Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia

Altuna Akalin, Francine E. Garrett-Bakelman, Matthias Kormaksson, Jennifer Busuttil, Lu Zhang, Irina Khrebtukova, Thomas A. Milne, Yongsheng Huang, Debabrata Biswas, Jay L. Hess, C. David Allis, Robert G. Roeder, Peter J M Valk, Bob Löwenberg, Ruud Delwel, Hugo F. Fernandez, Elisabeth M. Paietta, Martin S. Tallman, Gary P. Schroth, Christopher E. MasonAri Melnick, Maria E. Figueroa

Research output: Contribution to journalArticle

174 Citations (Scopus)

Abstract

We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage, which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands. Applying this method to primary human bone marrow specimens from patients with Acute Myelogeneous Leukemia (AML), we demonstrated that genetically distinct AML subtypes display diametrically opposed DNA methylation patterns. As compared to normal controls, we observed widespread hypermethylation in IDH mutant AMLs, preferentially targeting promoter regions and CpG islands neighboring the transcription start sites of genes. In contrast, AMLs harboring translocations affecting the MLL gene displayed extensive loss of methylation of an almost mutually exclusive set of CpGs, which instead affected introns and distal intergenic CpG islands and shores. When analyzed in conjunction with gene expression profiles, it became apparent that these specific patterns of DNA methylation result in differing roles in gene expression regulation. However, despite this subtype-specific DNA methylation patterning, a much smaller set of CpG sites are consistently affected in both AML subtypes. Most CpG sites in this common core of aberrantly methylated CpGs were hypermethylated in both AML subtypes. Therefore, aberrant DNA methylation patterns in AML do not occur in a stereotypical manner but rather are highly specific and associated with specific driving genetic lesions.

Original languageEnglish (US)
Article numbere1002781
JournalPLoS Genetics
Volume8
Issue number6
DOIs
StatePublished - Jun 2012

Fingerprint

myeloid leukemia
methylation
DNA methylation
DNA Methylation
leukemia
DNA Sequence Analysis
Acute Myeloid Leukemia
Epigenomics
epigenetics
Base Pairing
Leukemia
CpG Islands
DNA
gene expression
bisulfites
Transcription Initiation Site
gene expression regulation
Gene Expression Regulation
Transcriptome
Genetic Promoter Regions

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Akalin, A., Garrett-Bakelman, F. E., Kormaksson, M., Busuttil, J., Zhang, L., Khrebtukova, I., ... Figueroa, M. E. (2012). Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genetics, 8(6), [e1002781]. https://doi.org/10.1371/journal.pgen.1002781

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. / Akalin, Altuna; Garrett-Bakelman, Francine E.; Kormaksson, Matthias; Busuttil, Jennifer; Zhang, Lu; Khrebtukova, Irina; Milne, Thomas A.; Huang, Yongsheng; Biswas, Debabrata; Hess, Jay L.; Allis, C. David; Roeder, Robert G.; Valk, Peter J M; Löwenberg, Bob; Delwel, Ruud; Fernandez, Hugo F.; Paietta, Elisabeth M.; Tallman, Martin S.; Schroth, Gary P.; Mason, Christopher E.; Melnick, Ari; Figueroa, Maria E.

In: PLoS Genetics, Vol. 8, No. 6, e1002781, 06.2012.

Research output: Contribution to journalArticle

Akalin, A, Garrett-Bakelman, FE, Kormaksson, M, Busuttil, J, Zhang, L, Khrebtukova, I, Milne, TA, Huang, Y, Biswas, D, Hess, JL, Allis, CD, Roeder, RG, Valk, PJM, Löwenberg, B, Delwel, R, Fernandez, HF, Paietta, EM, Tallman, MS, Schroth, GP, Mason, CE, Melnick, A & Figueroa, ME 2012, 'Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia', PLoS Genetics, vol. 8, no. 6, e1002781. https://doi.org/10.1371/journal.pgen.1002781
Akalin, Altuna ; Garrett-Bakelman, Francine E. ; Kormaksson, Matthias ; Busuttil, Jennifer ; Zhang, Lu ; Khrebtukova, Irina ; Milne, Thomas A. ; Huang, Yongsheng ; Biswas, Debabrata ; Hess, Jay L. ; Allis, C. David ; Roeder, Robert G. ; Valk, Peter J M ; Löwenberg, Bob ; Delwel, Ruud ; Fernandez, Hugo F. ; Paietta, Elisabeth M. ; Tallman, Martin S. ; Schroth, Gary P. ; Mason, Christopher E. ; Melnick, Ari ; Figueroa, Maria E. / Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. In: PLoS Genetics. 2012 ; Vol. 8, No. 6.
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