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 language | English |
|---|---|
| Pages (from-to) | 4783-4791 |
| Number of pages | 9 |
| Journal | Nucleic Acids Research |
| Volume | 41 |
| Issue number | 9 |
| DOIs | |
| Publication status | Published - 2013 May 1 |
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ASJC Scopus subject areas
- Genetics
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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 journal › Article
}
TY - JOUR
T1 - Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes
AU - Chae, Heejoon
AU - Park, Jinwoo
AU - Lee, Seong Whan
AU - Nephew, Kenneth P.
AU - Kim, Sun
PY - 2013/5/1
Y1 - 2013/5/1
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gkt144
DO - 10.1093/nar/gkt144
M3 - Article
C2 - 23519616
AN - SCOPUS:84877301094
VL - 41
SP - 4783
EP - 4791
JO - The BMJ
JF - The BMJ
SN - 0730-6512
IS - 9
ER -