Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome

Bioinformatics

Volumn 25, Issue 10, 2009, Pages 1215-1218

  Wang, Xiangfeng ^a   Yu, Zhihui ^b   Yang, Xiaozeng ^b   Deng, Xing Wang ^a   Li, Lei ^b  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME STRUCTURE; CONTROLLED STUDY; GENE DUPLICATION; GENE EXPRESSION; GENE FUNCTION; GENETIC SELECTION; GENOME ANALYSIS; MICROARRAY ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; RICE; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; TRANSPOSON;

DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENOME, PLANT; ORYZA SATIVA; TRANSCRIPTION, GENETIC;

EID: 65549125469     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp147     Document Type: Article

References (21)

1. Bertone,P. et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science, 306 2242-2246.
2. Cheng,J. et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308, 1149-1154.
3. He,H. et al. (2007) Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray. Genome Res., 17, 1471-1477.
4. Hirschman,J.E. et al. (1988) Genetic evidence for promoter competition in Saccharomyces cerevisiae. Mol. Cell Biol., 8, 4608-4615.
5. Jiang,N. et al. (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature, 431, 569-573.
6. Juretic,N. et al. (2005) The evolutionary fate of MULE-mediated duplications of donor gene fragments in rice. Genome Res., 15 1292-1297.
7. Kim,T.H. et al. (2005) A high-resolution map of active promoters in the human genome. Nature, 436, 876-880.
8. Li,L. et al. (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat. Genet., 38, 124-129.
9. Li,L. et al. (2007) Global identification and characterization of transcriptionally active regions in the rice genome. PLoS ONE, 2, e294.
10. Li,L. et al. (2008) Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol., 9, R57.
11. Martens,JA. et al. (2005) Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev., 19, 2695-2704.
12. Mockler,T.C. and Ecker,J.R. (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics, 85, 1-15.
13. Ouyang,S. et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res., 35, D883-D887.
14. Radonjic,M. et al. (2005) Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol. Cell, 18, 171-183.
15. Rizzon,C. et al. (2006) Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput. Biol., 2, e115.
16. Samanta,M.P. et al. (2006) The transcriptome of the sea urchin embryo. Science, 314, 960-962.
17. Stolc,V et al. (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster. Science, 306, 655-660.
18. Wilhelm,B.T. et al. (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature, 453, 1239-1243.
19. Yamada,K. et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 302, 842-846.
20. Yu J. et al. (2005) The genomes of Oryza sativa: A history of duplications. PLoS Biol., 3, e38.
21. Zhang,Z. et al. (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evol. Biol., 6, 44.