TitleA Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations.
Publication TypeJournal Article
Year of Publication2016
AuthorsHan, Dali, Lu Xingyu, Shih Alan H., Nie Ji, You Qiancheng, Xu Meng Michelle, Melnick Ari M., Levine Ross L., and He Chuan
JournalMol Cell
Volume63
Issue4
Pagination711-719
Date Published2016 Aug 18
ISSN1097-4164
Keywords5-Methylcytosine, Animals, Cells, Cultured, Computational Biology, Databases, Genetic, Dioxygenases, DNA Methylation, DNA-Binding Proteins, Epigenesis, Genetic, fms-Like Tyrosine Kinase 3, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Gene Library, Genome-Wide Association Study, Hematopoiesis, Hematopoietic Stem Cells, High-Throughput Nucleotide Sequencing, Leukemia, Promyelocytic, Acute, Mice, Mutation, Nanotechnology, Proto-Oncogene Proteins, Time Factors
Abstract

<p>We present a highly sensitive and selective chemical labeling and capture approach for genome-wide profiling of 5-hydroxylmethylcytosine (5hmC) using DNA isolated from ∼1,000 cells (nano-hmC-Seal). Using this technology, we assessed 5hmC occupancy and dynamics across different stages of hematopoietic differentiation. Nano-hmC-Seal profiling of purified Tet2-mutant acute myeloid leukemia (AML) murine stem cells allowed us to identify leukemia-specific, differentially hydroxymethylated regions that harbor known and candidate disease-specific target genes with differential 5hmC peaks compared to normal stem cells. The change of 5hmC patterns in AML strongly correlates with differential gene expression, demonstrating the importance of dynamic alterations of 5hmC in regulating transcription in AML. Together, covalent 5hmC labeling offers an effective approach to study and detect DNA methylation dynamics in in vivo disease models and in limited clinical samples.</p>

DOI10.1016/j.molcel.2016.06.028
Alternate JournalMol Cell
PubMed ID27477909
PubMed Central IDPMC4992443
Grant ListP30 CA008748 / CA / NCI NIH HHS / United States
R01 CA173636 / CA / NCI NIH HHS / United States
R01 HG006827 / HG / NHGRI NIH HHS / United States
U54 CA193419 / CA / NCI NIH HHS / United States
/ HHMI / Howard Hughes Medical Institute / United States