Epigenetics articles within Nature Communications

Featured

  • Article
    | Open Access

    Development may be plastic and influenced by parental care. Here, the authors show that experimental reduction of maternal care in the small carpenter bee leads to extensive changes in gene expression and splicing, minor changes in methylation, and greater offspring aggression and social avoidance.

    • Samuel V. Arsenault
    • , Brendan G. Hunt
    •  & Sandra M. Rehan
  • Article
    | Open Access

    The role of Polycomb Repressive Complex 1 (PRC1) is well described in development. Here, the authors investigate canonical PRC1’s regulation of transcriptional programs in breast cancer where, in addition to its repressive function, it is also recruited to oncogenic active enhancers to regulate enhancer activity and chromatin accessibility.

    • Ho Lam Chan
    • , Felipe Beckedorff
    •  & Lluis Morey
  • Article
    | Open Access

    De novo DNA methylation during mouse oogenesis occurs within transcribed regions. Here the authors investigate the role of species-specific long terminal repeats (LTRs)-initiated transcription units in regulating the oocyte methylome, identifying syntenic regions in mouse, rat and human with divergent DNA methylation associated with private LITs.

    • Julie Brind’Amour
    • , Hisato Kobayashi
    •  & Matthew C. Lorincz
  • Article
    | Open Access

    Immunoglobulin E (IgE)-mediated food allergy is a major issue that affects 2–10% of infants. Here the authors study the epigenetic regulation of the naive CD4+ T cell activation response among children with IgE-mediated food allergy finding epigenetic dysregulation in the early stages of signal transduction through the T cell receptor complex.

    • David Martino
    • , Melanie Neeland
    •  & Richard Saffery
  • Article
    | Open Access

    Epigenetic modifications are a key contributor to cell identity, and their propagation is crucial for proper development. Here the authors use a super-resolution microscopy approach to reveal how histone variants are faithfully transmitted during genome duplication, and reveal an important role for the histone chaperone ASF1 in the redistribution of parental histones.

    • Camille Clément
    • , Guillermo A. Orsi
    •  & Geneviève Almouzni
  • Article
    | Open Access

    Myelin-forming cells derive from oligodendrocyte progenitors. Here the authors identify histone arginine methyl-transferase PRMT5 as critical for developmental myelination by modulating the cross-talk between histone arginine methylation and lysine acetylation, to favor differentiation.

    • Antonella Scaglione
    • , Julia Patzig
    •  & Patrizia Casaccia
  • Article
    | Open Access

    Genomic imprinting restricts transcription to predominantly one parental allele. Here the authors perform a screen for epigenetic factors involved in paternal allelic silencing at the Kcnq1ot1 imprinted domain in mouse extraembryonic endoderm stem cells and characterize a role for specific nucleoporins in mediating Kcnq1ot1 imprinted regulation.

    • Saqib S. Sachani
    • , Lauren S. Landschoot
    •  & Mellissa R. W. Mann
  • Article
    | Open Access

    ASXL1 gene is often mutated in myeloid malignancies. Here, the authors show that mutant ASXL1 and BAP1 are in a positive feedback loop such that BAP1 induces monoubiquitination of mutant ASXL1, which in turn enhances BAP1 activity to potentiate myeloid transformation via HOXA clusters and IRF8.

    • Shuhei Asada
    • , Susumu Goyama
    •  & Toshio Kitamura
  • Article
    | Open Access

    Uhrf1 is a known regulator of heterochromatin and DNA methylation in embryonic stem cells (ESCs). Here, the authors demonstrate that Uhrf1 acts together with the Set1/COMPASS complex regulator of active transcription to promote H3K4 methylation at bivalent loci and Uhrf1 loss results in disruption of differentiation.

    • Kun-Yong Kim
    • , Yoshiaki Tanaka
    •  & In-Hyun Park
  • Article
    | Open Access

    Sex differences in placental O-linked N-acetylglucosamine transferase (OGT) activity mediate the effects of prenatal stress on neurodevelopmental programming. Here authors provide evidence that OGT confers variation in vulnerability to prenatal insults by establishing sex-specific trophoblast gene expression via regulation of H3K27me3.

    • Bridget M. Nugent
    • , Carly M. O’Donnell
    •  & Tracy L. Bale
  • Article
    | Open Access

    Histone mark reader proteins bind to particular histone modifications and regulate chromatin state. Here, Qian et al. show that the SHORT LIFE reader has a unique ability to recognize both activating and repressive histone marks and that these interactions enable SHORT LIFE to repress flowering in plants.

    • Shuiming Qian
    • , Xinchen Lv
    •  & Jiamu Du
  • Article
    | Open Access

    Single cell ATAC-seq (scATAC-seq) data reveals cellular level epigenetic heterogeneity but its application in delineating distinct subpopulations is still challenging. Here, the authors develop scABC, a statistical method for unsupervised clustering of scATAC-seq data and identification of open chromatin regions specific to cell identity.

    • Mahdi Zamanighomi
    • , Zhixiang Lin
    •  & Wing Hung Wong
  • Article
    | Open Access

    To comprehend the genetic regulatory mechanisms underlying brain-related traits in humans, Qi et al. estimate the correlation of expression and DNA methylation QTL effects in cis between blood and brain and show that using blood eQTL/mQTL data of large sample size  can increase power in gene discovery for brain-related traits and diseases.

    • Ting Qi
    • , Yang Wu
    •  & Jian Yang
  • Article
    | Open Access

    Steatosis is characterized by initial accumulation of lipids, followed by inflammation and ultimately fibrosis. Here the authors show that the histone demethylase Plant Homeodomain Finger 2 protects liver form steatosis progression by acting as a co-activator of ChREBP, thus, favouring lipid accumulation without inflammation.

    • Julien Bricambert
    • , Marie-Clotilde Alves-Guerra
    •  & Renaud Dentin
  • Article
    | Open Access

    A proportion of neurodevelopmental disorder and congenital anomaly cases remain without a genetic diagnosis. Here, the authors study aberrations of DNA methylation in such cases and find that epivariations might provide an explanation for some of these undiagnosed patients.

    • Mafalda Barbosa
    • , Ricky S. Joshi
    •  & Andrew J. Sharp
  • Article
    | Open Access

    Here the authors show that a large fraction of the tissue-specific methylation pattern is generated postnatally. These changes, which occur in response to hormone signaling, appear to play a major role in the regulation of gene expression and tissue maturation in the liver.

    • Yitzhak Reizel
    • , Ofra Sabag
    •  & Howard Cedar
  • Article
    | Open Access

    Adoptive T cell therapy using an allogeneic T cell graft is an encouraging therapeutic approach in cancer, but issues such as graft-versus-host disease can hinder applicability. Here, the authors show that DOT1L inhibition or DUSP6 overexpression in T cells attenuates graft-versus-host disease but retains anti-tumour activity in mouse models.

    • Yuki Kagoya
    • , Munehide Nakatsugawa
    •  & Naoto Hirano
  • Article
    | Open Access

    Polycomb-group proteins are key regulators of transcriptional programs that maintain cell identity. Here the authors provide evidence that PCGF5, a subunit of Polycomb Repressor Complex 1, is important for the differentiation of mouse embryonic stem cells towards a neural cell fate.

    • Mingze Yao
    • , Xueke Zhou
    •  & Hongjie Yao
  • Article
    | Open Access

    In mammalian female germ cells, parent-specific epigenetic marks are erased and the X chromosome reactivated before entry into meiosis. Here, by combining parental haplotype reconstruction with single-cell transcriptomics of human female embryonic germ cells, the authors demonstrate that epigenetic reprogramming occurs in a heterogeneous fashion and during a broad time window up to week 14.

    • Ábel Vértesy
    • , Wibowo Arindrarto
    •  & Susana M. Chuva de Sousa Lopes
  • Article
    | Open Access

    Previous studies suggest that DNA methylation is the main mechanism to silence endogenous retroviruses (ERVs) in somatic cells. Here the authors provide evidence that distinctive sets of ERVs are silenced by Setdb1 in different types of somatic cells, suggesting a general function in ERV silencing.

    • Masaki Kato
    • , Keiko Takemoto
    •  & Yoichi Shinkai
  • Article
    | Open Access

    Repression of gene transcription using CRISPR-Cas9 has been achieved in vitro but not for delivery into adult animal models. Here, the authors use AAV8 to deliver the transcriptional repressor dSaCas9KRAB to the cholesterol regulator Pcsk9, and show repression up to 24 weeks and reduced cholesterol levels in mice.

    • Pratiksha I. Thakore
    • , Jennifer B. Kwon
    •  & Charles A. Gersbach
  • Article
    | Open Access

    Lysine methylation is increasingly being implicated in the modification of non-histone proteins. Here the authors find that the methylation of DNMT1 and E2F1 are recognized by the protein L3MBTL3 and the ubiquitin E3 ligase CRL4DCAF5, which cooperatively target these methylated proteins for ubiquitin-dependent proteolysis.

    • Feng Leng
    • , Jiekai Yu
    •  & Hui Zhang
  • Article
    | Open Access

    The inactive X chromosome condenses into a bipartite structure. Here the authors use cells with allelic deletions or inversions to show that the Dxz4 locus is necessary to maintain the bipartite structure and that Dxz4 orientation controls the distribution of contacts on the inactive X chromosome.

    • G. Bonora
    • , X. Deng
    •  & C. M. Disteche
  • Article
    | Open Access

    Cytosine methyltransferases (DNMTs) often silence transposons in eukaryotic genomes. Here the authors describe the recurrent acquisition of DNMTs by transposons from two distantly-related eukaryotes and suggest that methylation of CG dinucleotides by transposon DNMTs could modify the host epigenome in dinoflagellates.

    • Alex de Mendoza
    • , Amandine Bonnet
    •  & Ryan Lister
  • Article
    | Open Access

    Anteroposterior axis extension during gastrulation is dynamically coordinated, but how this is regulated at a molecular level is unclear. Here, the authors show in zebrafish that the chromatin factor Gon4l, encoded by ugly duckling, coordinates axis extension by modulating EpCAM and Integrinα3b expression.

    • Margot L. K. Williams
    • , Atsushi Sawada
    •  & Lilianna Solnica-Krezel
  • Article
    | Open Access

    The production of nitric oxide (NO) is required for early stage embryo implantation into the uterus. Here the authors show that during differentiation of naive mouse ESCs, early production of endogenous NO leads to a mesendoderm differentiation commitment pathway by inhibiting the action of the transcriptional repressor Zeb1.

    • Chiara Cencioni
    • , Francesco Spallotta
    •  & Carlo Gaetano
  • Article
    | Open Access

    DNA methylation is associated with breast cancer risk. Here the authors measure DNA methylation in the blood of individuals from 25 Australian families with multiple cases of breast cancer but not known mutations associated with breast cancer risk to identify possible heritable methylation markers.

    • Jihoon E. Joo
    • , James G. Dowty
    •  & Yoland Antill
  • Article
    | Open Access

    Most expression QTLs (eQTLs) co-occur with a DNA methylation QTL (meQTL), suggesting a common causal variant. Here the authors analyse DNA and RNA from blood and identify eQTL-meQTL pairs likely to share a causal variant, finding that expression and methylation are often genetically co-regulated.

    • Brandon L. Pierce
    • , Lin Tong
    •  & Habibul Ahsan
  • Article
    | Open Access

    Relationships between DNA methylation and transcription, and methylation and DNA accessibility can be probed but interrogating all three in the same single cells has not been possible. Here, the authors report the first single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling.

    • Stephen J. Clark
    • , Ricard Argelaguet
    •  & Wolf Reik
  • Article
    | Open Access

    Microrchidia CW-type zinc finger protein 2 (MORC2) is an effector of epigenetic silencing by the human silencing hub (HUSH). Here the authors present the crystal structures of MORC2 and disease-causing MORC2 mutants and give mechanistic insights into how MORC2 mediates HUSH-dependent silencing.

    • Christopher H. Douse
    • , Stuart Bloor
    •  & Yorgo Modis
  • Article
    | Open Access

    FGF21 exerts beneficial metabolic effects on multiple tissues. Here the authors show that the Fgf21 gene is demethylated during the postnatal suckling period, creating an epigenetic memory that determines the responsiveness of the Fgf21 gene to inducers such as PPARα activators or fasting in adulthood.

    • Xunmei Yuan
    • , Kazutaka Tsujimoto
    •  & Yoshihiro Ogawa
  • Article
    | Open Access

    The canonical histone variant H3.1 of vascular plants contains a conserved Phe residue at position 41 that is unique to the plant kingdom. Here, Lu et al. provide evidence that H3.1Phe41 acts collaboratively with the H3.1 core domain to restrict H3.1 deposition to silent regions of the genome.

    • Li Lu
    • , Xiangsong Chen
    •  & Xuehua Zhong
  • Article
    | Open Access

    CARM1 is an arginine methyltransferase often overexpressed in human cancer. Here, the authors show that EZH2 inhibition suppresses growth in CARM1-expressing epithelial ovarian cancer, and examine the mechanism of how CARM1 promotes EZH2-mediated tumor suppressor gene silencing.

    • Sergey Karakashev
    • , Hengrui Zhu
    •  & Rugang Zhang
  • Article
    | Open Access

    Plants use multiple cues to monitor seasonal temperatures. Here, the authors show that Arabidopsis requires not only prolonged cold, but the absence of temperature spikes above 15 °C to epigenetically silence FLC during winter.

    • Jo Hepworth
    • , Rea L. Antoniou-Kourounioti
    •  & Caroline Dean
  • Article
    | Open Access

    Satellite cells can differentiate both into myocytes and brown adipocytes. Here, the authors show that the histone demethylase Lsd1 prevents adipogenic differentiation of satellite cells by repressing expression of Glis1, and that its ablation changes satellite cell fate towards brown adipocytes and delays muscle regeneration in mice.

    • Milica Tosic
    • , Anita Allen
    •  & Roland Schüle