| dc.description.abstract | CpG islands are regulatory elements in a genome with high CpG dinucleotide density,
influencing gene expression and genomic stability. These regions are important to rice
biology. Despite the extensive body of research on CpG islands, the understanding of
their distribution and characteristics at the chromosomal level remains limited. Hence,
in silico analysis of chromosomal CpG islands in rice (Oryza sativa L. spp. japonica)
is a computational approach to elucidate the chromosomal distribution and distinctive
features of CpG islands within the genome of this agriculturally significant plant species.
Genomic data from the GenBank and EnsemblPlants databases were utilized, with contigs
NC_029256.1, NC_029257.1, NC_029258.1, NC_029259.1, NC_029260.1, NC_029261.1,
NC_029262.1, NC_029263.1, NC_029254.1, NC_029265.1, NC_029266.1, NC_029267.1
representing chromosomes 1 to 12, respectively. Consistent G+C percentages were observed across all chromosomes, with GpC showing a higher frequency compared to CpC,
CpG, and GpG. CpG islands were identified in the chromosomes using the Gardiner Garden and Frommer algorithm, based on a minimum 200-bp region with an observed
CpG/expected CpG (O/E ratio) of 0.6 or higher and a GC content greater than 50%. The
statistical analysis unveiled significant enrichment of CpG islands (O/E ratio > 0.6) across
all chromosomes. Additionally, the study employed the identification of CpG islands
within the genomic loci of all chromosomes, revealing that, on average a maximum
of 35% of these islands were situated within gene sequences. Chromosomes 11 and 12
exhibited comparatively lower proportions of CpG islands in contrast to the remaining
chromosomes. Notably, a minimum of 68% of genes spanning all chromosomes harboured CpG islands. Mostly positioned within gene promoters, CpG islands govern gene
expression through methylation, impacting growth, stress response, and development in
rice. Epigenetic inheritance of CpG patterns aids trait transmission. Thus, unravelling
CpG complexities promises better rice crops. In conclusion, this study offers invaluable
insights into the chromosomal-level characteristics of CpG islands in rice, facilitating the
advancement of our understanding of CpG island research and its intricate integration
with chromosomal organization. | en_US |
