High throughput characterizations of poly(A) site choice in plants

Methods

Volumn 67, Issue 1, 2014, Pages 74-83

  Ma, Liuyin ^a   Pati, Pratap Kumar ^b,c   Liu, Man ^d   Li, Qingshun Q ^d,e   Hunt, Arthur G ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

^b UNIVERSITY OF KENTUCKY   (United States)

^c GURU NANAK DEV UNIVERSITY   (India)

^d MIAMI UNIVERSITY   (United States)

^e XIAMEN UNIVERSITY   (China)

Author keywords

Alternative polyadenylation; Gene expression; High throughput sequencing

Indexed keywords

MESSENGER RNA; POLYADENYLIC ACID; ARABIDOPSIS PROTEIN; COMPLEMENTARY DNA; PLANT RNA;

3' UNTRANSLATED REGION; ARTICLE; DNA SEQUENCE; EUKARYOTE; GENE EXPRESSION REGULATION; NONHUMAN; PLANT GENETICS; POLYADENYLATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REPRODUCIBILITY; TECHNOLOGY; ARABIDOPSIS; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; METABOLISM; NUCLEOTIDE SEQUENCE; PLANT LEAF; PLANT SEED;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PLANT LEAVES; POLYADENYLATION; POLYMERASE CHAIN REACTION; RNA, MESSENGER; RNA, PLANT; SEEDS;

EID: 84899472795     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.06.037     Document Type: Article

References (38)

1. Sun Y., Fu Y., Li Y., Xu A. J. Mol. Cell Biol. 2012, 4(6):352-361.
2. Mueller A.A., Cheung T.H., Rando T.A. Curr. Opin. Cell Biol. 2013, 25(2):222-232.
3. Shi Y. RNA 2012, 18(12):2105-2117.
4. Lee J.Y., Yeh I., Park J.Y., Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. 2007, 35:D165-D168.
5. Loke J.C., Stahlberg E.A., Strenski D.G., Haas B.J., Wood P.C., Li Q.Q. Plant Physiol. 2005, 138(3):1457-1468.
6. Shen Y., Ji G., Haas B.J., Wu X., Zheng J., Reese G.J., Li Q.Q. Nucleic Acids Res. 2008, 36(9):3150-3161.
7. Shen Y., Venu R.C., Nobuta K., Wu X., Notibala V., Demirci C., Meyers B.C., Wang G.L., Ji G., Li Q.Q. Genome Res. 2011, 21(9):1478-1486.
8. Wu X., Liu M., Downie B., Liang C., Ji G., Li Q.Q., Hunt A.G. Proc. Natl. Acad. Sci. USA 2011, 108(30):12533-12538.
9. Lin Y., Li Z., Ozsolak F., Kim S.W., Arango-Argoty G., Liu T.T., Tenenbaum S.A., Bailey T., Monaghan A.P., Milos P.M., et al. Nucleic Acids Res. 2012, 40(17):8460-8471.
10. Mayr C., Bartel D.P. Cell 2009, 138(4):673-684.
11. Li Y., Sun Y., Fu Y., Li M., Huang G., Zhang C., Liang J., Huang S., Shen G., Yuan S., et al. Genome Res. 2012, 22(10):1899-1906.
12. Smibert P., Miura P., Westholm J.O., Shenker S., May G., Duff M.O., Zhang D., Eads B.D., Carlson J., Brown J.B., et al. Cell Rep. 2012, 1(3):277-289.
13. Miura P., Shenker S., Andreu-Agullo C., Westholm J.O., Lai E.C. Widespread and extensive lengthening of 3' UTRs in the mammalian brain. Genome Res 2013.
14. Jan C.H., Friedman R.C., Ruby J.G., Bartel D.P. Nature 2011, 469(7328):97-101.
15. Shepard P.J., Choi E.A., Lu J., Flanagan L.A., Hertel K.J., Shi Y. RNA 2011, 17(4):761-772.
16. Yoon O.K., Hsu T.Y., Im J.H., Brem R.B. PLoS Genet. 2012, 8(8):e1002882.
17. Hornyik C., Duc C., Rataj K., Terzi L.C., Simpson G.G. Biochem. Soc. Trans. 2010, 38(4):1077-1081.
18. Hornyik C., Terzi L.C., Simpson G.G. Dev. Cell 2010, 18(2):203-213.
19. Liu F., Marquardt S., Lister C., Swiezewski S., Dean C. Science 2010, 327(5961):94-97.
20. Simpson G.G., Dijkwel P.P., Quesada V., Henderson I., Dean C. Cell 2003, 113(6):777-787.
21. Terzi L.C., Simpson G.G. Curr. Top. Microbiol. Immunol. 2008, 326:201-218.
22. Thomas P.E., Wu X., Liu M., Gaffney B., Ji G., Li Q.Q., Hunt A.G. Plant Cell 2012, 24(11):4376-4388.
23. Zhang J., Addepalli B., Yun K.Y., Hunt A.G., Xu R., Rao S., Li Q.Q., Falcone D.L. PloS one 2008, 3(6):e2410.
24. Hunt A.G., Xing D., Li Q.Q. BMC Genomics 2012, 13:641.
25. Addepalli B., Meeks L.R., Forbes K.P., Hunt A.G. Biochim. Biophys. Acta 2004, 1679(2):117-128.
26. Addepalli B., Xu R., Dattaroy T., Li B., Bass W.T., Li Q.Q., Hunt A.G. Plant Mol. Biol. 2006, 61(3):383-397.
27. Meeks L.R., Addepalli B., Hunt A.G. PloS one 2009, 4(11):e8082.
28. Wan C.Y., Wilkins T.A. Anal. Biochem. 1994, 223(1):7-12.
29. Zhu Y.Y., Machleder E.M., Chenchik A., Li R., Siebert P.D. BioTechniques 2001, 30(4):892-897.
30. Nesi N., Jond C., Debeaujon I., Caboche M., Lepiniec L. Plant Cell 2001, 13(9):2099-2114.
31. Rajjou L., Gallardo K., Debeaujon I., Vandekerckhove J., Job C., Job D. Plant Physiol. 2004, 134(4):1598-1613.
32. L. Ma, The role of polyadenylation in seed germination. Ph. D. thesis. University of Kentucky, 2013.
33. Hoque M., Ji Z., Zheng D., Luo W., Li W., You B., Park J.Y., Yehia G., Tian B. Nat. Methods 2013, 10(2):133-139.
34. Ozsolak F., Kapranov P., Foissac S., Kim S.W., Fishilevich E., Monaghan A.P., John B., Milos P.M. Cell 2010, 143(6):1018-1029.
35. Sherstnev A., Duc C., Cole C., Zacharaki V., Hornyik C., Ozsolak F., Milos P.M., Barton G.J., Simpson G.G. Nat. Struct. Mol. Biol. 2012, 19(8):845-852.
36. Sparks K.A., Dieckmann C.L. Nucleic Acids Res. 1998, 26(20):4676-4687.
37. Sparks K.A., Mayer S.A., Dieckmann C.L. Mol. Cell. Biol. 1997, 17(8):4199-4207.
38. Wlotzka W., Kudla G., Granneman S., Tollervey D. EMBO J. 2011, 30(9):1790-1803.