Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers.
Enhancers are developmentally controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. In this study, we show by genome-wide mapping that the newly discovered deoxyribonucleic acid (DNA) modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells and during adipocyte differentiation of mouse 3T3-L1 cells. Functional annotation reveals that regions gaining 5hmC are associated with genes expressed either in neural tissues when P19 cells undergo neural differentiation or in adipose tissue when 3T3-L1 cells undergo adipocyte differentiation. Furthermore, distal regions gaining 5hmC together with H3K4me2 and H3K27ac in P19 cells behave as differentiation-dependent transcriptional enhancers. Identified regions are enriched in motifs for transcription factors regulating specific cell fates such as Meis1 in P19 cells and PPARγ in 3T3-L1 cells. Accordingly, a fraction of hydroxymethylated Meis1 sites were associated with a dynamic engagement of the 5-methylcytosine hydroxylase Tet1. In addition, kinetic studies of cytosine hydroxymethylation of selected enhancers indicated that DNA hydroxymethylation is an early event of enhancer activation. Hence, acquisition of 5hmC in cell-specific distal regulatory regions may represent a major event of enhancer progression toward an active state and participate in selective activation of tissue-specific genes.
Université de Rennes 1, CNRS UMR6290, Team SP@RTE, Campus de Beaulieu, Rennes F-35042, France.
Aurélien A
AA
Sérandour
Stéphane
S
Avner
Frédérik
F
Oger
Maud
M
Bizot
Frédéric
F
Percevault
Céline
C
Lucchetti-Miganeh
Gaëlle
G
Palierne
Céline
C
Gheeraert
Frédérique
F
Barloy-Hubler
Christine Le
CL
Péron
Thierry
T
Madigou
Emmanuelle
E
Durand
Philippe
P
Froguel
Bart
B
Staels
Philippe
P
Lefebvre
Raphaël
R
Métivier
Jérôme
J
Eeckhoute
Gilles
G
Salbert
D041721:3T3-L1 Cells; D044503:5-Methylcytosine / Q000031:analogs & derivatives; D000818:Animals; D001665:Binding Sites; D002454:Cell Differentiation / Q000235:genetics*; D045744:Cell Line, Tumor; D002843:Chromatin / Q000378:metabolism; D003596:Cytosine / Q000031:analogs & derivatives / Q000378:metabolism; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D018398:Homeodomain Proteins / Q000378:metabolism; D051379:Mice; D000075064:Myeloid Ecotropic Viral Integration Site 1 Protein; D009363:Neoplasm Proteins / Q000378:metabolism; D055495:Neurogenesis / Q000235:genetics; D011518:Proto-Oncogene Proteins / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism
D002843:Chromatin; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; C000616392:Meis1 protein, mouse; D000075064:Myeloid Ecotropic Viral Integration Site 1 Protein; D009363:Neoplasm Proteins; D011518:Proto-Oncogene Proteins; C540839:TET1 protein, mouse; D014157:Transcription Factors; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine