Now showing items 83-102 of 105

    • RAB5A and TRAPPC6B are novel targets for Shiga toxin 2a inactivation in kidney epithelial cells 

      Kouzel, Ivan; Kehl, Alexander; Berger, Petya; Liashkovich, Ivan; Steil, Daniel; Makalowski, Wojciech; Suzuki, Yutaka; Pohlentz, Gottfried; Karch, Helge; Mellmann, Alexander C.; Müthing, Johannes (Journal article; Peer reviewed, 2020-03-18)
      The cardinal virulence factor of human-pathogenic enterohaemorrhagic Escherichia coli (EHEC) is Shiga toxin (Stx), which causes severe extraintestinal complications including kidney failure by damaging renal endothelial ...
    • RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions 

      Bonetti, Alessandro; Agostini, Federico; Suzuki, Ana Maria; Hashimoto, Kosuke; Pascarella, Giovanni; Gimenez, Juliette; Roos, Leonie; Nash, Alex J.; Ghilotti, Marco; Cameron, Christopher J.  F.; Valentine, Matthew; Medvedeva, Yulia A.; Noguchi, Shuhei; Agirre, Eneritz; Kashi, Kaori; Samudyata, Samudyata; Luginbühl, Joachim; Cazzoli, Riccardo; Agrawal, Saumya; Luscombe, Nicholas M.; Blanchette, Mathieu; Kasukawa, Takeya; de Hoon, Michiel; Arner, Erik; Lenhard, Boris; Plessy, Charles; Castelo-Branco, Gonçalo; Orlando, Valerio; Carninci, Piero (Journal article; Peer reviewed, 2020)
      Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. ...
    • Regulation of Nematostella neural progenitors by SoxB, Notch and bHLH genes 

      Richards, Gemma Sian; Rentzsch, Fabian (Journal article; Peer reviewed, 2015-10-06)
      Notch signalling, SoxB and Group A bHLH ‘proneural’ genes are conserved regulators of the neurogenic program in many bilaterians. However, the ancestry of their functions and interactions is not well understood. We address ...
    • Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum 

      Bråte, Jon; Adamski, Marcin; Neumann, Ralf Stefan; Shalchian-Tabrizi, Kamran; Adamska, Maja (Journal article; Peer reviewed, 2015-12-23)
      Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation was important for the evolution of developmental complexity in animals. ...
    • Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes 

      Kikuta, Hiroshi; Fredman, David; Rinkwitz, Silke; Lenhard, Boris; Becker, Thomas S. (Journal article; Peer reviewed, 2007-10-31)
      A large-scale enhancer detection screen was performed in the zebrafish using a retroviral vector carrying a basal promoter and a fluorescent protein reporter cassette. Analysis of insertional hotspots uncovered areas around ...
    • A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species 

      Sinigaglia, Chiara; Thiel, Daniel; Houliston, Evelyn; Leclère, Lucas (Journal article, 2017)
      In situ hybridization is a widely employed technique allowing spatial visualization of gene expression in fixed specimens. It has proven to be essential to our understanding of biological processes, including developmental ...
    • Some like it hot: population-specific adaptations in venom production to abiotic stressors in a widely distributed cnidarian 

      Sachkova, Maria; Macrander, Jason; Surm, Joachim M.; Aharoni, Reuven; Menard-Harvey, Shelcie S.; Klock, Amy; Leach, Whitney B.; Reitzel, Adam M.; Moran, Yehu (Journal article; Peer reviewed, 2020-09)
      Background: In cnidarians, antagonistic interactions with predators and prey are mediated by their venom, whose synthesis may be metabolically expensive. The potentially high cost of venom production has been hypothesized ...
    • The study of Priapulus caudatus reveals conserved molecular patterning underlying different gut morphogenesis in the Ecdysozoa 

      Martin Duran, Jose Maria; Hejnol, Andreas (Journal article; Peer reviewed, 2015-04-21)
      Background The digestive systems of animals can become highly specialized in response to their exploration and occupation of new ecological niches. Although studies on different animals have revealed commonalities in gut ...
    • Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes 

      Dong, Xianjun; Fredman, David; Lenhard, Boris (Journal article; Peer reviewed, 2009-08-21)
      Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into ...
    • Toxin-like neuropeptides in the sea anemone Nematostella unravel recruitment from the nervous system to venom 

      Sachkova, Maria; Landau, Morani; Surm, Joachim M.; Macrander, Jason; Singer, Shir A.; Reitzel, Adam M.; Moran, Yehu (Journal article; Peer reviewed, 2020)
      The sea anemone Nematostella vectensis (Anthozoa, Cnidaria) is a powerful model for characterizing the evolution of genes functioning in venom and nervous systems. Although venom has evolved independently numerous times ...
    • Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR 

      Danks, Gemma Barbara; Galbiati, Heloisa; Raasholm, Martina; Torres Cleuren, Yamila Nicole; Valen, Eivind; Navratilova, Pavla; Thompson, Eric (Journal article; Peer reviewed, 2019)
      Background: In phylogenetically diverse organisms, the 5′ ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. Results: We ...
    • Transcription start site mapping using super-low input carrier-CAGE 

      Cvetesic, Nevena; Pahita, Elena; Lenhard, Boris (Journal article; Peer reviewed, 2019-06-26)
      Cap analysis of gene expression (CAGE) is a method used for single-nucleotide resolution detection of RNA polymerase II transcription start sites (TSSs). Accurate detection of TSSs enhances identification and discovery of ...
    • Transcriptional adaptation in caenorhabditis elegans 

      Serobyan, Vahan; Kontarakis, Zacharias; El-Brolosy, Mohamed A.; Welker, Jordan M.; Tolstenkov, Oleg; Saadeldein, Amr M.; Retzer, Nicholas; Gottschalk, Alexander; Wehman, Ann M; Stainier, Didier YR (Journal article; Peer reviewed, 2020-01)
      Transcriptional adaptation is a recently described phenomenon by which a mutation in one gene leads to the transcriptional modulation of related genes, termed adapting genes. At the molecular level, it has been proposed ...
    • Transdifferentiation is a driving force of regeneration in Halisarca dujardini (Demospongiae, Porifera) 

      Borisenko, Ilya E.; Adamska, Maja; Tokina, Daria B.; Ereskovsky, Alexander V. (Journal article; Peer reviewed, 2015-08-25)
      The ability to regenerate is widespread in the animal kingdom, but the regenerative capacities and mechanisms vary widely. To understand the evolutionary history of the diverse regeneration mechanisms, the regeneration ...
    • Translog, a web browser for studying the expression divergence of homologous genes 

      Dong, Xianjun; Akalin, Altuna; Sharma, Yogita; Lenhard, Boris (Journal article; Peer reviewed, 2010-01-18)
      Background: Increasing amount of data from comparative genomics, and newly developed technologies producing accurate gene expression data facilitate the study of the expression divergence of homologous genes. Previous ...
    • Transposon mediated transgenesis in a marine invertebrate chordate: Ciona intestinalis 

      Sasakura, Yasunori; Oogai, Yuichi; Matsuoka, Terumi; Satoh, Nori; Awazu, Satoko (Journal article; Peer reviewed, 2007-10-31)
      Achievement of transposon mediated germline transgenesis in a basal chordate, Ciona intestinalis, is discussed. A Tc1/mariner superfamily transposon, Minos, has excision and transposition activities in Ciona. Minos enables ...
    • Twenty million years of evolution: The embryogenesis of four Caenorhabditis species are indistinguishable despite extensive genome divergence 

      Memar, Nadin; Schiemann, Sabrina; Hennig, Christian; Findeis, Daniel; Conradt, Barbara; Schnabel, Ralf (Journal article; Peer reviewed, 2019-03-15)
      The four Caenorhabditis species C. elegans, C. briggsae, C. remanei and C. brenneri show more divergence at the genomic level than humans compared to mice (Stein et al., 2003; Cutter et al., 2006, 2008). However, the ...
    • Ultrastructural correlates of enhanced norepinephrine and neuropeptide y cotransmission in the spontaneously hypertensive rat brain 

      Kourtesis, Ioannis; Kasparov, Sergey; Verkade, Paul; Teschemacher, Anja G. (Journal article; Peer reviewed, 2015-10-29)
      The spontaneously hypertensive rat (SHR) replicates many clinically relevant features of human essential hypertension and also exhibits behavioral symptoms of attention-deficit/hyperactivity disorder and dementia. The SHR ...
    • Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks 

      Barešić, Anja; Nash, Alexander Jolyon; Dahoun, Tarik; Howes, Oliver; Lenhard, Boris (Journal article; Peer reviewed, 2019)
      Recent genome-wide association studies have identified numerous loci associated with neuropsychiatric disorders. The majority of these are in non-coding regions, and are commonly assigned to the nearest gene along the ...
    • A unified phylogeny-based nomenclature for histone variants 

      Talbert, Paul B.; Ahmad, Kami; Almouzni, Geneviève; Ausió, Juan; Berger, Frederic; Thompson, Eric M.; Bhalla, Prem L.; Bonner, William M.; Cande, W. Zacheus; Chadwick, Brian P.; Chan, Simon W. L.; Cross, George A. M.; Cui, Liwang; Dimitrov, Stefan I.; Doenecke, Detlef; Eirin-López, José M.; Gorovsky, Martin A.; Hake, Sandra B.; Hamkalo, Barbara A.; Holec, Sarah; Jacobsen, Steven E.; Kamieniarz, Kinga; Khochbin, Saadi; Ladurner, Andreas G.; Landsman, David; Latham, John A.; Loppin, Benjamin; Malik, Harmit S.; Marzluff, William F.; Pehrson, John R.; Postberg, Jan; Schneider, Robert; Singh, Mohan B.; Smith, M. M.; Torres-Padilla, Maria-Elena; Tremethick, David J.; Turner, Bryan M.; Waterborg, Jakob H.; Wollmann, Heike; Yelagandula, Ramesh; Zhu, Bing; Henikoff, Steven (Peer reviewed; Journal article, 2012-06-21)
      Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for ...