Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

Eun Joon Lee, Lirong Pei, Gyan Srivastava, Trupti Joshi, Garima Kushwaha, Jeong-Hyeon Choi, Keith D. Robertson, Xinguo Wang, John K. Colbourne, Lu Zhang, Gary P. Schroth, Dong Xu, Kun Zhang, Huidong Shi

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

We applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of ~1 million CpGs in more than 21408 CGIs and more than 15946 transcriptional regulatory regions. Of the CpGs analyzed, 77-84 fell on or near capture probe sequences; 69-75 fell within CGIs. More than 85 of capture probes successfully yielded quantitative DNA methylation information of targeted regions. Differentially methylated regions (DMRs) were identified in the 5′-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X-chromosome among the three breast cancer cell lines analyzed. We chose 46 candidate loci (762 CpGs) for confirmation with PCR-based bisulfite sequencing and demonstrated excellent correlation between two data sets. Targeted bisulfite sequencing of three DNA methyltransferase (DNMT) knockout cell lines and the wild-type HCT116 colon cancer cell line revealed a significant decrease in CpG methylation for the DNMT1 knockout and DNMT1, 3B double knockout cell lines, but not in DNMT3B knockout cell line. We demonstrated the targeted bisulfite sequencing approach to be a powerful method to uncover novel aberrant methylation in the cancer epigenome. Since all targets were captured and sequenced as a pool through a series of single-tube reactions, this method can be easily scaled up to deal with a large number of samples.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume39
Issue number19
DOIs
StatePublished - Oct 1 2011

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High-Throughput Nucleotide Sequencing
CpG Islands
Cell Line
Nucleic Acid Regulatory Sequences
Methylation
Intergenic DNA
Methyltransferases
X Chromosome
Human Genome
DNA Methylation
DNA Sequence Analysis
Colonic Neoplasms
hydrogen sulfite
Breast Neoplasms
Polymerase Chain Reaction
Neoplasms

ASJC Scopus subject areas

  • Genetics

Cite this

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. / Lee, Eun Joon; Pei, Lirong; Srivastava, Gyan; Joshi, Trupti; Kushwaha, Garima; Choi, Jeong-Hyeon; Robertson, Keith D.; Wang, Xinguo; Colbourne, John K.; Zhang, Lu; Schroth, Gary P.; Xu, Dong; Zhang, Kun; Shi, Huidong.

In: Nucleic Acids Research, Vol. 39, No. 19, 01.10.2011.

Research output: Contribution to journalArticle

Lee, EJ, Pei, L, Srivastava, G, Joshi, T, Kushwaha, G, Choi, J-H, Robertson, KD, Wang, X, Colbourne, JK, Zhang, L, Schroth, GP, Xu, D, Zhang, K & Shi, H 2011, 'Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing', Nucleic Acids Research, vol. 39, no. 19. https://doi.org/10.1093/nar/gkr598
Lee, Eun Joon ; Pei, Lirong ; Srivastava, Gyan ; Joshi, Trupti ; Kushwaha, Garima ; Choi, Jeong-Hyeon ; Robertson, Keith D. ; Wang, Xinguo ; Colbourne, John K. ; Zhang, Lu ; Schroth, Gary P. ; Xu, Dong ; Zhang, Kun ; Shi, Huidong. / Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. In: Nucleic Acids Research. 2011 ; Vol. 39, No. 19.
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