Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes

Heejoon Chae, Jinwoo Park, Seong Whan Lee, Kenneth P. Nephew, Sun Kim

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

CpG islands are GC-rich regions often located in the 5′ end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative analysis of all CpG island sequences in 10 mammalian genomes. As sequence similarity methods and character composition techniques such as information theory are particularly difficult to conduct, we used exact patterns in CpG island sequences and single character discrepancies to identify differences in CpG island sequences. First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes. Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers. In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.

Original languageEnglish
Pages (from-to)4783-4791
Number of pages9
JournalNucleic Acids Research
Volume41
Issue number9
DOIs
Publication statusPublished - 2013 May 1

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CpG Islands
Genes
Genome
GC Rich Sequence
Information Theory
Methylation
Mammals
Cytosine
Information theory
Transcription
Phylogeny
Epigenomics
Learning algorithms
Sequence Analysis
Learning systems
Conservation
History
Testing
Chemical analysis

ASJC Scopus subject areas

  • Genetics

Cite this

Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes. / Chae, Heejoon; Park, Jinwoo; Lee, Seong Whan; Nephew, Kenneth P.; Kim, Sun.

In: Nucleic Acids Research, Vol. 41, No. 9, 01.05.2013, p. 4783-4791.

Research output: Contribution to journalArticle

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