Segmental Distribution of Genes Harboring a CpG Island-like Region on Rice Chromosomes

Overview

Journal Mol Genet Genomics

Specialty Genetics

Date 2005 Nov 12

PMID 16283384

Citations 2

Authors

I Ashikawa

H Numa

K Sakata

Affiliations

Soon will be listed here.

Abstract

In plant genomes, there exist discrete regions rich in CpG dinucleotides, namely CpG clusters. In rice, most of these CpG clusters are associated with genes. Rice genes are grouped into one of the five classes according to the position of an associated CpG cluster. Among them, class 1 genes, which harbor a CpG cluster at the 5'-terminus, share similarities with human genes having CpG islands. In the present study, by analyzing plant genome sequence data, primarily from rice, we investigated the chromosomal distribution of genes of each class, mainly class 1 genes. Class 1 genes were not uniformly distributed across the rice genome, but were clustered into discrete chromosomal segments. EST-based analysis of the distribution of expressed genes indicates that this segmental distribution of class 1 genes caused a preferential distribution of expressed genes within class 1 gene-rich segments. We then compared the methylation status of genes of each class to examine the possibility that differential DNA methylation, if any, is relevant to the observed differential expression level of genes inside and outside the class 1 segments. The difference in the methylation level between these genes was revealed to be fairly small, which does not support the above-mentioned possibility.

Citing Articles

Epigenetic regulation of photoperiodic flowering.

Takeno K Plant Signal Behav. 2010; 5(7):788-91.

PMID: 20448475 PMC: 3115027. DOI: 10.4161/psb.5.7.11766.

Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants?.

Bousios A, Darzentas N, Tsaftaris A, Pearce S BMC Genomics. 2010; 11:89.

PMID: 20132532 PMC: 2829016. DOI: 10.1186/1471-2164-11-89.

References

Panstruga R, Buschges R, Piffanelli P, Schulze-Lefert P . A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res. 1998; 26(4):1056-62. PMC: 147355. DOI: 10.1093/nar/26.4.1056. View

Murray M, Thompson W . Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980; 8(19):4321-5. PMC: 324241. DOI: 10.1093/nar/8.19.4321. View

Sakata K, Nagamura Y, Numa H, Antonio B, Nagasaki H, Idonuma A . RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Res. 2001; 30(1):98-102. PMC: 99141. DOI: 10.1093/nar/30.1.98. View

Hashimshony T, Zhang J, Keshet I, Bustin M, Cedar H . The role of DNA methylation in setting up chromatin structure during development. Nat Genet. 2003; 34(2):187-92. DOI: 10.1038/ng1158. View

Sorensen M, Muller M, Skerritt J, Simpson D . Hordein promoter methylation and transcriptional activity in wild-type and mutant barley endosperm. Mol Gen Genet. 1996; 250(6):750-60. DOI: 10.1007/BF02172987. View

Ashikawa I . Gene-associated CpG islands and the expression pattern of genes in rice. DNA Res. 2002; 9(4):131-4. DOI: 10.1093/dnares/9.4.131. View

Bennetzen J, Schrick K, Springer P, Brown W, SanMiguel P . Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome. 1994; 37(4):565-76. DOI: 10.1139/g94-081. View

Bird A . DNA methylation patterns and epigenetic memory. Genes Dev. 2002; 16(1):6-21. DOI: 10.1101/gad.947102. View

Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N . Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science. 2003; 301(5631):376-9. DOI: 10.1126/science.1081288. View

10.

Finnegan E, Peacock W, Dennis E . DNA methylation, a key regulator of plant development and other processes. Curr Opin Genet Dev. 2000; 10(2):217-23. DOI: 10.1016/s0959-437x(00)00061-7. View

11.

Larsen F, Gundersen G, Lopez R, Prydz H . CpG islands as gene markers in the human genome. Genomics. 1992; 13(4):1095-107. DOI: 10.1016/0888-7543(92)90024-m. View

12.

Florea L, Hartzell G, Zhang Z, Rubin G, Miller W . A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 1998; 8(9):967-74. PMC: 310774. DOI: 10.1101/gr.8.9.967. View

13.

Langdale J, Taylor W, Nelson T . Cell-specific accumulation of maize phosphoenolpyruvate carboxylase is correlated with demethylation at a specific site greater than 3 kb upstream of the gene. Mol Gen Genet. 1991; 225(1):49-55. DOI: 10.1007/BF00282641. View

14.

Dunham I, Shimizu N, Roe B, Chissoe S, HUNT A, Collins J . The DNA sequence of human chromosome 22. Nature. 1999; 402(6761):489-95. DOI: 10.1038/990031. View

15.

Rombauts S, Florquin K, Lescot M, Marchal K, Rouze P, Van de Peer Y . Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol. 2003; 132(3):1162-76. PMC: 167057. DOI: 10.1104/pp.102.017715. View

16.

Ashikawa I . Gene-associated CpG islands in plants as revealed by analyses of genomic sequences. Plant J. 2001; 26(6):617-25. DOI: 10.1046/j.1365-313x.2001.01062.x. View

17.

Moore G, Abbo S, Cheung W, Foote T, Gale M, Koebner R . Key features of cereal genome organization as revealed by the use of cytosine methylation-sensitive restriction endonucleases. Genomics. 1993; 15(3):472-82. DOI: 10.1006/geno.1993.1097. View

18.

Turcotte K, Srinivasan S, Bureau T . Survey of transposable elements from rice genomic sequences. Plant J. 2001; 25(2):169-79. DOI: 10.1046/j.1365-313x.2001.00945.x. View

19.

Messeguer R, Ganal M, Steffens J, Tanksley S . Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Mol Biol. 1991; 16(5):753-70. DOI: 10.1007/BF00015069. View

20.

Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T . Functional annotation of a full-length Arabidopsis cDNA collection. Science. 2002; 296(5565):141-5. DOI: 10.1126/science.1071006. View