., Thomas M., Davis C.A., Shiekhattar R., Gingeras T.R., Hubbard T.J., Notredame C., Harrow J., Guigo R. Genome Research 2012, 22:1775-1789.
21. Novikova I.V., Hennelly S.P., Sanbonmatsu K.Y. Nucleic Acids Research 2012, 40:5034-5051.
22. Montange R.K., Batey R.T. Annual Review of Biophysics 2008, 37:117-133.
23. Winkler W., Nahvi A., Breaker R.R. Nature 2002, 419:952-956.
24. Tucker B.J., Breaker R.R. Current Opinion in Structural Biology 2005, 15:342-348.
25. Hennelly S.P., Sanbonmatsu K.Y. Nucleic Acids Research 2011, 39:2416-2431.
26. Stoddard C.D., Montange R.K., Hennelly S.P., Rambo R.P., Sanbonmatsu K.Y., Batey R.T. Structure 2010, 18:787-797.
27. Hayes R.L., Noel J.K., Mohanty U., Whitford P.C., Hennelly S.P., Onuchic J.N., Sanbonmatsu K.Y. Journal of the American Chemical Society 2012, 134:12043-12053.
28. Kino T., Hurt D.E., Ichijo T., Nader N., Chrousos G.P. Science signaling 2010, 3:ra8.
29. Batey R.T., Gilbert S.D., Montange R.K. Nature 2004, 432:411-415.
30. Montange R.K., Batey R.T. Nature 2006, 441:1172-1175.
31. Garst A.D., Heroux A., Rambo R.P., Batey R.T. Journal of Biological Chemistry 2008, 283:22347-22351.
32. Gilbert S.D., Rambo R.P., Van Tyne D., Batey R.T. Nature Structural and Molecular Biology 2008, 15:177-182.
33. Deigan K.E., Li T.W., Mathews D.H., Weeks K.M. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:97-102.
34. Hamada M., Sato K., Asai K. BMC Bioinformatics 2010, 11:586.
35. Hamada M., Sato K., Asai K. Nucleic Acids Research 2011, 39:393-402.
36. Rivas E., Lang R., Eddy S.R. RNA 2012, 18:193-212.
37. Bernhart S.H., Hofacker I.L., Will S., Gruber A.R., Stadler P.F. BMC Bioinformatics 2008, 9:474.
38. Turner D.H. Current Opinion in Structural Biology 1996, 6:299-304.
39. Kim J., Walter A.E., Turner D.H. Biochemistry 1996, 35:13753-13761.
40. Wu M., McDowell J.A., Turner D.H. Biochemistry 1995, 34:3204-3211.
41. Rivas E., Eddy S.R. Bioinformatics 2000, 16:583-605.
42. Wilkinson K.A., Gorelick R.J., Vasa S.M., Guex N., Rein A., Mathews D.H., Giddings M.C., Weeks K.M. PLoS Biology 2008, 6:e96.
43. Reuter J.S., Mathews D.H. BMC Bioinformatics 2010, 11:129.
44. Lucks J.B., Mortimer S.A., Trapnell C., Luo S., Aviran S., Schroth G.P., Pachter L., Doudna J.A., Arkin A.P. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:11063-11068.
45. Wan Y., Qu K., Ouyang Z., Kertesz M., Li J., Tibshirani R., Makino D.L., Nutter R.C., Segal E., Chang H.Y. Molecular Cell 2012, 48:169-181.
46. Ouyang Z., Snyder M.P., Chang H.Y. Genome Research 2013, 23:377-387.
47. Wan Y., Qu K., Ouyang Z., Chang H.Y. Natural Protocol 2013, 8:849-869.
48. Bernstein B.E., Birney E., Dunham I., Green E.D., Gunter C., Snyder M. Nature 2012, 489:57-74.
49. Hofacker I.L. Methods in Molecular Biology 2007, 395:527-544.
50. Vasa S.M., Guex N., Wilkinson K.A., Weeks K.M., Giddings M.C. RNA 2008, 14:1979-1990.
51. Karabiber F., McGinnis J.L., Favorov O.V., Weeks K.M. RNA 2013, 19:63-73.
52. Mercer T.R., Mattick J.S. Nature Structural and Molecular Biology 2013, 20:300-307.
53. Guttman M., Rinn J.L. Nature 2012, 482:339-346.
54. Kamalampeta R., Kothe U. Science Reports 2012, 2:663.
55. Jacobs E., Mills J.D., Janitz M. Journal of Genetics Genomics 2012, 39:535-543.
56. Griffiths-Jones S., Bateman A., Marshall M., Khanna A., Eddy S.R. Nucleic Acids Research 2003, 31:439-441.