Predicting DNA methylation susceptibility using CpG flanking sequences

S. Kim, M. Li, H. Pair, Kenneth Nephew, H. Shi, R. Kramer, D. Xu, T. H. Huang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

15 Citations (Scopus)

Abstract

DNA methylation is a type of chemical modification of DNA that adds a methyl group to DNA at the fifth carbon of the cytosine pyrimidine ring. In normal cells, methylation of CpG dinucleotides is extensively found across the genome. However, specific DNA regions known as the CpG islands, short CpG dinucleotide-rich stretches (500bp-2000bp), are commonly unmethylated. During tumorigenesis, on the other hand, global de-methylation and CpG island hypermethylation are widely observed. De novo hypermethylation at CpG dinucleotides is typically associated with loss of expression of flanking genes, thus it is believed to be an alternative to mutation and deletion in the inactivation of tumor suppressor genes. In this paper, we report that sequences flanking CpG sites can be used for predicting DNA methylation levels. DNA methylation levels were measured by utilizing a new high throughput sequencing technology (454) to sequence bisulfite treated DNA from four types of primary leukemia and lymphoma cells and normal peripheral blood lymphocytes. After measuring methylation levels at each CpG site, we used 30 bp flanking sequences to characterize methylation susceptibility in terms of character compositions and built predictive models for DNA methylation susceptibility, achieving up to 75% prediction accuracy in 10-fold cross validation tests. Our study is first of its kind to build predictive models for methylation susceptibility by utilizing CpG site specific methylation levels.

Original languageEnglish
Title of host publicationPacific Symposium on Biocomputing 2008, PSB 2008
Pages315-326
Number of pages12
StatePublished - 2008
Event13th Pacific Symposium on Biocomputing, PSB 2008 - Kohala Coast, HI, United States
Duration: Jan 4 2008Jan 8 2008

Other

Other13th Pacific Symposium on Biocomputing, PSB 2008
CountryUnited States
CityKohala Coast, HI
Period1/4/081/8/08

Fingerprint

Methylation
DNA Methylation
DNA
CpG Islands
Genes
Lymphocytes
Sequence Deletion
Cytosine
Chemical modification
Tumor Suppressor Genes
Tumors
Lymphoma
Carcinogenesis
Leukemia
Blood
Carbon
Throughput
Genome
Technology
Gene Expression

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • Medicine(all)

Cite this

Kim, S., Li, M., Pair, H., Nephew, K., Shi, H., Kramer, R., ... Huang, T. H. (2008). Predicting DNA methylation susceptibility using CpG flanking sequences. In Pacific Symposium on Biocomputing 2008, PSB 2008 (pp. 315-326)

Predicting DNA methylation susceptibility using CpG flanking sequences. / Kim, S.; Li, M.; Pair, H.; Nephew, Kenneth; Shi, H.; Kramer, R.; Xu, D.; Huang, T. H.

Pacific Symposium on Biocomputing 2008, PSB 2008. 2008. p. 315-326.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Kim, S, Li, M, Pair, H, Nephew, K, Shi, H, Kramer, R, Xu, D & Huang, TH 2008, Predicting DNA methylation susceptibility using CpG flanking sequences. in Pacific Symposium on Biocomputing 2008, PSB 2008. pp. 315-326, 13th Pacific Symposium on Biocomputing, PSB 2008, Kohala Coast, HI, United States, 1/4/08.
Kim S, Li M, Pair H, Nephew K, Shi H, Kramer R et al. Predicting DNA methylation susceptibility using CpG flanking sequences. In Pacific Symposium on Biocomputing 2008, PSB 2008. 2008. p. 315-326
Kim, S. ; Li, M. ; Pair, H. ; Nephew, Kenneth ; Shi, H. ; Kramer, R. ; Xu, D. ; Huang, T. H. / Predicting DNA methylation susceptibility using CpG flanking sequences. Pacific Symposium on Biocomputing 2008, PSB 2008. 2008. pp. 315-326
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