title: A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations.
abstract: 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.
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
authors.forename: Dali
authors.initials: D
authors.lastname: Han
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
authors.forename: Xingyu
authors.initials: X
authors.lastname: Lu
authors.affiliation: Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Alan H
authors.initials: AH
authors.lastname: Shih
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
authors.forename: Ji
authors.initials: J
authors.lastname: Nie
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
authors.forename: Qiancheng
authors.initials: Q
authors.lastname: You
authors.affiliation: Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Meng Michelle
authors.initials: MM
authors.lastname: Xu
authors.affiliation: Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA; Weill Cornell Medical College, Cornell University, 413 East 69th Street, BB-1462, New York, NY 10021, USA.
authors.forename: Ari M
authors.initials: AM
authors.lastname: Melnick
authors.affiliation: Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: leviner@mskcc.org.
authors.forename: Ross L
authors.initials: RL
authors.lastname: Levine
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA. Electronic address: chuanhe@uchicago.edu.
authors.forename: Chuan
authors.initials: C
authors.lastname: He
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D000818:Animals; D002478:Cells, Cultured; D019295:Computational Biology; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics; D030541:Databases, Genetic; D049308:Dioxygenases; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D015723:Gene Library; D055106:Genome-Wide Association Study; D006410:Hematopoiesis / Q000235:genetics*; D006412:Hematopoietic Stem Cells / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D015473:Leukemia, Promyelocytic, Acute / Q000235:genetics* / Q000378:metabolism; D051379:Mice; D009154:Mutation; D036103:Nanotechnology; D011518:Proto-Oncogene Proteins / Q000235:genetics; D013997:Time Factors; D051941:fms-Like Tyrosine Kinase 3 / Q000235:genetics
chemical_list: D004268:DNA-Binding Proteins; D011518:Proto-Oncogene Proteins; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D049308:Dioxygenases; C551914:Tet2 protein, mouse; C497971:Flt3 protein, mouse; D051941:fms-Like Tyrosine Kinase 3