title: Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis.
abstract: The genome-wide localization and function of endogenous Dnmt3a and Dnmt3b in adult stem cells are unknown. Here, we show that in human epidermal stem cells, the two proteins bind in a histone H3K36me3-dependent manner to the most active enhancers and are required to produce their associated enhancer RNAs. Both proteins prefer super-enhancers associated to genes that either define the ectodermal lineage or establish the stem cell and differentiated states. However, Dnmt3a and Dnmt3b differ in their mechanisms of enhancer regulation: Dnmt3a associates with p63 to maintain high levels of DNA hydroxymethylation at the center of enhancers in a Tet2-dependent manner, whereas Dnmt3b promotes DNA methylation along the body of the enhancer. Depletion of either protein inactivates their target enhancers and profoundly affects epidermal stem cell function. Altogether, we reveal novel functions for Dnmt3a and Dnmt3b at enhancers that could contribute to their roles in disease and tumorigenesis.
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain. Electronic address: lorenzo.rinaldi@irbbarcelona.org.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Rinaldi
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
authors.forename: Debayan
authors.initials: D
authors.lastname: Datta
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
authors.forename: Judit
authors.initials: J
authors.lastname: Serrat
authors.affiliation: Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
authors.forename: Lluis
authors.initials: L
authors.lastname: Morey
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
authors.forename: Guiomar
authors.initials: G
authors.lastname: Solanas
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Avgustinova
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Enrique
authors.initials: E
authors.lastname: Blanco
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
authors.forename: José Ignacio
authors.initials: JI
authors.lastname: Pons
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: David
authors.initials: D
authors.lastname: Matallanas
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: Alex
authors.initials: A
authors.lastname: Von Kriegsheim
authors.affiliation: ICREA, Passeig de Lluís Companys 23, 08010 Barcelona, Spain; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain. Electronic address: luciano.dicroce@crg.eu.
authors.forename: Luciano
authors.initials: L
authors.lastname: Di Croce
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig de Lluís Companys 23, 08010 Barcelona, Spain. Electronic address: salvador.aznar-benitah@irbbarcelona.org.
authors.forename: Salvador Aznar
authors.initials: SA
authors.lastname: Benitah
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives / Q000378:metabolism; D001483:Base Sequence; D002454:Cell Differentiation; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics; D000090205:DNA Methyltransferase 3A; D004268:DNA-Binding Proteins / Q000378:metabolism; D049308:Dioxygenases; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D000078404:Epidermal Cells; D006657:Histones / Q000378:metabolism; D006706:Homeostasis; D006801:Humans; D015603:Keratinocytes / Q000166:cytology; D008239:Lysine / Q000378:metabolism; D011485:Protein Binding; D011518:Proto-Oncogene Proteins / Q000378:metabolism; D013234:Stem Cells / Q000166:cytology* / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism; D025521:Tumor Suppressor Proteins / Q000378:metabolism; D000097584:DNA Methyltransferase 3B
chemical_list: D044503:5-Methylcytosine; D004248:DNA (Cytosine-5-)-Methyltransferases; D000090205:DNA Methyltransferase 3A; D004268:DNA-Binding Proteins; D049308:Dioxygenases; D006657:Histones; D008239:Lysine; D011518:Proto-Oncogene Proteins; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins; D000097584:DNA Methyltransferase 3B; C000717967:DNMT3A protein, human; C115051:TP63 protein, human; C011865:5-hydroxymethylcytosine; C541081:TET2 protein, human