Gene expression articles within Nature Communications

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  • Article
    | Open Access

    Conserved sets of transcription factors (TFs) regulate hematopoiesis. Here, Stadhouders et al. show that IRF2BP2 is a component of the LDB1 TF complex and together with its co-repressor ETO2, enhances transcriptional repression, which plays a crucial role at the erythroid progenitor stage.

    • Ralph Stadhouders
    • , Alba Cico
    •  & Eric Soler

  • Article
    | Open Access

    Measuring single-cell mRNA dynamics is critical to understand gene expression. Here, using RNA Spinach technique to detect very low abundant mRNAs, Guet et al. report an analysis of the osmotic shock response in live yeast by localizing induced transcription factors, target gene loci and corresponding transcripts.

    • David Guet
    • , Laura T. Burns
    •  & Catherine Dargemont

  • Article
    | Open Access

    Synthetic biology can be used to regulate target genes and uncover gene function in physiologically relevant settings. Here Robles-Oteiza et al. describe a new recombinase-based system for conditional inactivation and inducible restoration of gene function and develop new mouse models to study p53 and Rb.

    • Camila Robles-Oteiza
    • , Sarah Taylor
    •  & David M. Feldser

  • Article
    | Open Access

    The prolonged presence of cytokines is necessary to produce a robust pro-inflammatory response through the activation of p38 MAPK. Here, Tomidaet al. show that asynchronous oscillatory activation of p38 MAPK occurs at the single-cell level and is necessary for the proper expression of pro-inflammatory genes.

    • Taichiro Tomida
    • , Mutsuhiro Takekawa
    •  & Haruo Saito

  • Article
    | Open Access

    Transcription factor COUP-TFII is elevated in the hearts of non-ischaemic cardiomyopathy patients, but the nature of this correlation is unknown. Here the authors show that forced cardiac expression of COUP-TFII in mice causes dilated cardiomyopathy because of altered mitochondrial function and impaired metabolic remodelling.

    • San-Pin Wu
    • , Chung-Yang Kao
    •  & Sophia Y. Tsai

  • Article
    | Open Access

    Coenzyme B12 traditionally acts as cofactor to light-independent metabolic enzymes in bacteria and humans. Here, Kutta et al.present a time-resolved photochemical description of a B12-dependent photoreceptor protein, which represents a mechanistic foundation for B12 photobiology.

    • Roger J. Kutta
    • , Samantha J. O. Hardman
    •  & Alex R. Jones

  • Article
    | Open Access

    The first haematopoietic stem and progenitor cells arise from the hemogenic endothelium of arterial vascular beds. Here the authors describe the mechanism that regulates the endothelial-to-haematopoietic transition and show that Sox17 and Notch1, genes critical to arterial endothelium identity, are also crucial repressors of haematopoietic fate.

    • Carlos O. Lizama
    • , John S. Hawkins
    •  & Ann C. Zovein

  • Article
    | Open Access

    Infectious and chronic diseases display seasonal patterns, yet seasonal changes in physiology are rarely thought to affect human health. Here the authors show seasonal variation in all major blood cells and in gene and protein expression in diverse tissues, suggesting a mechanism for seasonal disease proneness and physiology.

    • Xaquin Castro Dopico
    • , Marina Evangelou
    •  & John A. Todd

  • Article
    | Open Access

    Screening genomic or metagenomic libraries for interesting products or activities is often hampered by poor gene expression in a heterologous host. Here the authors show that the expression of a Lactobacillus sigma factor greatly enhances transcription of heterologous and environmental DNA in E. coli.

    • Stefan M. Gaida
    • , Nicholas R. Sandoval
    •  & Eleftherios T. Papoutsakis

  • Article
    | Open Access

    The protein p16INK4a promotes senescence in tissue stem cells and thereby contributes to organismal ageing. Here the authors reveal that p16INK4a also downregulates expression of a-klotho, thereby revealing an additional ageing-promoting function of 16INK4athat is independent from its role in senescence.

    • Seidai Sato
    • , Yuka Kawamata
    •  & Eiji Hara

  • Article
    | Open Access

    STIM proteins sense calcium depletion in the endoplasmic reticulum and in response activate calcium influx through Orai1 channels located at the plasma membrane. Here, Miederer et al. identify a novel splice variant of STIM2 that fails to interact with and activate Orai1 and may act to fine-tune cellular calcium homeostasis by negatively regulating calcium influx.

    • Anna-Maria Miederer
    • , Dalia Alansary
    •  & Barbara A. Niemeyer

  • Article
    | Open Access

    Men and women differ in terms of their neurochemistry, behaviour and susceptibility to disease. Here the authors show that sex differences in gene expression and splicing are widespread in adult human brain, and that sex-biased expression is likely to have functional consequences.

    • Daniah Trabzuni
    • , Adaikalavan Ramasamy
    •  & Mina Ryten

  • Article |

    During embryonic development, midline fluid flow results in asymmetric nodal gene expression. Using genetic manipulations and mathematical modelling, Nakamura et al. find that expression of the nodal antagonist Cerl2 is regulated post-transcriptionally, and that asymmetry is maintained by Wnt-Cerl2 feedback loops.

    • Tetsuya Nakamura
    • , Daisuke Saito
    •  & Hiroshi Hamada

  • Article
    | Open Access

    Detailed analysis of axis development in mouse embryo has been limited. Morriset al. developed an in vitroculture technique that enables the real-time observation of an anterior visceral endoderm formation and show that cell marker asymmetry within the AVE subdomain dictates the direction of the AVE migration.

    • Samantha A. Morris
    • , Seema Grewal
    •  & Magdalena Zernicka-Goetz

  • Article |

    How retinoganglion cell axons project correctly to the superior colliculus is poorly understood. Here, projections are shown to require EphB1, EphB2 and ephrin-B1 to terminate in the medial superior colliculus, while ephrin-B2 is essential for the mapping of both dorsal and ventral axons.

    • Sonal Thakar
    • , George Chenaux
    •  & Mark Henkemeyer

  • Article
    | Open Access

    Chk2 is a kinase that is a potential chemotherapeutic target. Here, Chk2 and the kinase ERK are shown to functionally interact, and are elevated in expression in human diffuse B-cell lymphomas. Combinatorial inhibition of the kinases was also shown to block tumour growth in anin vivomouse model.

    • Bojie Dai
    • , X. Frank Zhao
    •  & Ronald B. Gartenhaus

  • Article |

    Soluble cytosolic proteins can be degraded in lysosomes by chaperone-mediated autophagy, however, the current method to measure this process requires isolation of lysosomes. Now, a fluorescent reporter is described that can measure this type of autophagy in intact cells.

    • Hiroshi Koga
    • , Marta Martinez-Vicente
    •  & Ana Maria Cuervo

  • Article
    | Open Access

    In vitrostudies have suggested that the ubiquitin ligase, Nedd4-2, regulates several proteins, including the epithelial sodium channel. Here by examining Nedd4-2-deficient mice, the authors demonstrate that Nedd4-2 is essential for epithelial sodium channel regulation, fetal and postnatal lung function and animal survival.

    • Natasha A. Boase
    • , Grigori Y. Rychkov
    •  & Sharad Kumar

  • Article
    | Open Access

    It was previously thought that the nerves in the pectoral fin of fish came solely from the spinal cord. Here, motoneurons in ray-finned fish are shown to also originate from the hindbrain, demonstrating that innervation was from both the hindbrain and the spinal cord in ancesteral vertebrates.

    • Leung-Hang Ma
    • , Edwin Gilland
    •  & Robert Baker

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