Plant simple sequence repeats: distribution, variation, and effects on gene expression.
Genome-wide simple sequence repeat (SSR) information was analyzed together with functional annotations of Arabidopsis genes and public gene expression data for Arabidopsis and rice. Analysis of more than 15,000 Arabidopsis and more than 16,000 rice SSRs indicated that SSRs may affect the expression of hundreds of genes. Data from experiments on DNA methylation, histone acetylation, and transcript turnover suggest that SSRs may affect gene expression at transcriptional and posttranscriptional levels. Members of some functional groups were shown to be enriched with SSRs and often contained similar but non-homologous repeats within the same gene regions. In addition, the distribution of perfect and imperfect SSRs in some Arabidopsis, maize, and rice genes was used to demonstrate how two-level control of SSR variation may contribute to protein evolution.
Sharopova
Natalya
N
250 Biological Sciences Building, 1445 Gortner Avenue, Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA. sharo002@umn.edu
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics; D010944:Plants / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000235:genetics
D014157:Transcription Factors