An exploration of 3′-end processing signals and their tissue distribution in Oryza sativa

Gene

Volumn 389, Issue 2, 2007, Pages 107-113

  Dong, Haitao ^a   Deng, Ye ^a   Chen, Jack ^b   Wang, Sheng ^a   Peng, Sihua ^c   Dai, Cheng'en ^a   Fang, Yongqi ^a   Shao, Jing ^a   Lou, Yichun ^a   Li, Debao ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^c ZHEJIANG UNIVERSITY   (China)

Author keywords

3 UTR; Cleavage site; Downstream sequences; Rice

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; PLANT RNA;

ARABIDOPSIS; ARTICLE; DNA FLANKING REGION; DNA LIBRARY; DNA SEQUENCE; ENDOSPERM; ENTROPY; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT LEAF; PLANT STEM; PLANT TISSUE; PRIORITY JOURNAL; RICE; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; TISSUE DISTRIBUTION; 3' UNTRANSLATED REGION; BIOLOGY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; METABOLISM; PLANT SEED; REGULATORY RNA SEQUENCE; RNA PROCESSING;

ARABIDOPSIS; EUKARYOTA; MAMMALIA; ORYZA SATIVA;

3' UNTRANSLATED REGIONS; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; ORYZA SATIVA; PLANT LEAVES; PLANT STEMS; RNA 3' POLYADENYLATION SIGNALS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; RNA, PLANT; SEEDS;

EID: 33846627322     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.10.015     Document Type: Article

References (24)

1. Beaudoing E., and Gautheret D. Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res. 11 (2001) 1520-1526
2. Colgan D.F., and Manley J.L. Mechanism and regulation of mRNA polyadenylation. Genes Dev. 11 (1997) 2755-2766
3. Dreyfus M., and Regnier P. The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell 111 (2002) 611-613
4. Edwalds-Gilbert G., Veraldi K.L., and Milcarek C. Alternative poly(A) site selection in complex transcription units: means to an end?. Nucleic Acids Res. 25 (1997) 2547-2561
5. Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome-wide expression patterns. PNAS 95 (1998) 14863-14868
6. Ewing B., Hillier L., Wendl M.C., and Green P. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8 (1998) 175-185
7. Gautheret D., Poirot O., Lopez F., Audic S., and Claverie J.M. Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. Genome Res. 8 (1998) 524-530
8. Goff S.A., et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296 (2002) 92-100
9. Graber J.H. Variations in yeast 3′-processing cis-elements correlate with transcript stability. Trends Genet. 19 (2003) 473-476
10. Graber J.H., Cantor C.R., Mohr S.C., and Smith T.F. In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 14055-14060
11. Kislauskis E.H., Zhu X., and Singer R.H. Sequences responsible for intracellular localization of beta-actin messenger RNA also affect cell phenotype. J. Cell Biol. 127 (1994) 441-451
12. Knirsch L., and Clerch L.B. A region in the 3′ UTR of MnSOD RNA enhances translation of a heterologous RNA. Biochem. Biophys. Res. Commun. 272 (2000) 164-168
13. Loke J.C., Stahlberg E.A., Strenski D.G., Haas B.J., Wood P.C., and Li Q.Q. Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol. 138 (2005) 1457-1468
14. Mazumder B., Seshadri V., and Fox P.L. Translational control by the 3′-UTR: the ends specify the means. Trends Biochem. Sci. 28 (2003) 91-98
15. Meyers B.C., et al. Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat. Biotechnol. 22 (2004) 1006-1011
16. Reinert G., Schbath S., and Waterman M.S. Probabilistic and statistical properties of words: an overview. J. Comput. Biol. 7 (2000) 1-46
17. Rothnie H.M. Plant mRNA 3′-end formation. Plant Mol. Biol. 32 (1996) 43-61
18. Schbath S. An overview on the distribution of word counts in Markov chains. J. Comput. Biol. 7 (2000) 193-201
19. Shannon, C.E., 1948. A mathematics theory of communication. Bell Syst. Tech. J. 27, 379-423-623-656.
20. van Helden J., del Olmo M., and Perez-Ortin J.E. Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res. 28 (2000) 1000-1010
21. Yan J., and Marr T.G. Computational analysis of 3′-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. Genome Res. 15 (2005) 369-375
22. Yu J., et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296 (2002) 79-92
23. Zhang Z., Schwartz S., Wagner L., and Miller W. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7 (2000) 203-214
24. Zhao J., Hyman L., and Moore C. Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63 (1999) 405-445