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Chromosome structure is a crucial regulatory factor for a wide range of nuclear processes. Chromosome conformation capture (3C)-based experiments combined with computational modelling are pivotal for unveiling 3D chromosome structure. Here, we introduce TADdyn, a tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements of genomic loci in a completely data-driven way. We apply TADdyn on in situ Hi-C time-course experiments studying the reprogramming of murine B cells to pluripotent cells, and characterize the structural rearrangements that take place upon changes in the transcriptional state of 21 genomic loci of diverse expression dynamics. By measuring various structural and dynamical properties, we find that during gene activation, the transcription starting site contacts with open and active regions in 3D chromatin domains. We propose that these 3D hubs of open and active chromatin may constitute a general feature to trigger and maintain gene transcription. ; This work was partially supported by the European Research Council under the 7th Framework Program FP7/2007-2013 (ERC grant agreement 609989 to M.A.M-R. and T.G.), the European Union's Horizon 2020 research and innovation programme (grant agreement 676556 to M.A.M-R.) and the Spanish Ministerio de Ciencia e Innovación (BFU2013-47736-P and BFU2017-85926-P to M.A.M-R. as well as IJCI-2015-23352 to I.F.). R.S. is supported by the Netherlands Organization for Scientific Research (VENI 91617114) and an Erasmus MC Fellowship. We also knowledge support from "Centro de Excelencia Severo Ochoa 2013-2017", SEV-2012-0208 the Spanish ministry of Science and Innovation to the EMBL partnership and the CERCA Programme/Generalitat de Catalunya to the CRG. We also acknowledge support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement and the Co-financing by the Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program to CNAG

The physical microenvironment regulates cell behavior during tissue development and homeostasis. How single cells decode information about their geometrical shape under mechanical stress and physical space constraints within tissues remains largely unknown. Here, using a zebrafish model, we show that the nucleus, the biggest cellular organelle, functions as an elastic deformation gauge that enables cells to measure cell shape deformations. Inner nuclear membrane unfolding upon nucleus stretching provides physical information on cellular shape changes and adaptively activates a calcium-dependent mechanotransduction pathway, controlling actomyosin contractility and migration plasticity. Our data support that the nucleus establishes a functional module for cellular proprioception that enables cells to sense shape variations for adapting cellular behavior to their microenvironment. ; Funding: V.V. acknowledges support from the ICFOstepstone PhD Programme funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement 665884. F.P. and Q.T.-R. acknowledge grants funded by Ministerio de Ciencia, Innovación y Universidades and Fondo Social Europeo (FSE) (BES2017-080523-SO, PRE2018-084393). M.A.V. acknowledges support from the Spanish Ministry of Science, Education and Universities through grant RTI2018-099718-B-100 and an institutional "Maria de Maeztu Programme" for Units of Excellence in R&D (CEX2018-000792-M) and FEDER funds.S.W. and M.K. acknowledge support from the Spanish Ministry of Economy and Competitiveness through the Severo Ochoa program for Centres of Excellence in R&D (CEX2019-000910-S), from Fundació Privada Cellex, Fundación Mig-Puig, and from Generalitat de Catalunya through the CERCA program and LaserLab (654148). M.K. acknowledges support through Spanish Ministry of Economy and Competitiveness (RYC-2015-17935, EQC2018-005048-P, AEI-010500-2018-228, and PGC2018-097882-A-I00),Generalitat de Catalunya (2017 SGR 1012), the ERC (715243), and the HFSPO (CDA00023/2018). S.W. acknowledges support through the Spanish Ministry of Economy and Competitiveness via MINECO's Plan Nacional (PGC2018-098532-A-I00). V.R. acknowledges support from the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the CERCA Programme/Generalitat de Catalunya, and the MINECO's Plan Nacional (BFU2017-86296-P)

S'adjunta carta al director publicada al Vol. 99 núm. 7 ; Lymphoma patients with persistent disease undergoing autologous transplantation have a very poor prognosis in the rituximab era. The addition of radioimmunotherapy to the conditioning regimen may improve the outcome for these patients. In a prospective, phase 2 study, we evaluated the safety and efficacy of the addition of 90Y-ibritumomab tiuxetan to the conditioning chemotherapy in patients with refractory diffuse large B-cell lymphoma. Thirty patients with induction failure (primary refractory; n=18) or refractory to salvage immunochemotherapy at relapse (n=12) were included in the study. The median age of the patients was 53 years (range, 25-67). All patients were given 90Y-ibritumomab tiuxetan at a fixed dose of 0.4 mCi/kg (maximum dose 32 mCi) 14 days prior to the preparative chemotherapy regimen. Histological examination showed that 22 patients had de novo diffuse large B-cell lymphoma and eight had transformed diffuse large B-cell lymphoma. All patients had persistent disease at the time of transplantation, with 25 patients considered to be chemorefractory. The median time to neutrophil recovery (>500 white blood cells/μL) was 11 days (range, 9-21), while the median time to platelet recovery (>20,000 platelets/μL) was 13 days (range, 11-35). The overall response rate at day +100 was 70% (95% CI, 53.6-86.4) with 60% (95% CI, 42.5-77.5) of patients obtaining a complete response. After a median follow-up of 31 months for alive patients (range, 16-54), the estimated 3-year overall and progression-free survival rates are 63% (95% CI, 48-82) and 61% (95% CI, 45-80), respectively. We conclude that autologous transplantation with conditioning including 90Y-ibritumomab tiuxetan is safe and results in a very high response rate with promising survival in this group of patients with refractory diffuse large B-cell lymphoma with a very poor prognosis. Study registered at European Union Drug Regulating Authorities Clinical Trials (EudraCT) N. 2007-003198-22.

Glioblastoma multiforme is resistant to conventional anti-tumoral treatments due to its infiltrative nature and capability of relapse; therefore, research efforts focus on characterizing gliomagenesis and identifying molecular targets useful on therapy. New therapeutic strategies are being tested in patients, such as Histone deacetylase inhibitors (HDACi) either alone or in combination with other therapies. Here two HDACi included in clinical trials have been tested, suberanilohydroxamic acid (SAHA) and valproic acid (VPA), to characterize their effects on glioma cell growth in vitro and to determine the molecular changes that promote cancer cell death. We found that both HDACi reduce glioma cell viability, proliferation and clonogenicity. They have multiple effects, such as inducing the production of reactive oxygen species (ROS) and activating the mitochondrial apoptotic pathway, nevertheless cell death is not prevented by the pan-caspase inhibitor Q-VD-OPh. Importantly, we found that HDACi alter cell cycle progression by decreasing the expression of G2 checkpoint kinases Wee1 and checkpoint kinase 1 (Chk1). In addition, HDACi reduce the expression of proteins involved in DNA repair (Rad51), mitotic spindle formation (TPX2) and chromosome segregation (Survivin) in glioma cells and in human glioblastoma multiforme primary cultures. Therefore, HDACi treatment causes glioma cell entry into mitosis before DNA damage could be repaired and to the formation of an aberrant mitotic spindle that results in glioma cell death through mitotic catastrophe-induced apoptosis. ; This work was supported by the Spanish Ministry of Health grant ISCIII and the European Fund for Regional Development (FEDER) PS09/00140 to ML, ISCIII-PI080790 to JH and Programa de Suport a Grups de Recerca from the Government of Catalonia (AGAUR) (2009-SGR-346) to ML, DS and JXC.

Bi-species, fusion-mediated, somatic cell reprogramming allows precise, organism-specific tracking of unknown lineage drivers. The fusion of Tcf7l1-/- murine embryonic stem cells with EBV-transformed human B cell lymphocytes, leads to the generation of bi-species heterokaryons. Human mRNA transcript profiling at multiple time points permits the tracking of the reprogramming of B cell nuclei to a multipotent state. Interrogation of a human B cell regulatory network with gene expression signatures identifies 8 candidate master regulator proteins. Of these 8 candidates, ectopic expression of BAZ2B, from the bromodomain family, efficiently reprograms hematopoietic committed progenitors into a multipotent state and significantly enhances their long-term clonogenicity, stemness, and engraftment in immunocompromised mice. Unbiased systems biology approaches let us identify the early driving events of human B cell reprogramming. ; This work was supported by Human Frontier Science Program Grant 2010 (to M.P.C. and A.C.); the European Union's Horizon 2020 Research and Innovation Programme (CellViewer no. 686637 to M.P.C); Ministerio de Ciencia e Innovación grant no. BFU2017-86760-P (AEI/FEDER, UE); AGAUR grant from Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya ( 2017 SGR 689 to M.P.C.); Guangzhou Key Projects of Brain Science and Brain-Like Intelligence Technology ( 20200730009 to M.P.C.); Juan de la Cierva Fellowship (to K.A.); BIST Master Fellowship (to X.T.); and the R35CA197745 outstanding NCI investigator award to A.C. We acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa , and the CERCA Programme (to M.P.C.), and the two instrumentation grants S10OD012351 and S10OD021764 to A.C. supporting the analytical work

Nucleosomes form heterogeneous groups in vivo, named clutches. Clutches are smaller and less dense in mouse embryonic stem cells (ESCs) compared to neural progenitor cells (NPCs). Using coarse-grained modeling of the pluripotency Pou5f1 gene, we show that the genome-wide clutch differences between ESCs and NPCs can be reproduced at a single gene locus. Larger clutch formation in NPCs is associated with changes in the compaction and internucleosome contact probability of the Pou5f1 fiber. Using single-molecule tracking (SMT), we further show that the core histone protein H2B is dynamic, and its local mobility relates to the structural features of the chromatin fiber. H2B is less stable and explores larger areas in ESCs compared to NPCs. The amount of linker histone H1 critically affects local H2B dynamics. Our results have important implications for how nucleosome organization and H2B dynamics contribute to regulate gene activity and cell identity. ; This work was supported by a University of Pennsylvania Epigenetics Pilot Award (M.L.); an NSF Center for Engineering and Mechanobiology (CEMB) Pilot Award (M.L.); a Linda Pechenik Montague Investigator Award (M.L.); the European Union's Horizon 2020 Research and Innovation Programme (CellViewer grant 686637 to M.L., M.P.C., and E.M.); Ministerio de Ciencia, Innovación y Universidades ( BFU2017-86760-P [AEI/FEDER, UE]) and Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya (AGAUR grant 2017 SGR 689 to M.P.C.); National NSFC grant 319711771003712 (M.P.C.); National Institutes of Health , National Institute of General Medical Sciences awards R01-GM055264 and R35-GM122562 ; People Program (Marie Curie Actions) FP7/2007–2013 under REA grant 608959 (M.V.N.); and Juan de la Cierva-Incorporación 2017 (M.V.N.)

Collisions between the DNA replication machinery and co-transcriptional R-loops can impede DNA synthesis and are a major source of genomic instability in cancer cells. How cancer cells deal with R-loops to proliferate is poorly understood. Here we show that the ATP-dependent chromatin remodelling INO80 complex promotes resolution of R-loops to prevent replication-associated DNA damage in cancer cells. Depletion of INO80 in prostate cancer PC3 cells leads to increased R-loops. Overexpression of the RNA:DNA endonuclease RNAse H1 rescues the DNA synthesis defects and suppresses DNA damage caused by INO80 depletion. R-loops co-localize with and promote recruitment of INO80 to chromatin. Artificial tethering of INO80 to a LacO locus enabled turnover of R-loops in cis. Finally, counteracting R-loops by INO80 promotes proliferation and averts DNA damage-induced death in cancer cells. Our work suggests that INO80-dependent resolution of R-loops promotes DNA replication in the presence of transcription, thus enabling unlimited proliferation in cancers. ; Work in MPC lab is supported by Liverpool University, Newcastle University and a Wellcome Institutional Support Fund Award. Work done in A.G.'s lab was supported by Bulgarian National Science Fund grant # DN11/17. Work in the PP lab is supported by grants from the Agence Nationale pour la Recherche (ANR), the Ligue Contre le Cancer (équipe labellisée), SIRIC Montpellier Cancer (INCa Inserm DGOS 12553) and the MSDAvenir fund. ULM was funded by the Royal Society RG170342. IHL was funded from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754510. Work in the DR lab is supported by a Wellcome Trust Seed Award in Science (206103/Z/17/Z). Work of JMGH was funded by a Wellcome Trust Investigator Award [106951/Z/15/Z] and a Royal Society Wolfson Research Merit Award

The origin of eukaryotes stands as a major conundrum in biology. Current evidence indicates that the last eukaryotic common ancestor already possessed many eukaryotic hallmarks, including a complex subcellular organization. In addition, the lack of evolutionary intermediates challenges the elucidation of the relative order of emergence of eukaryotic traits. Mitochondria are ubiquitous organelles derived from an alphaproteobacterial endosymbiont. Different hypotheses disagree on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host are debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Most competing scenarios can be roughly grouped into either mito-early, which consider the driving force of eukaryogenesis to be mitochondrial endosymbiosis into a simple host, or mito-late, which postulate that a significant complexity predated mitochondrial endosymbiosis. Here we provide evidence for late mitochondrial endosymbiosis. We use phylogenomics to directly test whether proto-mitochondrial proteins were acquired earlier or later than other proteins of the last eukaryotic common ancestor. We find that last eukaryotic common ancestor protein families of alphaproteobacterial ancestry and of mitochondrial localization show the shortest phylogenetic distances to their closest prokaryotic relatives, compared with proteins of different prokaryotic origin or cellular localization. Altogether, our results shed new light on a long-standing question and provide compelling support for the late acquisition of mitochondria into a host that already had a proteome of chimaeric phylogenetic origin. We argue that mitochondrial endosymbiosis was one of the ultimate steps in eukaryogenesis and that it provided the definitive selective advantage to mitochondria-bearing eukaryotes over less complex forms. ; T.G. group research is funded in part by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161), a grant from the European Union FP7 FP7-PEOPLE-2013-ITN-606786 and a grant from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC (Grant Agreement number ERC-2012-StG-310325)

MOTIVATION: The evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism. RESULTS: We present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons. AVAILABILITY AND IMPLEMENTATION: https://github.com/Gabaldonlab/EvolClust/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. ; This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) for the EMBL partnership and grants 'Centro de Excelencia Severo Ochoa' SEV-2012-0208 and BFU2015-67107 cofounded by European Regional Development Fund (ERDF); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857 and grant from the European Union's Horizon 2020 research and innovation programme under the grant agreement ERC-2016-724173 the Marie Sklodowska-Curie grant agreement No H2020-MSCA-ITN-2014-642095. The group also receives support from a INB Grant (PT17/0009/0023–ISCIII-SGEFI/ERDF)

Protein arginine deimination leading to the non-coded amino acid citrulline remains a key question in the field of post-translational modifications ever since its discovery by Rogers and Simmonds in 1958. Citrullination is catalyzed by a family of enzymes called peptidyl arginine deiminases (PADIs). Initially, increased citrullination was associated with autoimmune diseases, including rheumatoid arthritis and multiple sclerosis, as well as other neurological disorders and multiple types of cancer. During the last decade, research efforts have focused on how citrullination contributes to disease pathogenesis by modulating epigenetic events, pluripotency, immunity and transcriptional regulation. However, our knowledge regarding the functional implications of citrullination remains quite limited, so we still do not completely understand its role in physiological and pathological conditions. Here, we review the recently discovered functions of PADI2-mediated citrullination of the C-terminal domain of RNA polymerase II in transcriptional regulation in breast cancer cells and the proposed mechanisms to reshape the transcription regulatory network that promotes cancer progression. ; This work was supported by Spanish MEC (SAF2016–75006), the Catalan Government (2017–2019 SGR 747_MBeato), and the European Research Council Synergy Grant "4DGenome" (609989). Also, we acknowledge the support of the Spanish Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa" and the CERCA Programme/Generalitat de Catalunya"

Since the recent discovery of taxol and other taxanes in Corylus avellana, this plant species has attracted interest as a potential new source of these compounds. However, its low taxane content in comparison with Taxus spp. has restricted research to analytical identification or global quantitation. A feasible and sensitive method based on liquid chromatography-tandem mass spectrometry using a triple quadrupole analyzer was developed for the analysis of taxol and four other taxanes in a Corylus avellana cell suspension medium. Taxanes were extracted from the cell culture medium with dichloromethane and analyzed using electrospray ionization and quantified by multiple-reaction monitoring mode. Methanol and matrix-matching calibration curves using docetaxel as the internal standard were analyzed. Linearity was confirmed over the whole calibration range (0.3–2.1 μg mL−1). The inter- and intra-day precision of taxanes ranged from 80% to 120% and the recovery rates were higher than 80%. Limits of detection were between 0.24–38 ng mL−1 and the limits of quantification were between 0.8–125 ng mL−1. The low detection and quantitation values obtained allowed us to detect small quantities of the released taxanes (120 ng mL−1 of B, 151 ng mL−1 of CF and 105 ng mL−1 of T), which correspond to about 0.5 ng mL−1 of each taxane, in the 20 mL Corylus avellana cell suspension culture medium extracted, even at the beginning of the culture. These results were confirmed by high resolution mass spectrometry. ; This research has been supported by a grant from the Spanish MEC (BIO2011-29856-CO2-01) and a grant from the Catalan Government (2014SGR215). A. Gallego was supported by a fellowship from the University Pompeu Fabra.

A high level of subcellular compartmentalization is a hallmark of eukaryotic cells. This intricate internal organization was present already in the common ancestor of all extant eukaryotes, and the determination of the origins and early evolution of the different organelles remains largely elusive. Organellar proteomes are determined through regulated pathways that target proteins produced in the cytosol to their final subcellular destinations. This internal sorting of proteins can vary across different physiological conditions, cell types and lineages. Evolutionary retargeting - the alteration of a subcellular localization of a protein in the course of evolution - has been rampant in eukaryotes and involves any possible combination of organelles. This fact adds another layer of difficulty to the reconstruction of the origins and evolution of organelles. In this review we discuss current themes in relation to the origin and evolution of organellar proteomes. Throughout the text, a special focus is set on the evolution of mitochondrial and peroxisomal proteomes, which are two organelles for which extensive proteomic and evolutionary studies have been performed. ; TG group research is funded in part by a grant from the Spanish ministry of Economy and Competitiveness (BIO2012-37161), a Grant from the Qatar National Research Fund grant (NPRP 5-298-3-086), and a grant from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ ERC (Grant Agreement n. ERC-2012-StG-310325).

The Notch pathway is an essential regulator of cell proliferation and differentiation during development. Its involvement in insect oogenesis has been examined in insect species with meroistic ovaries, and it is known to play a fundamental role in cell fate decisions and the induction of the mitosis-to-endocycle switch in follicular cells (FCs). This work reports the functions of the main components of the Notch pathway (Notch and its ligands Delta and Serrate) during oogenesis in Blattella germanica, a phylogenetically basal species with panoistic ovary. As is revealed by RNAi-based analyses, Notch and Delta were found to contribute towards maintaining the FCs in an immature, non-apoptotic state. This ancestral function of Notch appears in opposition to the induction of transition from mitosis to endocycle that Notch exerts in Drosophila melanogaster, a change in the Notch function that might be in agreement with the evolution of the insect ovary types. Notch was also shown to play an active role in inducing ovarian follicle elongation via the regulation of the cytoskeleton. In addition, Delta and Notch interactions were seen to determine the differentiation of the posterior population of FCs. Serrate levels were found to be Notch-dependent and are involved in the control of the FC programme, although they would appear to play no crucial role in panoistic ovary oogenesis. ; This work was supported by the Ministry of Science and Innovation, Spain (grant no. BFU2011-22404), by the Catalan Regional Government (grant no. 2014 SGR 619), and by CONICYT + PAI Concurso Nacional Apoyo al Retorno de Investigadores desde el Extranjero, Convocatoria 2013 + 821320046. P.I. is the recipient of a postdoctoral research grant (BECAS CHILE from CONICYT. N.E. is the recipient of a JAE pre-doctoral research grant from the Consejo Superior de Investigaciones Científicas (CSIC)

HIV viral reservoirs are established very early during infection. Resident memory T cells (TRM) are present in tissues such as the lower female genital tract, but the contribution of this subset of cells to the pathogenesis and persistence of HIV remains unclear. Here, we show that cervical CD4+TRM display a unique repertoire of clusters of differentiation, with enrichment of several molecules associated with HIV infection susceptibility, longevity and self-renewing capacities. These protein profiles are enriched in a fraction of CD4+TRM expressing CD32. Cervical explant models show that CD4+TRM preferentially support HIV infection and harbor more viral DNA and protein than non-TRM. Importantly, cervical tissue from ART-suppressed HIV+ women contain high levels of viral DNA and RNA, being the TRM fraction the principal contributor. These results recognize the lower female genital tract as an HIV sanctuary and identify CD4+TRM as primary targets of HIV infection and viral persistence. Thus, strategies towards an HIV cure will need to consider TRM phenotypes, which are widely distributed in tissues. ; We would like to thank all the patients who participated in the study and their providers. We thank José L. Poza, Mª Elena Suárez, Mª Assumpció Pérez-Benavente and Cristina Carrato for referral of patients and sample collection, Irian Lorencés and Laia Pérez-Roca from the Tumor Bank of the IGTP-HUGTiP for sample management, Alba Ruiz and Ruth Peña for generating the viral stock R5-Bal and Gerard Requena from the Flow Cytometry Facility at the IGTP for excellent technical assistance, as well as Isabel Crespo from the Flow Cytometry Platform at the IDIBAPS for her excellent technical assistance on Amnis technology. This work was primarily supported by grants from the Spanish "Ministerio de Economía y Competitividad, Instituto de Salud Carlos III" (ISCIII, PI14/01235 and PI17/01470) and a fellowship award from the Dexeus foundation for women's health research to M.G., grants R21AI118411 and SAF2015-67334-R (from the Spanish Secretariat of Science and Innovation and FEDER funds) to M.J.B and grants from the ISCIII (PI14/01058 and PI17/00164) to J.G.P. M.G., M.J.B., and. J.G.P. are supported by the Spanish AIDS network Red Temática Cooperativa de Investigación en SIDA (RD16/0025/0007) M.G. is currently supported by the "Pla estratègic de recerca i innovació en salut" (PERIS, SLT002/16/00353), from the Catalan government, while the Miguel Servet program from the ISCIII supports M.J.B. (CP17/00179) and J.G.P. (CP15/00014).

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. ; The S.A.B. laboratory research is supported by the European Research Council (ERC), the Worldwide Cancer Research Foundation, the Foundation La Marató de TV3, the Spanish Ministry of Economy and Development, the Foundation Vencer el Cancer (''Beat Cancer''), the Government of Cataluña (SGR and Mario Salvia' grants), the Foundation Fundación Botín, and the Institute for Research in Biomedicine (IRB-Barcelona). L.R. is a La Caixa Foundation Ph.D. fellow. G.S. was supported by an AXA postdoctoral fellowship. IRB Barcelona is the recipient of a Severo Ochoa Award of Excellence from MINECO (Government of Spain). L.D.C. was supported by grants from the Spanish Ministerio de Educación y Ciencia (SAF2013-48926-P) and the European Commission's 7th Framework Program 4DCellFate grant number 277899. We are grateful to the Common Fund's Epigenomic Program from the NIH (USA) for providing the bisulphite whole genome sequencing data of human EpSCs