Transcriptional regulatory elements articles within Nature Communications

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  • Article
    | Open Access

    Transcription factors of the AP-1 family can play diverse roles despite recognizing the same DNA sequence. Here the authors investigate the DNA binding activities of AP-1 members in mouse macrophages and apply a machine learning approach to identify motifs predicted to drive factor-specific binding profiles.

    • Gregory J. Fonseca
    • , Jenhan Tao
    •  & Christopher K. Glass

  • Article
    | Open Access

    Hydra regenerate various body parts on amputation by activation of the appropriate organiser, but how head formation is controlled is unclear. Here, the authors identify the transcription factor Sp5 as restricting head formation, by being activated by beta-catenin and then acting as a repressor of Wnt3.

    • Matthias C. Vogg
    • , Leonardo Beccari
    •  & Brigitte Galliot

  • Article
    | Open Access

    Quantification of genomic responses to environmental stimuli by current genome-scale assays is limited to indirect measurements or requires knowledge of the transcription factors involved. Here, the authors use genome-wide high-throughput reporter assays to agnostically map enhancer activity in response to glucocorticoid treatment across the human genome.

    • Graham D. Johnson
    • , Alejandro Barrera
    •  & Timothy E. Reddy

  • Article
    | Open Access

    Transcription preinitiation complex assembly begins with the recognition of the gene promoter by the TATA-box Binding Protein-containing TFIID complex. Here the authors present a Cryo-EM structure of promoter-bound yeast TFIID complex, providing a detailed view of its subunit organization and promoter DNA contacts.

    • Olga Kolesnikova
    • , Adam Ben-Shem
    •  & Gabor Papai

  • Article
    | Open Access

    AUXIN RESPONSE FACTORS (ARFs) are a family of plant-specific transcriptional factors involved in auxin signaling. Here, the authors adapt DAP-seq technology to show the binding landscape of 14 maize ARFs and reveal class-specific binding properties and transcriptional coordination by ARFs from different classes.

    • Mary Galli
    • , Arjun Khakhar
    •  & Andrea Gallavotti

  • Article
    | Open Access

    Chr3q26 rearrangements cause overexpression of EVI1 and associate with myeloid neoplasms, but the mechanism behind this association is unclear. Here, using a novel mouse model they show that EVI1 causes premalignant myeloid expansion with suppression of other lineages through upregulation of Spi1/PU.1.

    • Edward Ayoub
    • , Michael P. Wilson
    •  & Archibald S. Perkins

  • Article
    | Open Access

    The role of the genome structure in the establishment of the embryonic and trophoblast lineages is still not well understood. Here the authors perform promoter capture Hi-C in mouse trophoblast and embryonic stem cells and find divergent networks of repressive and active chromatin interactions between the two lineages.

    • Stefan Schoenfelder
    • , Borbala Mifsud
    •  & Miguel R. Branco

  • Article
    | Open Access

    Enhancers and promoters are different types of regulatory elements with shared architectural and functional features. Here the authors perform integrated cross-mammalian analyses of DNase hypersensitivity, chromatin modification and transcriptional data, to provide evidence of regulatory repurposing during evolution.

    • Francesco N. Carelli
    • , Angélica Liechti
    •  & Henrik Kaessmann

  • Article
    | Open Access

    Tightly regulated promoters with strong inducibility and scalability are highly desirable for biological applications. Here the authors describe ‘Jungle Express’, a EilR repressor-based broad host system activated by cationic dyes.

    • Thomas L. Ruegg
    • , Jose H. Pereira
    •  & Michael P. Thelen

  • Article
    | Open Access

    HLX transcription factor regulates haematopoietic stem and progenitor cell (HSPC) differentiation and is overexpressed in acute myeloid leukemia. Here the authors show that HLX overexpression leads to myeloid differentiation block in zebrafish and human HSPCs by direct regulation of metabolic pathways.

    • Indre Piragyte
    • , Thomas Clapes
    •  & Eirini Trompouki

  • Article
    | Open Access

    CRISPRa is an attractive tool for cellular reprogramming due to its multiplexing capacity and direct targeting of genomic loci. Here the authors demonstrate the reprogramming of human fibroblasts into iPSCs, which is enhanced by targeting a conserved Alu-motif.

    • Jere Weltner
    • , Diego Balboa
    •  & Timo Otonkoski

  • 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

    Very little is known regarding the molecular mechanisms involved in gastric cancer development. Here the authors show estrogen-related receptor gamma (ESRRG) is a tumor suppressor in gastric cancer and suggest the mechanism of this tumor suppression function involves the inhibition of Wnt signaling.

    • Myoung-Hee Kang
    • , Hyunji Choi
    •  & Yun-Yong Park

  • 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

    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

    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

    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

    In breast cancer GATA3 is known to be frequently mutated, but the function of these mutations is unclear. Here, the authors utilise CRISPR-Cas9 to model frame-shift mutations in zinc finger 2 of GATA3, highlighting that GATA3 mutation can have gain- or loss-of function effects in breast cancer.

    • Motoki Takaku
    • , Sara A. Grimm
    •  & Paul A. Wade

  • Article
    | Open Access

    Transcription of lncRNAs is known to regulate local gene expression. Here the authors describe how orchestrated transcription of two contiguous lncRNAs facilitates a regulatory circuit by which the master regulator for entry into meiosis, IME1, directs the decision to enter meiosis in yeast.

    • Fabien Moretto
    • , N. Ezgi Wood
    •  & Folkert J. van Werven

  • Article
    | Open Access

    Methyl metabolites in the one-carbon cycle, such as phosphatidylcholines and S-adenosylmethionine, play a role in hepatic triglyceride regulation. Here Kim et al. show that AhR and SHP are both involved in the expression of several key enzymes of one-carbon metabolism, with the former regulating them early after feeding and the latter inhibiting AhR at later stages.

    • Young-Chae Kim
    • , Sunmi Seok
    •  & Jongsook Kim Kemper

  • Article
    | Open Access

    Transcript cleavage factors such as eukaryotic TFIIS assist the resumption of transcription following RNA pol II backtracking. Here the authors find that one of the Sulfolobus solfataricus TFIIS homolog—TFS4—has evolved into a potent RNA polymerase inhibitor potentially involved in antiviral defense.

    • Thomas Fouqueau
    • , Fabian Blombach
    •  & Finn Werner

  • Article
    | Open Access

    The repertoire of tissue-specific distal regulators of gene transcription enhancers defines homeostasis or disease. Here, the authors reveal the enhancer and super-enhancer signature of vascular smooth muscle cells under normal and angiotensin II stimuli, providing new insight into the transcriptional regulation of vascular pathologies.

    • Sadhan Das
    • , Parijat Senapati
    •  & Rama Natarajan

  • Article
    | Open Access

    Zbtb16-encoded transcription factor PLZF directs the differentiation of multiple innate and innate-like cell lineages, but how Zbtb16 itself is regulated remains unclear. Here the authors show, using CRISPR gene editing, ATAC-seq and ChIP-seq, that specific Runx1-bound enhancer elements critically modulate lineage-dependent expressions of PLZF.

    • Ai-Ping Mao
    • , Isabel E. Ishizuka
    •  & Albert Bendelac

  • Article
    | Open Access

    “Each olfactory sensory neuron expresses a single odorant receptor gene from either class I or class II genes. Here, the authors identify an enhancer for mouse class I genes, that is highly conserved, and regulates most class I genes expression by acting over ~ 3 megabases within the whole cluster.”

    • Tetsuo Iwata
    • , Yoshihito Niimura
    •  & Junji Hirota

  • Article
    | Open Access

    The transcription factor ERG is key to endothelial lineage specification and vascular homeostasis. Here the authors show that ERG balances TGFβ signalling through the SMAD1 and SMAD3 pathways, protecting the endothelium from endothelial-to-mesenchymal transition and consequent liver fibrosis in mice via a SMAD3-dependent mechanism.

    • Neil P. Dufton
    • , Claire R. Peghaire
    •  & Anna M. Randi

  • Article
    | Open Access

    HDAC3 is a critical mediator of hepatic lipid metabolism and its loss leads to fatty liver. Here, the authors characterize the liver HDAC3 interactome in vivo, provide evidence that HDAC3 interacts with PROX1, and show that HDAC3 and PROX1 control expression of genes regulating lipid homeostasis.

    • Sean M. Armour
    • , Jarrett R. Remsberg
    •  & Mitchell A. Lazar

  • Article
    | Open Access

    HIV insertions in hematopoietic cells are enriched in BACH2 or MLK2 genes, but the selective advantages conferred are unknown. Here, the authors show that BACH2 and additionally STAT5B are activated by viral insertions, generating chimeric mRNAs specifically enriched in T regulatory cells favoring their persistence.

    • Daniela Cesana
    • , Francesca R. Santoni de Sio
    •  & Eugenio Montini

  • Article
    | Open Access

    Cancer driver mutations can occur within noncoding genomic sequences. Here, the authors develop a statistical approach to identify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experimentally demonstrate they are regulatory elements of known cancer genes.

    • Matteo D′Antonio
    • , Donate Weghorn
    •  & Kelly A Frazer

  • Article
    | Open Access

    Zinc homeostasis in most bacteria is achieved by a set of regulators, each responding to a certain level of intracellular zinc. Here the authors show that, inStreptomyces coelicolor, the Zur regulator modulates the expression of genes for zinc import and export over a large range of zinc concentrations.

    • Seung-Hwan Choi
    • , Kang-Lok Lee
    •  & Jung-Hye Roe

  • Article
    | Open Access

    LDL receptor-related protein 1 (LRP1) is an endocytic receptor involved in cell signalling and energy homeostasis. Here Maoet al. demonstrate that endothelial Lrp1 modulates lipid and glucose metabolism by binding the nuclear receptor Pparγ and promoting its transcriptional activity.

    • Hua Mao
    • , Pamela Lockyer
    •  & Xinchun Pi

  • Article
    | Open Access

    The molecular pathways regulating the cardioprotective activity of deacetylase sirtuin-1 are unknown. Here, Yanget al. show that histone H3K9 methyltransferase SUV39H and HP1gamma cooperatively methylate H3K9 on the sirtuin-1 promoter and inhibit sirtuin-1 transcription, and show that inhibition of SUV39H in mice is cardioprotective.

    • Guang Yang
    • , Xinyu Weng
    •  & Aijun Sun

  • Article
    | Open Access

    Genome wide association studies have identified multiple risk loci for multiple myeloma. Here, the authors show that the expression of CDCA7Lis associated with patient survival and expression of the gene is influenced by a risk variant at 7p15.3, which creates a transcription factor binding site for IRF4.

    • Ni Li
    • , David C. Johnson
    •  & Richard S. Houlston

  • Article
    | Open Access

    How archaeal viruses perturb host transcription machinery is poorly understood. Here, the authors provide evidence that the archaeo-viral transcription factor ORF145/RIP targets host RNA polymerase, repressing its activity.

    • Carol Sheppard
    • , Fabian Blombach
    •  & Finn Werner

  • Article
    | Open Access

    The chromatin-associated protein AKAP95 is known for its chromatin-related functions including enhancing transcription. Here the authors show that AKAP95 interacts with the splicing regulatory factors as well as RNAs to regulate the inclusion of exons and pre-mRNA splicing.

    • Jing Hu
    • , Alireza Khodadadi-Jamayran
    •  & Hao Jiang

  • Article
    | Open Access

    Identification of non-coding variants has outstripped our ability to annotate and interpret them. Dickel et al. present a compendium of over 80,000 putative human heart enhancers and demonstrate that two conserved enhancers are required for proper cardiac function in mice.

    • Diane E. Dickel
    • , Iros Barozzi
    •  & Len A. Pennacchio

  • Article
    | Open Access

    Chromatin architecture is a key regulator of transcriptional processes, however current methods to investigate it have technical limitations. Here, the authors describe a novel chromatin capture technique, CATCH, which can be used to identify and characterize complex genomic interaction networks.

    • Ryan J. Bourgo
    • , Hari Singhal
    •  & Geoffrey L. Greene

  • Article
    | Open Access

    To modulate gene expression, the glucocorticoid receptor binds to response elements (RE) that vary in sequence. Here, the authors show that RE sequences can modulate glucocorticoid receptor structure and activity, which might provide regulatory specificity towards individual target genes.

    • Stefanie Schöne
    • , Marcel Jurk
    •  & Sebastiaan H. Meijsing

  • Article
    | Open Access

    The Fur protein regulates transcription of bacterial genes in response to metal ions. Here, the authors show that the Fur protein from Helicobacter pylorirepresses transcription by iron-responsive oligomerization and DNA compaction, encasing the transcriptional start site in a macromolecular complex.

    • Davide Roncarati
    • , Simone Pelliciari
    •  & Alberto Danielli

  • Article
    | Open Access

    CtBP1-S/BARS is required for fission of endomembrane compartments including the Golgi. Here the authors show that CtBP1-S/BARS activates a trans-Golgi lysophosphatidic acid acyltransferase that catalyses the production of phosphatidic acid and is required for fission of the post-Golgi carrier membrane.

    • Alessandro Pagliuso
    • , Carmen Valente
    •  & Alberto Luini

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