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Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer

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Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer. / Bhattacharyya, Sanchari; Yu, Yiting; Suzuki, Masako; Campbell, Nathaniel; Mazdo, Jozef; Vasanthakumar, Aparna; Bhagat, Tushar D; Nischal, Sangeeta; Christopeit, Maximilian; Parekh, Samir; Steidl, Ulrich; Godley, Lucy; Maitra, Anirban; Greally, John M; Verma, Amit.

In: NUCLEIC ACIDS RES, Vol. 41, No. 16, 09.2013, p. e157.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Bhattacharyya, S, Yu, Y, Suzuki, M, Campbell, N, Mazdo, J, Vasanthakumar, A, Bhagat, TD, Nischal, S, Christopeit, M, Parekh, S, Steidl, U, Godley, L, Maitra, A, Greally, JM & Verma, A 2013, 'Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer', NUCLEIC ACIDS RES, vol. 41, no. 16, pp. e157. https://doi.org/10.1093/nar/gkt601

APA

Bhattacharyya, S., Yu, Y., Suzuki, M., Campbell, N., Mazdo, J., Vasanthakumar, A., Bhagat, T. D., Nischal, S., Christopeit, M., Parekh, S., Steidl, U., Godley, L., Maitra, A., Greally, J. M., & Verma, A. (2013). Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer. NUCLEIC ACIDS RES, 41(16), e157. https://doi.org/10.1093/nar/gkt601

Vancouver

Bhattacharyya S, Yu Y, Suzuki M, Campbell N, Mazdo J, Vasanthakumar A et al. Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer. NUCLEIC ACIDS RES. 2013 Sep;41(16):e157. https://doi.org/10.1093/nar/gkt601

Bibtex

@article{c4662814f6cb4475b758c6b1653a5d60,
title = "Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer",
abstract = "5-hydroxymethylcytosine (5-hmC) is a recently discovered epigenetic modification that is altered in cancers. Genome-wide assays for 5-hmC determination are needed as many of the techniques for 5-methylcytosine (5-mC) determination, including methyl-sensitive restriction digestion and bisulfite sequencing cannot distinguish between 5-mC and 5-hmC. Glycosylation of 5-hmC residues by beta-glucosyl transferase (β-GT) can make CCGG residues insensitive to digestion by MspI. Restriction digestion by HpaII, MspI or MspI after β-GT conversion, followed by adapter ligation, massive parallel sequencing and custom bioinformatic analysis allowed us determine distribution of 5-mC and 5-hmC at single base pair resolution at MspI restriction sites. The resulting HpaII tiny fragment Enrichment by Ligation-mediated PCR with β-GT (HELP-GT) assay identified 5-hmC loci that were validated at global level by liquid chromatography-mass spectrometry (LC-MS) and the locus-specific level by quantitative reverse transcriptase polymerase chain reaction of 5-hmC pull-down DNA. Hydroxymethylation at both promoter and intragenic locations correlated positively with gene expression. Analysis of pancreatic cancer samples revealed striking redistribution of 5-hmC sites in cancer cells and demonstrated enrichment of this modification at many oncogenic promoters such as GATA6. The HELP-GT assay allowed global determination of 5-hmC and 5-mC from low amounts of DNA and with the use of modest sequencing resources. Redistribution of 5-hmC seen in cancer highlights the importance of determination of this modification in conjugation with conventional methylome analysis.",
keywords = "5-Methylcytosine, Animals, Cell Line, Tumor, Cell Transformation, Neoplastic, Cytosine, DNA, Neoplasm, Gene Expression, Genome, Human, Genomics, Glycosyltransferases, Humans, Mice, Pancreatic Neoplasms, Polymerase Chain Reaction",
author = "Sanchari Bhattacharyya and Yiting Yu and Masako Suzuki and Nathaniel Campbell and Jozef Mazdo and Aparna Vasanthakumar and Bhagat, {Tushar D} and Sangeeta Nischal and Maximilian Christopeit and Samir Parekh and Ulrich Steidl and Lucy Godley and Anirban Maitra and Greally, {John M} and Amit Verma",
year = "2013",
month = sep,
doi = "10.1093/nar/gkt601",
language = "English",
volume = "41",
pages = "e157",
journal = "NUCLEIC ACIDS RES",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "16",

}

RIS

TY - JOUR

T1 - Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer

AU - Bhattacharyya, Sanchari

AU - Yu, Yiting

AU - Suzuki, Masako

AU - Campbell, Nathaniel

AU - Mazdo, Jozef

AU - Vasanthakumar, Aparna

AU - Bhagat, Tushar D

AU - Nischal, Sangeeta

AU - Christopeit, Maximilian

AU - Parekh, Samir

AU - Steidl, Ulrich

AU - Godley, Lucy

AU - Maitra, Anirban

AU - Greally, John M

AU - Verma, Amit

PY - 2013/9

Y1 - 2013/9

N2 - 5-hydroxymethylcytosine (5-hmC) is a recently discovered epigenetic modification that is altered in cancers. Genome-wide assays for 5-hmC determination are needed as many of the techniques for 5-methylcytosine (5-mC) determination, including methyl-sensitive restriction digestion and bisulfite sequencing cannot distinguish between 5-mC and 5-hmC. Glycosylation of 5-hmC residues by beta-glucosyl transferase (β-GT) can make CCGG residues insensitive to digestion by MspI. Restriction digestion by HpaII, MspI or MspI after β-GT conversion, followed by adapter ligation, massive parallel sequencing and custom bioinformatic analysis allowed us determine distribution of 5-mC and 5-hmC at single base pair resolution at MspI restriction sites. The resulting HpaII tiny fragment Enrichment by Ligation-mediated PCR with β-GT (HELP-GT) assay identified 5-hmC loci that were validated at global level by liquid chromatography-mass spectrometry (LC-MS) and the locus-specific level by quantitative reverse transcriptase polymerase chain reaction of 5-hmC pull-down DNA. Hydroxymethylation at both promoter and intragenic locations correlated positively with gene expression. Analysis of pancreatic cancer samples revealed striking redistribution of 5-hmC sites in cancer cells and demonstrated enrichment of this modification at many oncogenic promoters such as GATA6. The HELP-GT assay allowed global determination of 5-hmC and 5-mC from low amounts of DNA and with the use of modest sequencing resources. Redistribution of 5-hmC seen in cancer highlights the importance of determination of this modification in conjugation with conventional methylome analysis.

AB - 5-hydroxymethylcytosine (5-hmC) is a recently discovered epigenetic modification that is altered in cancers. Genome-wide assays for 5-hmC determination are needed as many of the techniques for 5-methylcytosine (5-mC) determination, including methyl-sensitive restriction digestion and bisulfite sequencing cannot distinguish between 5-mC and 5-hmC. Glycosylation of 5-hmC residues by beta-glucosyl transferase (β-GT) can make CCGG residues insensitive to digestion by MspI. Restriction digestion by HpaII, MspI or MspI after β-GT conversion, followed by adapter ligation, massive parallel sequencing and custom bioinformatic analysis allowed us determine distribution of 5-mC and 5-hmC at single base pair resolution at MspI restriction sites. The resulting HpaII tiny fragment Enrichment by Ligation-mediated PCR with β-GT (HELP-GT) assay identified 5-hmC loci that were validated at global level by liquid chromatography-mass spectrometry (LC-MS) and the locus-specific level by quantitative reverse transcriptase polymerase chain reaction of 5-hmC pull-down DNA. Hydroxymethylation at both promoter and intragenic locations correlated positively with gene expression. Analysis of pancreatic cancer samples revealed striking redistribution of 5-hmC sites in cancer cells and demonstrated enrichment of this modification at many oncogenic promoters such as GATA6. The HELP-GT assay allowed global determination of 5-hmC and 5-mC from low amounts of DNA and with the use of modest sequencing resources. Redistribution of 5-hmC seen in cancer highlights the importance of determination of this modification in conjugation with conventional methylome analysis.

KW - 5-Methylcytosine

KW - Animals

KW - Cell Line, Tumor

KW - Cell Transformation, Neoplastic

KW - Cytosine

KW - DNA, Neoplasm

KW - Gene Expression

KW - Genome, Human

KW - Genomics

KW - Glycosyltransferases

KW - Humans

KW - Mice

KW - Pancreatic Neoplasms

KW - Polymerase Chain Reaction

U2 - 10.1093/nar/gkt601

DO - 10.1093/nar/gkt601

M3 - SCORING: Journal article

C2 - 23861445

VL - 41

SP - e157

JO - NUCLEIC ACIDS RES

JF - NUCLEIC ACIDS RES

SN - 0305-1048

IS - 16

ER -