Molecular biology articles within Nature Communications

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  • 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

    Arsenic resistance protein 2 (ARS2) plays an important role in nuclear RNA metabolism and interacts with the nuclear cap-binding complex (CBC). Here the authors present the human ARS2 structure and identify regions important for its interactions with binding partners supporting that mutually exclusive higher order CBC-ARS2 complexes are formed.

    • Wiebke Manuela Schulze
    • , Frank Stein
    •  & Stephen Cusack

  • 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

    Many SNPs associated with inflammatory bowel disease are located in non-coding genomic regions. Here, the authors perform CAGE-sequencing on descending colon biopsies of Crohn’s disease and ulcerative colitis patients to map transcription start sites and enhancer activity for analysis of regulatory regions.

    • Mette Boyd
    • , Malte Thodberg
    •  & Albin Sandelin

  • Article
    | Open Access

    The nuclear pore complex is crucial for mediating nucleocytoplasmic exchanges. Here the authors use budding yeast to reveal a mechanism responsible of maintaining nucleoporin homeostasis by sensing changes in the complex integrity and further altering the metabolism of the corresponding mRNAs.

    • Jérôme O. Rouvière
    • , Manuel Bulfoni
    •  & Benoit Palancade

  • Article
    | Open Access

    The functional role of dissociation of long ncRNAs from chromatin is poorly understood. Here, the authors provide evidence that release of the long ncRNA AROD from chromatin enhances DKK1 transcription, and suggest that this regulatory mechanism of transcription applies to a subset of long ncRNAs.

    • Evgenia Ntini
    • , Annita Louloupi
    •  & Ulf Andersson Vang Ørom

  • 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 maintenance of chromatin integrity during replication is critical for cell viability. Here the authors study how dividing cells respond to alterations in chromatin structure and find that these elicit a range of responses in the dynamics of DNA replication and consequences on replicative stress.

    • Ricardo Almeida
    • , José Miguel Fernández-Justel
    •  & María Gómez

  • Article
    | Open Access

    As a circadian organ, liver functions are regulated by circadian clock. Here, the authors present a comprehensive proteomics landscape of the mouse liver, including transcription factor binding profiles, phosphorylation and ubiquitylation patterns, nuclear and whole proteome, and the transcriptome.

    • Yunzhi Wang
    • , Lei Song
    •  & Chen Ding

  • Article
    | Open Access

    Histone variant H3.3 is incorporated at transcriptionally active genes and is associated with active marks. Here, the authors investigate H3.3 deposition during reprogramming and find that initially H3.3 helps maintain parental cell fate and is later required for establishment of the cell lineages.

    • Hai-Tong Fang
    • , Chadi A. EL Farran
    •  & Yuin-Han Loh

  • Article
    | Open Access

    Dinoflagellates are known to use dinoflagellate-viral-nucleoproteins (DVNPs) in place of histones, yet this evolutionary transition is not well understood. Here, Irwin et al. use yeast expressing DVNP to show that DVNP displaces histones and that histone reduction allows cells to cope with DVNP.

    • Nicholas A. T. Irwin
    • , Benjamin J. E. Martin
    •  & LeAnn J. Howe

  • Article
    | Open Access

    Plants use nucleotide excision repair to maintain genome integrity in response to damage caused by stresses such as UV radiation. Here Oztas et al. use genome-wide profiling to show that excision repair in Arabidopsis is strongly coupled to transcription and reflects circadian patterns of gene expression.

    • Onur Oztas
    • , Christopher P. Selby
    •  & Ogun Adebali

  • Article
    | Open Access

    Hypoxia-inducible transcription factor HIF-1α promotes glycolysis allowing cell survival under stress. Here the authors show, using both cell lines and animal models, that in cutaneous squamous cell carcinoma HOXA9 acts as a tumor suppressor and inhibits glycolysis by associating with CRIP2 to repress HIF-1α binding to target genes.

    • Liang Zhou
    • , Yinghui Wang
    •  & Zhenhua Ding

  • Article
    | Open Access

    RNA synthesis by bacterial RNA polymerase is interrupted by pauses but their role in RNA synthesis is poorly understood. Here the authors use single-molecule FRET and biochemical analysis to show that pausing regulates branching between the abortive and productive outcomes of initial transcription.

    • David Dulin
    • , David L. V. Bauer
    •  & Achillefs N. Kapanidis

  • Article
    | Open Access

    The heat shock protein 90 (Hsp90) chaperone undergoes large conformational changes during its functional cycle. Here the authors combine in vivo, biochemical, biophysical and computational approaches and provide insights into the allosteric regulation of Hsp90 by identifying and characterizing a switch point in the Hsp90 middle domain.

    • Daniel Andreas Rutz
    • , Qi Luo
    •  & Johannes Buchner

  • Article
    | Open Access

    Although CTCF binding has been implicated in the formation of topologically associated domains (TADs) the mechanisms folding the genome into TADs are not fully understood. Here the authors investigate the TAD boundary on lncRNA locus Firre, which has ~ 15 CTCF binding sites, and its organization.

    • A. Rasim Barutcu
    • , Philipp G. Maass
    •  & John L. Rinn

  • 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

    Feingold syndrome is a skeletal dysplasia caused by mutations in MYCN or MIR17HG, but it is not clear if these mutations lead to pathology via a common molecular mechanism. Here, the authors show that mutations in MIR17HG lead to upregulated TGF-β signaling in limb mesenchymal cells, while mutations in MYCN downregulate PI3K signaling.

    • Fatemeh Mirzamohammadi
    • , Anastasia Kozlova
    •  & Tatsuya Kobayashi

  • 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

    Nucleosomes are dynamic and can move along DNA in an uncatalyzed manner but little is known about the mechanisms of histone octamer translocation. Here the authors present cryo-EM structures of nucleosomes in differently organized histone octamer and DNA states and show how histone octamers translocate DNA.

    • Silvija Bilokapic
    • , Mike Strauss
    •  & Mario Halic

  • Article
    | Open Access

    Glucocorticoid receptor (GR) regulates immunity and inflammation but the mechanisms by which GR represses proinflammatory genes are still being debated. Here the authors use a multidisciplinary approach and show that GR binds to a cryptic site within genome-wide NFκB DNA response elements to repress pro-inflammatory genes.

    • William H. Hudson
    • , Ian Mitchelle S. de Vera
    •  & Eric A. Ortlund

  • Article
    | Open Access

    Promyelocytic leukemia protein (PML) is a scaffolding protein that organizes PML nuclear bodies. Here the authors present the tetrameric crystal structure of the PML RING domain and show that RING tetramerization is functionally important for nuclear body formation and PML sumoylation.

    • Pengran Wang
    • , Shirine Benhenda
    •  & Guoyu Meng

  • 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

    Histone chaperone ASF1A is often dysregulated in cancers, however the regulation of its abundance is unclear. Here, the authors show that USP52 promotes ASF1A stability through deubiquitination while impairment of this stability reduces breast tumorigenesis and confers sensitivity to DNA damage.

    • Shangda Yang
    • , Ling Liu
    •  & Lei Shi

  • Article
    | Open Access

    Activation-induced deaminase (AID) is important for inducing desirable mutations at the B cell receptor genes for effective antibody responses. Here the authors show that three key arginine residues of AID link AID-chromatin association with transcription elongation to license AID for specific mutagenesis in B cells.

    • Stephen P. Methot
    • , Ludivine C. Litzler
    •  & Javier M. Di Noia

  • Article
    | Open Access

    Migratory locusts shift between aggregating together during gregarious phases and living individually during solitary phases. Here, the authors find that the D1-like dopamine receptor regulates the olfactory attraction underlying this behavioral switch via microRNA-9a and adenylyl cyclase.

    • Xiaojiao Guo
    • , Zongyuan Ma
    •  & Le Kang

  • Article
    | Open Access

    Varicella-zoster virus (VZV) establishes lifelong infection in the majority of the population, but mechanisms underlying latency remain unclear. Here, the authors use ultra-deep RNA sequencing, enriched for viral RNAs, of latently infected human trigeminal ganglia and identify a spliced, latency-associated VZV mRNA.

    • Daniel P. Depledge
    • , Werner J. D. Ouwendijk
    •  & Judith Breuer

  • Article
    | Open Access

    Type I interferon signaling is critical for the control of infection. Here the authors show that zinc finger RNA-binding protein (ZFR) can control type I interferon responses, and that this control is itself regulated by distinct ZFR truncation patterns that differ between monocytes and macrophages.

    • Nazmul Haque
    • , Ryota Ouda
    •  & J. Robert Hogg

  • Article
    | Open Access

    The NuA4 histone acetyltransferase complex is important for gene regulation, DNA repair processes and cell cycle progression. Here the authors give molecular insights into the NuA4 complex by presenting the cryo-EM structures of the NuA4 TEEAA (Tra1, Eaf1, Eaf5, actin, and Arp4) and TEEAA-piccolo NuA4 assemblies.

    • Xuejuan Wang
    • , Salar Ahmad
    •  & Gang Cai

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