Compositional bias is a major determinant of the distribution pattern of palindromes in Drosophila

• 作 者: Guoqing Liu Bingjie Zhang Jia Liu
• 机 构: SchoolofMathematics,PhysicsandBiologicalEngineering,InnerMongoliaUniversityofScienceandTechnology,Ba
• 出 处: 第五届全国生物信息学与系统生物学学术大会
• 发表日期: 2012年8期
• 关键词: Palindrome Compositional bias Recombination

　　Background: Palindromic sequences are important DNA motifs relating to gene regulation, DNA replication and recombination.Thus, investigating the mechanisms that have shaped the palindrome distribution and abundance in genomes is substantially important.Results: We investigated the palindrome distribution and abundance in Drosophila melanogaster.The results show that: (1) Short palindromes (<6 bp) are under-represented, while relatively long palindromes (>6 bp) are over-represented as compared to those in random sequences ; (2) The genomic distribution of palindromes is associated with recombination rate, gene density and GC content ; (3) Partial correlation analysis indicates that the majority of the palindrome density variation across the genome is explained by GC content, and the most of the correlation between palindrome density and recombination rate is likely to be the side-product of the effect of GC content on palindrome density, indicating that compositional bias is a major determinant of the distribution pattern and abundance of palindromes in Drosophila melanogaster.Conclusion: Our data implicate that compositional bias might be a major determinant of palindrome abundance in eukaryotic genomes and at least in part resulted in the contemporary pattern of palindrome abundance, such as the short palindrome avoidance and overrepresentation of long palindromes, in the D.melanogaster genome .