PubMed Central (PMC3 - NLM DTD)
Archive of life sciences journal literature at the U.S. National Institutes of Health (NIH), developed and managed by NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM).
R-loops induce repressive chromatin marks over mammalian gene terminators - Skourti-Stathaki, Konstantina; Kamieniarz-Gdula, Kinga; Proudfoot, Nicholas J.
The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potential harmful effects on genome integrity, due to the fragility of the displaced DNA coding strand1. However R-loops may also possess beneficial effects as their widespread formation has been detected over CpG island promoters in human genes2,3. Furthermore we have previously shown that R-loops are particularly enriched over G-rich terminator elements. These facilitate RNA polymerase II (Pol II) pausing prior to efficient termination4. Here we reveal an unanticipated link...
Functionalized olefin cross-coupling to construct carbon–carbon bonds - Lo, Julian C.; Gui, Jinghan; Yabe, Yuki; Pan, Chung-Mao; Baran, Phil S.
Carbon–carbon (C–C) bonds form the backbone of many important molecules, including polymers, dyes, and pharmaceutical agents. The development of new methods to create these essential connections in a rapid and practical fashion has been the focus of numerous organic chemists. This endeavor heavily relies on the ability to form C–C bonds in the presence of sensitive functional groups and congested structural environments. Here we report a fundamentally new chemical transformation that allows for the facile construction of highly substituted and uniquely functionalized C–C bonds. Using a simple iron catalyst, an inexpensive silane, and a benign solvent under an ambient atmosphere,...
Image-guided radiotherapy platform using single nodule conditional lung cancer mouse models - Herter-Sprie, Grit S.; Korideck, Houari; Christensen, Camilla L.; Herter, Jan M.; Rhee, Kevin; Berbeco, Ross I.; Bennett, David G.; Akbay, Esra A.; Kozono, David; Mak, Raymond H.; Makrigiorgos, G. Mike; Kimmelman, Alec C.; Wong, Kwok-Kin
Close resemblance of murine and human trials is essential to achieve the best predictive value of animal-based translational cancer research. Kras-driven genetically engineered mouse models of non-small cell lung cancer faithfully predict the response of human lung cancers to systemic chemotherapy. Due to development of multifocal disease, however, these models have not been usable in studies of outcomes following focal radiotherapy (RT). We report the development of a preclinical platform to deliver state-of-the-art image-guided RT in these models. Presence of a single tumour as usually diagnosed in patients is modelled by confined injection of adenoviral Cre recombinase. Furthermore, three-dimensional conformal...
Mitochondrial UPR-regulated innate immunity provides resistance to pathogen infection - Pellegrino, Mark W.; Nargund, Amrita M.; Kirienko, Natalia V.; Gillis, Reba; Fiorese, Christopher J.; Haynes, Cole M.
Metazoans identify and eliminate bacterial pathogens in microbe-rich environments such as the intestinal lumen, however the mechanisms are unclear. Potentially, host cells employ intracellular surveillance or stress response programs to detect pathogens that target monitored cellular activities to initiate innate immune responses1–3. Mitochondrial function is evaluated by monitoring mitochondrial protein import efficiency of the transcription factor ATFS-1, which mediates the mitochondrial unfolded protein response (UPRmt). During mitochondrial stress, import is impaired4 allowing ATFS-1 to traffic to the nucleus where it mediates a transcriptional response to re-establish mitochondrial homeostasis5. Here, we examined the role of ATFS-1 during pathogen exposure because in...
In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system - Maddalo, Danilo; Manchado, Eusebio; Concepcion, Carla P.; Bonetti, Ciro; Vidigal, Joana A.; Han, Yoon-Chi; Ogrodowski, Paul; Crippa, Alessandra; Rekhtman, Natasha; de Stanchina, Elisa; Lowe, Scott W.; Ventura, Andrea
Chromosomal rearrangements play a central role in the pathogenesis of human cancers and often result in the expression of therapeutically actionable gene fusions1. A recently discovered example is a fusion between the Echinoderm Microtubule-associated Protein-like 4 (EML4) and the Anaplastic Lymphoma Kinase (ALK) genes, generated by an inversion on the short arm of chromosome 2: inv(2)(p21p23). The EML4-ALK oncogene is detected in a subset of human non-small cell lung cancers (NSCLC)2 and is clinically relevant because it confers sensitivity to ALK inhibitors3. Despite their importance, modeling such genetic events in mice has proven challenging and requires complex manipulation of the...
Modeling human development and disease in pluripotent stem cell-derived gastric organoids - McCracken, Kyle W.; Catá, Emily M.; Crawford, Calyn M.; Sinagoga, Katie L.; Schumacher, Michael; Rockich, Briana E.; Tsai, Yu-Hwai; Mayhew, Christopher N.; Spence, Jason R.; Zavros, Yana; Wells, James M.
Gastric diseases, including peptic ulcer disease and gastric cancer, affect 10% of the world’s population and are largely due to chronic H. pylori infection1–3. Species differences in embryonic development and architecture of the adult stomach make animal models suboptimal for studying human stomach organogenesis and pathogenesis4, and there is no experimental model of normal human gastric mucosa. Here we report the de novo generation of three-dimensional human gastric tissue in vitro through the directed differentiation of human pluripotent stem cells (hPSCs). We identified that temporal manipulation of the FGF, WNT, BMP, retinoic acid and EGF signaling pathways and three-dimensional growth...
Translocation between PI(4,5)P2-poor and PI(4,5)P2-rich microdomains during store depletion determines STIM1 conformation and Orai1 gating - Maléth, Jozsef; Choi, Seok; Muallem, Shmuel; Ahuja, Malini
The Orai1-STIM1 current undergoes slow Ca2+-dependent inactivation (SCDI) mediated by binding of SARAF to STIM1. Here, we report the use of SCDI by SARAF as a probe of the conformation and microdomain localization of the Orai1-STIM1 complex. We find that interaction of STIM1 with Orai1 C terminus and the STIM1 K-domain are required for interaction of SARAF with STIM1 and SCDI. STIM1-Orai1 must be in a PM/ER microdomain tethered by E-Syt1, stabilized by Septin4 and enriched in PI(4,5)P2 for STIM1-SARAF interaction. Targeting STIM1 to PI(4,5)P2 rich and poor microdomains reveals that SARAF-dependent SCDI is observed only when STIM1-Orai1 are within...
Identification of gravitropic response indicator genes in Arabidopsis inflorescence stems - Taniguchi, Masatoshi; Nakamura, Moritaka; Tasaka, Masao; Morita, Miyo Terao
Differential organ growth during gravitropic response is caused by differential accumulation of auxin, that is, relative higher auxin concentration in lower flanks than in upper flanks of responding organs. Auxin responsive reporter systems such as DR5::GUS and DR5::GFP have usually been used as indicators of gravitropic response in roots and hypocotyls of Arabidopsis. However, in the inflorescence stems, the reporter systems don’t work well to monitor gravitropic response. Here, we aim to certify appropriate gravitropic response indicators (GRIs) in inflorescence stems. We performed microarray analysis comparing gene expression profiles between upper and lower flanks of Arabidopsis inflorescence stems after gravistimulation....
Nuclear ARRB1 induces pseudohypoxia and cellular metabolism reprogramming in prostate cancer - Zecchini, Vincent; Madhu, Basetti; Russell, Roslin; Pértega-Gomes, Nelma; Warren, Anne; Gaude, Edoardo; Borlido, Joana; Stark, Rory; Ireland-Zecchini, Heather; Rao, Roheet; Scott, Helen; Boren, Joan; Massie, Charlie; Asim, Mohammad; Brindle, Kevin; Griffiths, John; Frezza, Christian; Neal, David E; Mills, Ian G
Tumour cells sustain their high proliferation rate through metabolic reprogramming, whereby cellular metabolism shifts from oxidative phosphorylation to aerobic glycolysis, even under normal oxygen levels. Hypoxia-inducible factor 1A (HIF1A) is a major regulator of this process, but its activation under normoxic conditions, termed pseudohypoxia, is not well documented. Here, using an integrative approach combining the first genome-wide mapping of chromatin binding for an endocytic adaptor, ARRB1, both in vitro and in vivo with gene expression profiling, we demonstrate that nuclear ARRB1 contributes to this metabolic shift in prostate cancer cells via regulation of HIF1A transcriptional activity under normoxic conditions through...