Showing papers by "Yun Huang published in 2014"
TL;DR: Extended regions of low methylation (canyons) are discovered that span conserved domains frequently containing transcription factors and are distinct from CpG islands and shores and may contribute to leukemia development.
Abstract: Gains and losses in DNA methylation are prominent features of mammalian cell types. To gain insight into the mechanisms that promote shifts in DNA methylation and contribute to changes in cell fate, including malignant transformation, we performed genome-wide mapping of 5-methylcytosine and 5-hydroxymethylcytosine in purified mouse hematopoietic stem cells. We discovered extended regions of low methylation (canyons) that span conserved domains frequently containing transcription factors and are distinct from CpG islands and shores. About half of the genes in these methylation canyons are coated with repressive histone marks, whereas the remainder are covered by activating histone marks and are highly expressed in hematopoietic stem cells (HSCs). Canyon borders are demarked by 5-hydroxymethylcytosine and become eroded in the absence of DNA methyltransferase 3a (Dnmt3a). Genes dysregulated in human leukemias are enriched for canyon-associated genes. The new epigenetic landscape we describe may provide a mechanism for the regulation of hematopoiesis and may contribute to leukemia development.
287 citations
TL;DR: An overview of loss-of-function mutations and abnormal expression and regulation of TET proteins in hematological malignancies and solid tumors is presented, and the potential prognostic value of assessing TET mutations and 5hmC levels in cancer patients are discussed.
228 citations
TL;DR: The data point to a complex interplay between Tet1 and Tet2 in mESC, and to distinct roles for these two proteins in regulating promoter, exon, and polyadenylation site usage in cells.
Abstract: Dioxygenases of the Ten-Eleven Translocation (TET) family are 5-methylcytosine oxidases that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. We show that Tet1 and Tet2 have distinct roles in regulating 5hmC in mouse embryonic stem cells (mESC). Tet1 depletion diminishes 5hmC levels at transcription start sites (TSS), whereas Tet2 depletion is predominantly associated with decreased 5hmC in gene bodies. Enrichment of 5hmC is observed at the boundaries of exons that are highly expressed, and Tet2 depletion results in substantial loss of 5hmC at these boundaries. In contrast, at promoter/TSS regions, Tet2 depletion results in increased 5hmC, potentially because of the redundant activity of Tet1. Together, the data point to a complex interplay between Tet1 and Tet2 in mESC, and to distinct roles for these two proteins in regulating promoter, exon, and polyadenylation site usage in cells.
225 citations
TL;DR: The first genome-wide mapping of 5-hydroxymethylcytosine in T cells during sequential steps of lineage commitment in the thymus and the periphery is presented, finding that 5hmC is enriched at gene bodies and cell type-specific enhancers, that its levels in the gene body correlate strongly with gene expression and histone modifications, and that its Levels change dynamically during the course of T-cell development and differentiation.
Abstract: The discovery of Ten Eleven Translocation proteins, enzymes that oxidize 5-methylcytosine (5mC) in DNA, has revealed novel mechanisms for the regulation of DNA methylation. We have mapped 5-hydroxymethylcytosine (5hmC) at different stages of T-cell development in the thymus and T-cell differentiation in the periphery. We show that 5hmC is enriched in the gene body of highly expressed genes at all developmental stages and that its presence correlates positively with gene expression. Further emphasizing the connection with gene expression, we find that 5hmC is enriched in active thymus-specific enhancers and that genes encoding key transcriptional regulators display high intragenic 5hmC levels in precursor cells at those developmental stages where they exert a positive effect. Our data constitute a valuable resource that will facilitate detailed analysis of the role of 5hmC in T-cell development and differentiation.
135 citations
TL;DR: The central role of predicted Ca2+-binding site 1 within the hinge region of the extracellular domain (ECD) of CaSR and its interaction with other Ca2-binding sites within the ECD in tuning functional positive homotropic cooperativity caused by changes in [Ca2+]o is reported.
33 citations
TL;DR: Functional evaluation of intercellular interactions between leukemia cells and their microenvironment identifies a selective dependency of ALL cells on stromal metabolism for a relevant subgroup of cases, providing new opportunities to develop more personalized approaches to leukemia treatment.
Abstract: // Jeannette Boutter 1, 8, * , Yun Huang 1, 8, * , Blerim Marovca 1, 8 , Andreas Vonderheit 2 , Michael A. Grotzer 1, 8 , Cornelia Eckert 3 , Gunnar Cario 4 , Bernd Wollscheid 5 , Peter Horvath 6, 7 , Beat C. Bornhauser 1, 8, * , Jean-Pierre Bourquin 1, 8, * 1 Department of Pediatric Oncology, University Children’s Hospital Zurich, Zurich, Switzerland 2 Institute of Molecular Biology, Mainz, Germany 3 Department of Pediatric Oncology/Hematology, Charite Universitatsmedizin Berlin, Germany 4 Department of Pediatrics, University Medical Centre Schleswig-Holstein, Kiel, Germany 5 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland 6 Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary 7 Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland 8 Children's Research Center (CRC), University Children's Hospital Zurich, Zurich, Switzerland * These authors contributed equally to this work Correspondence to: Jean-Pierre Bourquin, email: Jean-Pierre.Bourquin@kispi.uzh.ch Keywords: acute lymphoblastic leukemia, bone marrow stroma, microenvironment, oxidative stress, RNAi screen Received: September 02, 2014 Accepted: October 03, 2014 Published: November 01, 2014 ABSTRACT Interactions with the bone marrow microenvironment are essential for leukemia survival and disease progression. We developed an imaging-based RNAi platform to identify protective cues from bone marrow derived mesenchymal stromal cells (MSC) that promote survival of primary acute lymphoblastic leukemia (ALL) cells. Using a candidate gene approach, we detected distinct responses of individual ALL cases to RNA interference with stromal targets. The strongest effects were observed when interfering with solute carrier family 3 member 2 (SLC3A2) expression, which forms the cystine transporter x c − when associated with SLC7A11. Import of cystine and metabolism to cysteine by stromal cells provides the limiting substrate to generate and maintain glutathione in ALL. This metabolic interaction reduces oxidative stress in ALL cells that depend on stromal x c − . Indeed, cysteine depletion using cysteine dioxygenase resulted in leukemia cell death. Thus, functional evaluation of intercellular interactions between leukemia cells and their microenvironment identifies a selective dependency of ALL cells on stromal metabolism for a relevant subgroup of cases, providing new opportunities to develop more personalized approaches to leukemia treatment.
30 citations
TL;DR: The study provides evidence for the emergence of an epigenetic regulatory system through recruitment of selfish elements in a eukaryotic lineage and describes a method for simultaneous mapping of the three different species of oxi-mCs at near–base-pair resolution.
Abstract: TET/JBP enzymes oxidize 5-methylpyrimidines in DNA. In mammals, the oxidized methylcytosines (oxi-mCs) function as epigenetic marks and likely intermediates in DNA demethylation. Here we present a method based on diglucosylation of 5-hydroxymethylcytosine (5hmC) to simultaneously map 5hmC, 5-formylcytosine, and 5-carboxylcytosine at near-base-pair resolution. We have used the method to map the distribution of oxi-mC across the genome of Coprinopsis cinerea, a basidiomycete that encodes 47 TET/JBP paralogs in a previously unidentified class of DNA transposons. Like 5-methylcytosine residues from which they are derived, oxi-mC modifications are enriched at centromeres, TET/JBP transposons, and multicopy paralogous genes that are not expressed, but rarely mark genes whose expression changes between two developmental stages. Our study provides evidence for the emergence of an epigenetic regulatory system through recruitment of selfish elements in a eukaryotic lineage, and describes a method to map all three different species of oxi-mCs simultaneously.
28 citations