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  • Mutations in DNM1L, as in OPA1, result indominant optic atrophy despite opposite effectson mitochondrial fusion and fission
    Brain (IF 10.292) Pub Date : 2017-09-23
    Sylvie Gerber, Majida Charif, Arnaud Chevrollier, Tanguy Chaumette, Claire Angebault, Mariame Selma Kane, Aurélien Paris, Jennifer Alban, Mélanie Quiles, Cécile Delettre, Dominique Bonneau, Vincent Procaccio, Patrizia Amati-Bonneau, Pascal Reynier, Stéphanie Leruez, Raphael Calmon, Nathalie Boddaert, Benoit Funalot, Marlène Rio, Didier Bouccara, Isabelle Meunier, Hiromi Sesaki, Josseline Kaplan, Christian P. Hamel, Jean-Michel Rozet, Guy Lenaers

    Dominant optic atrophy is a blinding disease due to the degeneration of the retinal ganglion cells, the axons of which form the optic nerves. In most cases, the disease is caused by mutations in OPA1, a gene encoding a mitochondrial large GTPase involved in cristae structure and mitochondrial network fusion. Using exome sequencing, we identified dominant mutations in DNM1L on chromosome 12p11.21 in three large families with isolated optic atrophy, including the two families that defined the OPA5 locus on chromosome 19q12.1-13.1, the existence of which is denied by the present study. Analyses of patient fibroblasts revealed physiological abundance and homo-polymerization of DNM1L, forming aggregates in the cytoplasm and on highly tubulated mitochondrial network, whereas neither structural difference of the peroxisome network, nor alteration of the respiratory machinery was noticed. Fluorescence microscopy of wild-type mouse retina disclosed a strong DNM1L expression in the ganglion cell layer and axons, and comparison between 3-month-old wild-type and Dnm1l+/− mice revealed increased mitochondrial length in retinal ganglion cell soma and axon, but no degeneration. Thus, our results disclose that in addition to OPA1, OPA3, MFN2, AFG3L2 and SPG7, dominant mutations in DNM1L jeopardize the integrity of the optic nerve, suggesting that alterations of the opposing forces governing mitochondrial fusion and fission, similarly affect retinal ganglion cell survival.

    更新日期:2017-09-23
  • TOR1A variants cause a severe arthrogryposis with developmental delay, strabismus and tremor
    Brain (IF 10.292) Pub Date : 2017-09-23
    Ariana Kariminejad, Martin Dahl-Halvarsson, Gianina Ravenscroft, Fariba Afroozan, Elham Keshavarz, Hayley Goullée, Mark R. Davis, Mehrshid Faraji Zonooz, Hossein Najmabadi, Nigel G Laing, Homa Tajsharghi

    Autosomal dominant torsion dystonia-1 is a disease with incomplete penetrance most often caused by an in-frame GAG deletion (p.Glu303del) in the endoplasmic reticulum luminal protein torsinA encoded by TOR1A. We report an association of the homozygous dominant disease-causing TOR1A p.Glu303del mutation, and a novel homozygous missense variant (p.Gly318Ser) with a severe arthrogryposis phenotype with developmental delay, strabismus and tremor in three unrelated Iranian families. All parents who were carriers of the TOR1A variant showed no evidence of neurological symptoms or signs, indicating decreased penetrance similar to families with autosomal dominant torsion dystonia-1. The results from cell assays demonstrate that the p.Gly318Ser substitution causes a redistribution of torsinA from the endoplasmic reticulum to the nuclear envelope, similar to the hallmark of the p.Glu303del mutation. Our study highlights that TOR1A mutations should be considered in patients with severe arthrogryposis and further expands the phenotypic spectrum associated with TOR1A mutations.

    更新日期:2017-09-23
  • Neuroinflammation and its relationship to changes in brain volume and white matter lesions in multiple sclerosis
    Brain (IF 10.292) Pub Date : 2017-09-23
    Gourab Datta, Alessandro Colasanti, Eugenii A. Rabiner, Roger N. Gunn, Omar Malik, Olga Ciccarelli, Richard Nicholas, Eline Van Vlierberghe, Wim Van Hecke, Graham Searle, Andre Santos-Ribeiro, Paul M. Matthews

    Brain magnetic resonance imaging is an important tool in the diagnosis and monitoring of multiple sclerosis patients. However, magnetic resonance imaging alone provides limited information for predicting an individual patient’s disability progression. In part, this is because magnetic resonance imaging lacks sensitivity and specificity for detecting chronic diffuse and multi-focal inflammation mediated by activated microglia/macrophages. The aim of this study was to test for an association between 18 kDa translocator protein brain positron emission tomography signal, which arises largely from microglial activation, and measures of subsequent disease progression in multiple sclerosis patients. Twenty-one patients with multiple sclerosis (seven with secondary progressive disease and 14 with a relapsing remitting disease course) underwent T1- and T2-weighted and magnetization transfer magnetic resonance imaging at baseline and after 1 year. Positron emission tomography scanning with the translocator protein radioligand 11C-PBR28 was performed at baseline. Brain tissue and lesion volumes were segmented from the T1- and T2-weighted magnetic resonance imaging and relative 11C-PBR28 uptake in the normal-appearing white matter was estimated as a distribution volume ratio with respect to a caudate pseudo-reference region. Normal-appearing white matter distribution volume ratio at baseline was correlated with enlarging T2-hyperintense lesion volumes over the subsequent year (ρ = 0.59, P = 0.01). A post hoc analysis showed that this association reflected behaviour in the subgroup of relapsing remitting patients (ρ = 0.74, P = 0.008). By contrast, in the subgroup of secondary progressive patients, microglial activation at baseline was correlated with later progression of brain atrophy (ρ = 0.86, P = 0.04). A regression model including the baseline normal-appearing white matter distribution volume ratio, T2 lesion volume and normal-appearing white matter magnetization transfer ratio for all of the patients combined explained over 90% of the variance in enlarging lesion volume over the subsequent 1 year. Glial activation in white matter assessed by translocator protein PET significantly improves predictions of white matter lesion enlargement in relapsing remitting patients and is associated with greater brain atrophy in secondary progressive disease over a period of short term follow-up.

    更新日期:2017-09-23
  • IMMOBILIZATION ALTERS HEPARIN CLEAVING PROPERTIES OF HEPARINASE I
    Glycobiology (IF 3.112) Pub Date : 2017-08-22
    Indu Bhushan, Alhumaidi Alabbas, Balagurunathan Kuberan, Ram B. Gupta, Umesh R. Desai

    We report here a novel observation that immobilization of heparinase I on CNBr-activated Sepharose results in heparin degradation properties that are different from heparinase I in the free solution form. Studies over a range of pHs (5–8) and temperatures (5–50°C) as well as under batch and flow conditions show that immobilized heparinase 1 displays altered pH and temperature optima, and a higher propensity for generation of longer chains (hexa- and octa-) with variable sulfation as compared to that in the free form, which is known to yield disaccharides. The immobilized enzyme retained good eliminase activity over at least five cycles of reuse. In combination, results suggest that heparinase I immobilization may offer a more productive route to longer, variably sulfated sequences.

    更新日期:2017-09-23
  • Family of Bioactive Heparin-Coated Iron Oxide Nanoparticles with Positive Contrast in Magnetic Resonance Imaging for Specific Biomedical Applications
    Biomacromolecules (IF 5.246) Pub Date : 2017-09-22
    Hugo Groult, Nicolas Poupard, Fernando Herranz, Egle Conforto, Nicolas Bridiau, Fréderic Sannier, Stéphanie Bordenave, Jean-Marie Piot, Jesús Ruiz-Cabello, Ingrid Fruitier-Arnaudin, Thierry Maugard
    更新日期:2017-09-23
  • Automatic identification and quantification of extra-well fluorescence in microarray images
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-22
    Robert Rivera, Jie Wang, xiaobo yu, Gokhan Demirkan, Marika Hopper, Xiaofang Bian, Tasnia Tahsin, D. Mitchell Magee, Ji Qiu, Joshua LaBaer, Garrick Wallstrom

    In recent studies involving NAPPA microarrays, extra-well fluorescence is used as a key measure for identifying disease biomarkers since there is evidence to support that it is better correlated with strong antibody responses than statistical analysis involving intra-spot intensity. Since this feature is not well quantified by traditional image analysis software, identification and quantification of extra-well fluorescence is performed manually, which is both time consuming and highly susceptible to variation between raters. A system that could automate this task efficiently and effectively would greatly improve the process of data acquisition in microarray studies, thereby accelerating the discovery of disease biomarkers. In this study, we experimented with different machine learning methods, as well as novel heuristics, for identifying spots exhibiting extra-well fluorescence (rings) in microarray images, and assigning each ring a grade of 1-5 based on its intensity and morphology. The sensitivity of our final system for identifying rings was found to be 72% at 99% specificity and 98% at 92% specificity. Our system performs this task significantly faster than a human, while maintaining high performance, and therefore, represents a valuable tool for microarray image analysis.

    更新日期:2017-09-23
  • Attachment Site Cysteine Thiol pKa Is a Key Driver for Site-Dependent Stability of THIOMAB Antibody–Drug Conjugates
    Bioconjugate Chem. (IF 4.818) Pub Date : 2017-09-22
    Breanna S. Vollmar, Binqing Wei, Rachana Ohri, Jianhui Zhou, Jintang He, Shang-Fan Yu, Douglas Leipold, Ely Cosino, Sharon Yee, Aimee Fourie-O’Donohue, Guangmin Li, Gail L. Phillips, Katherine R. Kozak, Amrita Kamath, Keyang Xu, Genee Lee, Greg A. Lazar, Hans K. Erickson
    更新日期:2017-09-23
  • Proteolytic Unlocking of Ultrastable Twin-Acylhydrazone Linkers for Lysosomal Acid-Triggered Release of Anticancer Drugs
    Bioconjugate Chem. (IF 4.818) Pub Date : 2017-09-22
    Yiwu Zheng, Jing Ren, Yaqi Wu, Xiaoting Meng, Yibing Zhao, Chuanliu Wu
    更新日期:2017-09-23
  • Cationic Poly(benzyl ether)s as Self-Immolative Antimicrobial Polymers
    Biomacromolecules (IF 5.246) Pub Date : 2017-09-22
    Cansu Ergene, Edmund F. Palermo
    更新日期:2017-09-23
  • 更新日期:2017-09-23
  • Reversible Dimerization of Polymeric Amphiphiles Acts as a Molecular Switch of Enzymatic Degradability
    Biomacromolecules (IF 5.246) Pub Date : 2017-09-22
    Ido Rosenbaum, Ram Avinery, Assaf J. Harnoy, Gadi Slor, Einat Tirosh, Uri Hananel, Roy Beck, Roey J. Amir
    更新日期:2017-09-23
  • The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-22
    Jochen M Schwenk, Gilbert S Omenn, Zhi Sun, David S Campbell, Mark S. Baker, Christopher M Overall, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch

    Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization’s Human Plasma Proteome Project (HPPP) has been promoting advances in the study and understanding of the full protein complement of human plasma and on determining the abundance and modifications of its components. In 2017, we review the history of the HPPP and the advances of human plasma proteomics in general, including several recent achievements. We then present the latest 2017-04 build of Human Plasma PeptideAtlas, which yields ~43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments at a 1% protein-level FDR globally across all experiments. Applying the latest Human Proteome Project Data Interpretation Guidelines, we catalog 3509 proteins that have at least two non-nested uniquely-mapping peptides of 9 amino acids or more and >1300 additional proteins with ambiguous evidence. We apply the same two-peptide guideline to historical PeptideAtlas builds going back to 2006 and examine the progress made in the past ten years in plasma proteome coverage. We also compare the distribution of proteins in historical PeptideAtlas builds in various RNA-abundance and cellular localization categories. We then discuss advances in plasma proteomics based on targeted mass spectrometry as well as affinity assays, which during early 2017 target ~2000 proteins. Finally we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.

    更新日期:2017-09-23
  • Generation of Clickable Pittsburgh Compound B for the Detection and Capture of β-Amyloid in Alzheimer’s Disease Brain
    Bioconjugate Chem. (IF 4.818) Pub Date : 2017-09-22
    Ian Diner, Jeromy Dooyema, Marla Gearing, Lary C. Walker, Nicholas T. Seyfried
    更新日期:2017-09-23
  • Urinary metabolic phenotyping of women with lower urinary tract symptoms
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-22
    Rhiannon Bray, Stefano Cacciatore, Beatriz Jimenez, Rufus Cartwright, Alex Digesu, Ruwan Fernando, Elaine Holmes, Jeremy Kirk Nicholson, Phillip R. Bennett, David A. MacIntyre, Vik Khullar

    Lower urinary tract symptoms (LUTS), including urinary incontinence, urgency and nocturia, affect approximately half of women worldwide. Current diagnostic methods for LUTS are invasive and costly, while available treatments are limited by side effects leading to poor patient compliance. In this study, we aimed to identify urine metabolic signatures associated with LUTS using proton nuclear magnetic resonance (1H-NMR) spectroscopy. A total of 214 urine samples were collected from women attending tertiary urogynaecology clinics (cases; n=176) and healthy control women attending general gynecology clinics (n=36). Despite high variation in the urine metabolome across the cohort, associations between urine metabolic profiles and BMI, parity, overactive bladder syndrome, frequency, straining and bladder storage were identified using KODAMA (knowledge discovery by accuracy maximization). Four distinct urinary metabotypes were identified, one of which was associated with increased urinary frequency and low BMI. Urine from these patients was characterized by increased levels of isoleucine and decreased levels of hippurate. Our study suggests that metabolic profiling of urine samples from LUTS patients offers the potential to identify differences in underlying aetiology, which may permit stratification of patient populations and the design of more personalized treatment strategies.

    更新日期:2017-09-23
  • His-Tag-Mediated Dimerization of Chemoreceptors Leads to Assembly of Functional Nanoarrays
    Biochemistry (IF 2.938) Pub Date : 2017-09-22
    Elizabeth R. Haglin, Wen Yang, Ariane Briegel, Lynmarie K. Thompson
    更新日期:2017-09-23
  • Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis
    Biochemistry (IF 2.938) Pub Date : 2017-09-22
    Nilkamal Mahanta, Graham A. Hudson, Douglas A. Mitchell
    更新日期:2017-09-23
  • Vigilance or Subversion? Constitutive and Inducible M Cells in Mucosal Tissues
    Trends Immunol. (IF 13.287) Pub Date : 2017-09-22
    David D. Lo

    Microfold (M) cells are epithelial cells present in mucosal tissues and specialized for the capture of luminal microparticles and their delivery to underlying immune cells; thus, they are crucial participants in mucosal immune surveillance. Multiple phenotypic subsets of M cells have now been described, all sharing a unique apical morphology that provides clues to their ability to capture microbial particles. The existence of diverse M cell phenotypes, especially inflammation-inducible M cells, provides an intriguing puzzle: some variants may augment luminal surveillance to boost mucosal immunity, while others may promote microbial access to tissues. Here, I consider the unique induction requirements of each M cell subset and functional differences, highlighting the potentially distinct consequences in mucosal immunity.

    更新日期:2017-09-23
  • Vigilance or Subversion? Constitutive and Inducible M Cells in Mucosal Tissues
    Trends Immunol. (IF 13.287) Pub Date : 2017-09-22
    David D. Lo
    更新日期:2017-09-23
  • “Juice monsters”: sub-ohm vaping and toxic volatile aldehyde emissions
    Chem. Res. Toxicol. (IF 3.278) Pub Date : 2017-09-22
    Soha Talih, Rola Salman, Nareg Karaoghlanian, Ahmad El-Hellani, Najat Aoun Saliba, Thomas Eissenberg, Alan Shihadeh

    An emerging category of electronic cigarettes (ECIGs) are sub-Ohm devices (SODs) that operate at ten or more times the power of conventional ECIGs. Because carcinogenic volatile aldehyde (VAs) emissions increase sharply with power, SODs may expose users to greater VAs. In this study, we compared VA emissions from several SODs and found that across device, VAs and power were un-correlated unless power was normalized by coil surface area. VA emissions and liquid consumed were correlated highly. Analyzed in light of EU regulations limiting ECIG liquid nicotine concentration, these findings suggest potential regulatory levers and pitfalls for protecting public health.

    更新日期:2017-09-23
  • Investigation of Dioscorea bulbifera Rhizome-Induced Hepatotoxicity in Rats by a Multisample Integrated Metabolomics Approach
    Chem. Res. Toxicol. (IF 3.278) Pub Date : 2017-09-22
    Dong-Sheng Zhao, Li-Long Jiang, Ya-Xi Fan, Ling-Li Wang, Zhuo-Qing Li, Wei Shi, Ping Li, Hui-Jun Li
    更新日期:2017-09-23
  • Coordination and Substitution of DNA Polymerases in Response to Genomic Obstacles
    Chem. Res. Toxicol. (IF 3.278) Pub Date : 2017-09-22
    Michael A. Trakselis, Matthew T. Cranford, Aurea M. Chu
    更新日期:2017-09-23
  • Rational Design of an Anticalin-Type Sugar-Binding Protein Using a Genetically Encoded Boronate Side Chain
    ACS Synth. Biol. (IF 5.382) Pub Date : 2017-09-22
    Selvakumar Edwardraja, Andreas Eichinger, Ina Theobald, Carina Andrea Sommer, Andreas J. Reichert, Arne Skerra

    The molecular recognition of carbohydrates plays a fundamental role in many biological processes. However, the development of carbohydrate-binding reagents for biomedical research and use poses a challenge due to the generally poor affinity of proteins towards sugars in aqueous solution. Here, we describe the effective molecular recognition of pyranose monosaccharides (in particular, galactose and mannose) by a rationally designed protein receptor based on the human lipocalin scaffold (Anticalin). Complexation relies on reversible covalent cis-diol boronate diester formation with a genetically encoded L-boronophenylalanine (Bpa) residue which was incorporated as a non-natural amino acid at a sterically permissive position in the binding site of the Anticalin, as confirmed by X-ray crystallography. Com-pared with the metal-ion and/or avidity-dependent oligovalent lectins that prevail in nature, our approach offers a novel and promising route to generate tight sugar-binding reagents both as research reagents and for biomedical applications.

    更新日期:2017-09-23
  • Genome-wide identification of bacterial plant colonization genes
    PLOS Bio. (IF 9.797) Pub Date : 2017-09-22
    Benjamin J. Cole, Meghan E. Feltcher, Robert J. Waters, Kelly M. Wetmore, Tatiana S. Mucyn, Elizabeth M. Ryan, Gaoyan Wang, Sabah Ul-Hasan, Meredith McDonald, Yasuo Yoshikuni, Rex R. Malmstrom, Adam M. Deutschbauer, Jeffery L. Dangl, Axel Visel
    更新日期:2017-09-23
  • A new discrete dynamic model of ABA-induced stomatal closure predicts key feedback loops
    PLOS Bio. (IF 9.797) Pub Date : 2017-09-22
    Réka Albert, Biswa R. Acharya, Byeong Wook Jeon, Jorge G. T. Zañudo, Mengmeng Zhu, Karim Osman, Sarah M. Assmann
    更新日期:2017-09-23
  • Early afterdepolarisation tendency as a simulated pro-arrhythmic risk indicator
    Toxicol. Res. (IF 1.969) Pub Date : 2017-09-14
    Beth McMillan, David J. Gavaghan, Gary R. Mirams
    更新日期:2017-09-23
  • CarSite: identifying carbonylated sites of human proteins based on a one-sided selection resampling method
    Mol. Biosyst. (IF 2.781) Pub Date : 2017-08-31
    Yun Zuo, Cang-Zhi Jia
    更新日期:2017-09-22
  • Structural step forward for NHEJ
    Cell Res. (IF 15.606) Pub Date : 2017-09-19
    Go Watanabe, Michael R Lieber, Dewight Williams

    In a recent paper published in Cell Research, a cryo-EM structure reveals the interface between DNA-PKcs and the Ku70/80:DNA complex, together forming the DNA-dependent protein kinase holoenzyme in non-homologous DNA end joining. Insight from this structure suggests how an allosteric rearrangement of DNA-PKcs driven by Ku70/80:DNA binding regulates kinase activity in this largest member of a family of structurally homologous phosphoinositide 3-kinase-related protein kinases that includes mTOR, ATR, and ATM.

    更新日期:2017-09-22
  • Fine-tuning type I IFN signaling: A new chapter in the IFN saga
    Cell Res. (IF 15.606) Pub Date : 2017-09-19
    Hideyuki Yanai, Tadatsugu Taniguchi

    Type I interferon (IFN) signaling is critical for intracellular antimicrobial programmes, affecting both innate and adaptive immune responses. The paper recently published in Cell demonstrates a new regulatory mechanism of the type I IFN signaling pathway by histone-lysine N-methyltransferase SETD2.

    更新日期:2017-09-22
  • 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers
    Cell Res. (IF 15.606) Pub Date : 2017-09-19
    Wenshuai Li, Xu Zhang, Xingyu Lu, Lei You, Yanqun Song, Zhongguang Luo, Jun Zhang, Ji Nie, Wanwei Zheng, Diannan Xu, Yaping Wang, Yuanqiang Dong, Shulin Yu, Jun Hong, Jianping Shi, Hankun Hao, Fen Luo, Luchun Hua, Peng Wang, Xiaoping Qian, Fang Yuan, Lianhuan Wei, Ming Cui, Taiping Zhang, Quan Liao, Menghua Dai, Ziwen Liu, Ge Chen, Katherine Meckel, Sarbani Adhikari, Guifang Jia, Marc B Bissonnette, Xinxiang Zhang, Yupei Zhao, Wei Zhang, Chuan He, Jie Liu

    DNA modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are epigenetic marks known to affect global gene expression in mammals. Given their prevalence in the human genome, close correlation with gene expression and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology, we report here the genome-wide profiling of 5hmC in circulating cell-free DNA (cfDNA) and in genomic DNA (gDNA) of paired tumor and adjacent tissues collected from a cohort of 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver or thyroid cancer and normal tissues from 90 healthy individuals. 5hmC was mainly distributed in transcriptionally active regions coincident with open chromatin and permissive histone modifications. Robust cancer-associated 5hmC signatures were identified in cfDNA that were characteristic for specific cancer types. 5hmC-based biomarkers of circulating cfDNA were highly predictive of colorectal and gastric cancers and were superior to conventional biomarkers and comparable to 5hmC biomarkers from tissue biopsies. Thus, this new strategy could lead to the development of effective, minimally invasive methods for diagnosis and prognosis of cancer from the analyses of blood samples.

    更新日期:2017-09-22
  • Size matters: Finding growth pathways that protect the heart
    Cell Res. (IF 15.606) Pub Date : 2017-09-19
    J Sawalla Guseh, Anthony Rosenzweig

    In a recent paper published in Cell Research, Abdul-Ghani and colleagues show that the cytokine, cardiotrophin-1 (CT1), drives a protective form of reversible cardiac hypertrophy that acts through a nonapoptotic caspase-dependent mechanism. Since CT1 can be delivered as exogenous protein, these studies provide new biological insights and potential translational opportunities.

    更新日期:2017-09-22
  • A vital sugar code for ricin toxicity
    Cell Res. (IF 15.606) Pub Date : 2017-09-19
    Jasmin Taubenschmid, Johannes Stadlmann, Markus Jost, Tove Irene Klokk, Cory D Rillahan, Andreas Leibbrandt, Karl Mechtler, James C Paulson, Julian Jude, Johannes Zuber, Kirsten Sandvig, Ulrich Elling, Thorsten Marquardt, Christian Thiel, Christian Koerner, Josef M Penninger

    Ricin is one of the most feared bioweapons in the world due to its extreme toxicity and easy access. Since no antidote exists, it is of paramount importance to identify the pathways underlying ricin toxicity. Here, we demonstrate that the Golgi GDP-fucose transporter Slc35c1 and fucosyltransferase Fut9 are key regulators of ricin toxicity. Genetic and pharmacological inhibition of fucosylation renders diverse cell types resistant to ricin via deregulated intracellular trafficking. Importantly, cells from a patient with SLC35C1 deficiency are also resistant to ricin. Mechanistically, we confirm that reduced fucosylation leads to increased sialylation of Lewis X structures and thus masking of ricin-binding sites. Inactivation of the sialyltransferase responsible for modifications of Lewis X (St3Gal4) increases the sensitivity of cells to ricin, whereas its overexpression renders cells more resistant to the toxin. Thus, we have provided unprecedented insights into an evolutionary conserved modular sugar code that can be manipulated to control ricin toxicity.

    更新日期:2017-09-22
  • Identification of Siglec Ligands Using a Proximity Labeling Method
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-22
    Lanyi Chang, Yi-Ju Chen, Chan-Yo Fan, Chin-Ju Tang, Yi-Hsiu Chen, Penk-Yeir Low, Albert Ventura, Chun-Cheng Lin, Yu-Ju Chen, Takashi Angata
    更新日期:2017-09-22
  • Periplasmic Binding Protein Dimer Has a Second Allosteric Event Tied to Ligand Binding
    Biochemistry (IF 2.938) Pub Date : 2017-09-22
    Le Li, Sudipa Ghimire-Rijal, Sarah L. Lucas, Christopher B. Stanley, Edward Wright, Pratul K. Agarwal, Dean A. Myles, Matthew J. Cuneo
    更新日期:2017-09-22
  • Systematic integration of biomedical knowledge prioritizes drugs for repurposing
    eLife (IF 7.725) Pub Date : 2017-09-22
    Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini

    The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval. This study describes Project Rephetio to systematically model drug efficacy based on 755 existing treatments. First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. Data was integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects, and symptoms. Next, we identified network patterns that distinguish treatments from non-treatments. Then we predicted the probability of treatment for 209,168 compound-disease pairs (het.io/repurpose). Our predictions validated on two external sets of treatment and provided pharmacological insights on epilepsy, suggesting they will help prioritize drug repurposing candidates. This study was entirely open and received realtime feedback from 40 community members.

    更新日期:2017-09-22
  • Systematic integration of biomedical knowledge prioritizes drugs for repurposing
    eLife (IF 7.725) Pub Date : 2017-09-22
    Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini

    The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval. This study describes Project Rephetio to systematically model drug efficacy based on 755 existing treatments. First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. Data was integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects, and symptoms. Next, we identified network patterns that distinguish treatments from non-treatments. Then we predicted the probability of treatment for 209,168 compound-disease pairs (het.io/repurpose). Our predictions validated on two external sets of treatment and provided pharmacological insights on epilepsy, suggesting they will help prioritize drug repurposing candidates. This study was entirely open and received realtime feedback from 40 community members.

    更新日期:2017-09-22
  • Tributylphosphate (TBP) and tris (2-butoxyethyl) phosphate (TBEP) induced apoptosis and cell cycle arrest in HepG2 cells
    Toxicol. Res. (IF 1.969) Pub Date : 2017-08-29
    Guofa Ren, Jingwen Hu, Yu Shang, Yufang Zhong, Zhiqiang Yu, Jing An
    更新日期:2017-09-22
  • Multidrug Resistance Protein 4 (MRP4/ABCC4) Protects Cells from the Toxic Effects of Halobenzoquinones
    Chem. Res. Toxicol. (IF 3.278) Pub Date : 2017-09-22
    Jinhua Li, Madlen Bauer, Birget Moe, Elaine M. Leslie, Xing-Fang Li
    更新日期:2017-09-22
  • Duodenal cytochrome b (Cybrd1) ferric reductase functional studies in cells
    Metallomics (IF 3.975) Pub Date : 2017-09-15
    F. Schlottmann, M. Vera-Aviles, G. O. Latunde-Dada
    更新日期:2017-09-22
  • Stereoselective Differences between the Reinforcing and Motivational Effects of Cathinone-Derived 4-Methylmethcathinone (Mephedrone) In Self-Administering Rats
    ACS Chem. Neurosci. (IF 3.883) Pub Date : 2017-09-22
    Helene L. Philogene-Khalid, Steven J. Simmons, Sunil Nayak, Rose M. Martorana, Shu H. Su, Yohanka Caro, Brona Ranieri, Kathryn DiFurio, Lili Mo, Taylor A. Gentile, Ali Murad, Allen B. Reitz, John W. Muschamp, Scott M. Rawls
    更新日期:2017-09-22
  • A synthetic DNA-binding inhibitor of SOX2 guides human induced pluripotent stem cells to differentiate into mesoderm
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-31
    Junichi Taniguchi, Ganesh N. Pandian, Takuya Hidaka, Kaori Hashiya, Toshikazu Bando, Kyeong Kyu Kim, Hiroshi Sugiyama

    Targeted differentiation of human induced pluripotent stem cells (hiPSCs) using only chemicals would have value-added clinical potential in the regeneration of complex cell types including cardiomyocytes. Despite the availability of several chemical inhibitors targeting proteins involved in signaling pathways, no bioactive synthetic DNA-binding inhibitors, targeting key cell fate-controlling genes such as SOX2, are yet available. Here, we demonstrate a novel DNA-based chemical approach to guide the differentiation of hiPSCs using pyrrole–imidazole polyamides (PIPs), which are sequence-selective DNA-binding synthetic molecules. Harnessing knowledge about key transcriptional changes during the induction of cardiomyocyte, we developed a DNA-binding inhibitor termed PIP-S2, targeting the 5′-CTTTGTT-3′ and demonstrated that inhibition of SOX2–DNA interaction by PIP-S2 triggers the mesoderm induction in hiPSCs. Genome-wide gene expression analyses revealed that PIP-S2 induced mesoderm by targeted alterations in SOX2-associated gene regulatory networks. Also, employment of PIP-S2 along with a Wnt/β-catenin inhibitor successfully generated spontaneously contracting cardiomyocytes, validating our concept that DNA-binding inhibitors could drive the directed differentiation of hiPSCs. Because PIPs can be fine-tuned to target specific DNA sequences, our DNA-based approach could be expanded to target and regulate key transcription factors specifically associated with desired cell types.

    更新日期:2017-09-21
  • Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-17
    Alexey K. Shaytan, Hua Xiao, Grigoriy A. Armeev, Carl Wu, David Landsman, Anna R. Panchenko

    Nucleosomes are the most abundant protein–DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical footprinting (HRF) of protein–DNA complexes is a chemical technique that probes nucleosome organization in solution with a high precision unattainable by other methods. In this work we propose an integrative modeling method for constructing high-resolution atomistic models of nucleosomes based on HRF experiments. Our method precisely identifies DNA positioning on nucleosome by combining HRF data for both DNA strands with the pseudo-symmetry constraints. We performed high-resolution HRF for Saccharomyces cerevisiae centromeric nucleosome of unknown structure and characterized it using our integrative modeling approach. Our model provides the basis for further understanding the cooperative engagement and interplay between Cse4p protein and the A-tracts important for centromere function.

    更新日期:2017-09-21
  • Automatic identification of informative regions with epigenomic changes associated to hematopoiesis
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-17
    Enrique Carrillo-de-Santa-Pau, David Juan, Vera Pancaldi, Felipe Were, Ignacio Martin-Subero, Daniel Rico, Alfonso Valencia

    Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify 42 human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability: https://github.com/david-juan/ChromDet.

    更新日期:2017-09-21
  • CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-08-09
    Zijun Zhang, Yi Xing

    Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation–maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein–RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome.

    更新日期:2017-09-21
  • Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-08-04
    Andrey Tvardovskiy, Veit Schwämmle, Stefan J. Kempf, Adelina Rogowska-Wrzesinska, Ole N. Jensen

    Deposition of replication-independent histone variant H3.3 into chromatin is essential for many biological processes, including development and reproduction. Unlike replication-dependent H3.1/2 isoforms, H3.3 is expressed throughout the cell cycle and becomes enriched in postmitotic cells with age. However, lifelong dynamics of H3 variant replacement and the impact of this process on chromatin organization remain largely undefined. Using quantitative middle-down proteomics we demonstrate that H3.3 accumulates to near saturation levels in the chromatin of various mouse somatic tissues by late adulthood. Accumulation of H3.3 is associated with profound changes in global levels of both individual and combinatorial H3 methyl modifications. A subset of these modifications exhibit distinct relative abundances on H3 variants and remain stably enriched on H3.3 throughout the lifespan, suggesting a causal relationship between H3 variant replacement and age-dependent changes in H3 methylation. Furthermore, the H3.3 level is drastically reduced in human hepatocarcinoma cells as compared to nontumoral hepatocytes, suggesting the potential utility of the H3.3 relative abundance as a biomarker of abnormal cell proliferation activity. Overall, our study provides the first quantitative characterization of dynamic changes in H3 proteoforms throughout lifespan in mammals and suggests a role for H3 variant replacement in modulating H3 methylation landscape with age.

    更新日期:2017-09-21
  • A comprehensive, cell specific microRNA catalogue of human peripheral blood
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-08-11
    Simonas Juzenas, Geetha Venkatesh, Matthias Hübenthal, Marc P. Hoeppner, Zhipei Gracie Du, Maren Paulsen, Philip Rosenstiel, Philipp Senger, Martin Hofmann-Apitius, Andreas Keller, Limas Kupcinskas, Andre Franke, Georg Hemmrich-Stanisak

    With this study, we provide a comprehensive reference dataset of detailed miRNA expression profiles from seven types of human peripheral blood cells (NK cells, B lymphocytes, cytotoxic T lymphocytes, T helper cells, monocytes, neutrophils and erythrocytes), serum, exosomes and whole blood. The peripheral blood cells from buffy coats were typed and sorted using FACS/MACS. The overall dataset was generated from 450 small RNA libraries using high-throughput sequencing. By employing a comprehensive bioinformatics and statistical analysis, we show that 3′ trimming modifications as well as composition of 3′ added non-templated nucleotides are distributed in a lineage-specific manner—the closer the hematopoietic progenitors are, the higher their similarities in sequence variation of the 3′ end. Furthermore, we define the blood cell-specific miRNA and isomiR expression patterns and identify novel cell type specific miRNA candidates. The study provides the most comprehensive contribution to date towards a complete miRNA catalogue of human peripheral blood, which can be used as a reference for future studies. The dataset has been deposited in GEO and also can be explored interactively following this link: http://134.245.63.235/ikmb-tools/bloodmiRs.

    更新日期:2017-09-21
  • The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-06-15
    Fernando Gómez-Herreros, Thanasis Margaritis, Olga Rodríguez-Galán, Vicent Pelechano, Victoria Begley, Gonzalo Millán-Zambrano, Macarena Morillo-Huesca, Mari Cruz Muñoz-Centeno, José E. Pérez-Ortín, Jesús de la Cruz, Frank C. P. Holstege, Sebastián Chávez

    Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis. We found that the in vivo depletion of one of these factors, Arb1, activated transcription elongation in the set of genes involved directly in ribosome assembly. Under these depletion conditions, Spt6 was physically targeted to the up-regulated genes, where it helped maintain their chromatin integrity and the synthesis of properly stable mRNAs. The mRNA profiles of a large set of ribosome biogenesis mutants confirmed the existence of a feedback regulatory network among ribosome assembly genes. The transcriptional response in this network depended on both the specific malfunction and the role of the regulated gene. In accordance with our screening, Spt6 positively contributed to the optimal operation of this global network. On the whole, this work uncovers a feedback control of ribosome biogenesis by fine-tuning transcription elongation in ribosome assembly factor-coding genes.

    更新日期:2017-09-21
  • Identification of multiple roles for histone acetyltransferase 1 in replication-coupled chromatin assembly
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-06-28
    Paula A. Agudelo Garcia, Michael E. Hoover, Pei Zhang, Prabakaran Nagarajan, Michael A. Freitas, Mark R. Parthun

    Histone acetyltransferase 1 (Hat1) catalyzes the acetylation of newly synthesized histone H4 at lysines 5 and 12 that accompanies replication-coupled chromatin assembly. The acetylation of newly synthesized H4 occurs in the cytoplasm and the function of this acetylation is typically ascribed to roles in either histone nuclear import or deposition. Using cell lines from Hat1+/+ and Hat1−/− mouse embryos, we demonstrate that Hat1 is not required for either histone nuclear import or deposition. We employed quantitative proteomics to characterize Hat1-dependent changes in the composition of nascent chromatin structure. Among the proteins depleted from nascent chromatin isolated from Hat1−/− cells are several bromodomain-containing proteins, including Brg1, Baz1A and Brd3. Analysis of the binding specificity of their bromodomains suggests that Hat1-dependent acetylation of H4 is directly involved in their recruitment. Hat1−/− nascent chromatin is enriched for topoisomerase 2α and 2β. The enrichment of topoisomerase 2 is functionally relevant as Hat1−/− cells are hyper-sensitive to topoisomerase 2 inhibition suggesting that Hat1 is required for proper chromatin topology. In addition, our results indicate that Hat1 is transiently recruited to sites of chromatin assembly, dissociating prior to the maturation of chromatin structure.

    更新日期:2017-09-21
  • XIAP upregulates expression of HIF target genes by targeting HIF1α for Lys63-linked polyubiquitination
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-06-28
    Catherine V. Park, Iglika G. Ivanova, Niall S. Kenneth

    The cellular response to hypoxia is characterised by a switch in the transcriptional program, mediated predominantly by the hypoxia inducible factor family of transcription factors (HIF). Regulation of HIF1 is primarily controlled by post-translational modification of the HIF1α subunit, which can alter its stability and/or activity. This study identifies an unanticipated role for the X-linked inhibitor of apoptosis (XIAP) protein as a regulator of Lys63-linked polyubiquitination of HIF1α. Lys63-linked ubiquitination of HIF1α by XIAP is dependent on the activity of E2 ubiquitin conjugating enzyme Ubc13. We find that XIAP and Ubc13 dependent Lys63-linked polyubiquitination promotes HIF1α nuclear retention leading to an increase in the expression of HIF1 responsive genes. Inhibition of the Lys63-linked polyubiquitination pathway leads to reduced levels of nuclear HIF1α, promoter occupancy, HIF-dependent gene expression and cell viability. Our data reveals an additional and significant level of control of the HIF1 by XIAP, with important implications in understanding the role of HIF1 and XIAP in human disease.

    更新日期:2017-09-21
  • Crosstalk between histone modifications indicates that inhibition of arginine methyltransferase CARM1 activity reverses HIV latency
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-06-20
    Zheng Zhang, Bryan C. Nikolai, Leah A. Gates, Sung Yun Jung, Edward B. Siwak, Bin He, Andrew P. Rice, Bert W. O’Malley, Qin Feng

    In eukaryotic cells, the gene expression status is strictly controlled by epigenetic modifications on chromatin. The repressive status of chromatin largely contributes to HIV latency. Studies have shown that modification of histone H3K27 acts as a key molecular switch for activation or suppression of many cellular genes. In this study, we found that K27-acetylated histone H3 specifically recruited Super Elongation Complex (SEC), the transcriptional elongation complex essential for HIV-1 long terminal repeat (LTR)-mediated and general cellular transcription. Interestingly, H3K27 acetylation further stimulates H3R26 methylation, which subsequently abrogates the recruitment of SEC, forming a negative feedback regulatory loop. Importantly, by inhibiting methyltransferase activity of CARM1, the enzyme responsible for H3R26 methylation, HIV-1 transcription is reactivated in several HIV latency cell models, including a primary resting CD4+ T cell model. When combined with other latency disrupting compounds such as JQ1 or vorinostat/SAHA, the CARM1 inhibitor achieved synergistic effects on HIV-1 activation. This study suggests that coordinated and dynamic modifications at histone H3K27 and H3R26 orchestrate HIV-1 LTR-mediated transcription, and potentially opens a new avenue to disrupt latent HIV-1 infection by targeting specific epigenetic enzymes.

    更新日期:2017-09-21
  • Recruitment and delivery of the fission yeast Rst2 transcription factor via a local genome structure counteracts repression by Tup1-family corepressors
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-06-27
    Ryuta Asada, Miki Umeda, Akira Adachi, Satoshi Senmatsu, Takuya Abe, Hiroshi Iwasaki, Kunihiro Ohta, Charles S. Hoffman, Kouji Hirota

    Transcription factors (TFs) determine the transcription activity of target genes and play a central role in controlling the transcription in response to various environmental stresses. Three dimensional genome structures such as local loops play a fundamental role in the regulation of transcription, although the link between such structures and the regulation of TF binding to cis-regulatory elements remains to be elucidated. Here, we show that during transcriptional activation of the fission yeast fbp1 gene, binding of Rst2 (a critical C2H2 zinc-finger TF) is mediated by a local loop structure. During fbp1 activation, Rst2 is first recruited to upstream-activating sequence 1 (UAS1), then it subsequently binds to UAS2 (a critical cis-regulatory site located approximately 600 base pairs downstream of UAS1) through a loop structure that brings UAS1 and UAS2 into spatially close proximity. Tup11/12 (the Tup-family corepressors) suppress direct binding of Rst2 to UAS2, but this suppression is counteracted by the recruitment of Rst2 at UAS1 and following delivery to UAS2 through a loop structure. These data demonstrate a previously unappreciated mechanism for the recruitment and expansion of TF-DNA interactions within a promoter mediated by local three-dimensional genome structures and for timely TF-binding via counteractive regulation by the Tup-family corepressors.

    更新日期:2017-09-21
  • Regulation of chromatin folding by conformational variations of nucleosome linker DNA
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-06-27
    Jenna M. Buckwalter, Davood Norouzi, Anna Harutyunyan, Victor B. Zhurkin, Sergei A. Grigoryev

    Linker DNA conformational variability has been proposed to direct nucleosome array folding into more or less compact chromatin fibers but direct experimental evidence for such models are lacking. Here, we tested this hypothesis by designing nucleosome arrays with A-tracts at specific locations in the nucleosome linkers to induce inward (AT-IN) and outward (AT-OUT) bending of the linker DNA. Using electron microscopy and analytical centrifugation techniques, we observed spontaneous folding of AT-IN nucleosome arrays into highly compact structures, comparable to those induced by linker histone H1. In contrast, AT-OUT nucleosome arrays formed less compact structures with decreased nucleosome interactions similar to wild-type nucleosome arrays. Adding linker histone H1 further increased compaction of the A-tract arrays while maintaining structural differences between them. Furthermore, restriction nuclease digestion revealed a strongly reduced accessibility of nucleosome linkers in the compact AT-IN arrays. Electron microscopy analysis and 3D computational Monte Carlo simulations are consistent with a profound zigzag linker DNA configuration and closer nucleosome proximity in the AT-IN arrays due to inward linker DNA bending. We propose that the evolutionary preferred positioning of A-tracts in DNA linkers may control chromatin higher-order folding and thus influence cellular processes such as gene expression, transcription and DNA repair.

    更新日期:2017-09-21
  • Cohesin acetyltransferase Esco2 regulates SAC and kinetochore functions via maintaining H4K16 acetylation during mouse oocyte meiosis
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-06-27
    Yajuan Lu, Xiaoxin Dai, Mianqun Zhang, Yilong Miao, Changyin Zhou, Zhaokang Cui, Bo Xiong

    Sister chromatid cohesion, mediated by cohesin complex and established by the acetyltransferases Esco1 and Esco2, is essential for faithful chromosome segregation. Mutations in Esco2 cause Roberts syndrome, a developmental disease characterized by severe prenatal retardation as well as limb and facial abnormalities. However, its exact roles during oocyte meiosis have not clearly defined. Here, we report that Esco2 localizes to the chromosomes during oocyte meiotic maturation. Depletion of Esco2 by morpholino microinjection leads to the precocious polar body extrusion, the escape of metaphase I arrest induced by nocodazole treatment and the loss of BubR1 from kinetochores, indicative of inactivated SAC. Furthermore, depletion of Esco2 causes a severely impaired spindle assembly and chromosome alignment, accompanied by the remarkably elevated incidence of defective kinetochore-microtubule attachments which consequently lead to the generation of aneuploid eggs. Notably, we find that the involvement of Esco2 in SAC and kinetochore functions is mediated by its binding to histone H4 and acetylation of H4K16 both in vivo and in vitro. Thus, our data assign a novel meiotic function to Esco2 beyond its role in the cohesion establishment during mouse oocyte meiosis.

    更新日期:2017-09-21
  • A novel requirement for DROSHA in maintenance of mammalian CG methylation
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-08-03
    Athanasia Stathopoulou, Jyoti B. Chhetri, John C. Ambrose, Pierre-Olivier Estève, Lexiang Ji, Hediye Erdjument-Bromage, Guoqiang Zhang, Thomas A. Neubert, Sriharsa Pradhan, Javier Herrero, Robert J. Schmitz, Steen K.T. Ooi

    In mammals, faithful inheritance of genomic methylation patterns ensures proper gene regulation and cell behaviour, impacting normal development and fertility. Following establishment, genomic methylation patterns are transmitted through S-phase by the maintenance methyltransferase Dnmt1. Using a protein interaction screen, we identify Microprocessor component DROSHA as a novel DNMT1-interactor. Drosha-deficient embryonic stem (ES) cells display genomic hypomethylation that is not accounted for by changes in the levels of DNMT proteins. DNMT1-mediated methyltransferase activity is also reduced in these cells. We identify two transcripts that are specifically upregulated in Drosha- but not Dicer-deficient ES cells. Regions within these transcripts predicted to form stem–loop structures are processed by Microprocessor and can inhibit DNMT1-mediated methylation in vitro. Our results highlight DROSHA as a novel regulator of mammalian DNA methylation and we propose that DROSHA-mediated processing of RNA is necessary to ensure full DNMT1 activity. This adds to the DROSHA repertoire of non-miRNA dependent functions as well as implicating RNA in regulating DNMT1 activity and correct levels of genomic methylation.

    更新日期:2017-09-21
  • Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-12
    Nilisha Pokhrel, Sofia Origanti, Eric Parker Davenport, Disha Gandhi, Kyle Kaniecki, Ryan A. Mehl, Eric C. Greene, Chris Dockendorff, Edwin Antony

    An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance.

    更新日期:2017-09-21
  • Human DNA polymerase delta double-mutant D316A;E318A interferes with DNA mismatch repair in vitro
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-14
    Dekang Liu, Jane H. Frederiksen, Sascha E. Liberti, Anne Lützen, Guido Keijzers, Javier Pena-Diaz, Lene Juel Rasmussen

    DNA mismatch repair (MMR) is a highly-conserved DNA repair mechanism, whose primary role is to remove DNA replication errors preventing them from manifesting as mutations, thereby increasing the overall genome stability. Defects in MMR are associated with increased cancer risk in humans and other organisms. Here, we characterize the interaction between MMR and a proofreading-deficient allele of the human replicative DNA polymerase delta, PolδD316A;E318A, which has a higher capacity for strand displacement DNA synthesis than wild type Polδ. Human cell lines overexpressing PolδD316A;E318A display a mild mutator phenotype, while nuclear extracts of these cells exhibit reduced MMR activity in vitro, and these defects are complemented by overexpression or addition of exogenous human Exonuclease 1 (EXO1). By contrast, another proofreading-deficient mutant, PolδD515V, which has a weaker strand displacement activity, does not decrease the MMR activity as significantly as PolδD316A;E318A. In addition, PolδD515V does not increase the mutation frequency in MMR-proficient cells. Based on our findings, we propose that the proofreading activity restricts the strand displacement activity of Polδ in MMR. This contributes to maintain the nicks required for EXO1 entry, and in this manner ensures the dominance of the EXO1-dependent MMR pathway.

    更新日期:2017-09-21
  • Phosphorylation regulates human polη stability and damage bypass throughout the cell cycle
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-24
    Federica Bertoletti, Valentina Cea, Chih-Chao Liang, Taiba Lanati, Antonio Maffia, Mario D.M. Avarello, Lina Cipolla, Alan R. Lehmann, Martin A. Cohn, Simone Sabbioneda

    DNA translesion synthesis (TLS) is a crucial damage tolerance pathway that oversees the completion of DNA replication in the presence of DNA damage. TLS polymerases are capable of bypassing a distorted template but they are generally considered inaccurate and they need to be tightly regulated. We have previously shown that polη is phosphorylated on Serine 601 after DNA damage and we have demonstrated that this modification is important for efficient damage bypass. Here we report that polη is also phosphorylated by CDK2, in the absence of damage, in a cell cycle-dependent manner and we identify serine 687 as an important residue targeted by the kinase. We discover that phosphorylation on serine 687 regulates the stability of the polymerase during the cell cycle, allowing it to accumulate in late S and G2 when productive TLS is critical for cell survival. Furthermore, we show that alongside the phosphorylation of S601, the phosphorylation of S687 and S510, S512 and/or S514 are important for damage bypass and cell survival after UV irradiation. Taken together our results provide new insights into how cells can, at different times, modulate DNA TLS for improved cell survival.

    更新日期:2017-09-21
  • STN1–POLA2 interaction provides a basis for primase-pol α stimulation by human STN1
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-19
    Swapna Ganduri, Neal F. Lue

    The CST (CTC1–STN1–TEN1) complex mediates critical functions in maintaining telomere DNA and overcoming genome-wide replication stress. A conserved biochemical function of the CST complex is its primase-Pol α (PP) stimulatory activity. In this report, we demonstrate the ability of purified human STN1 alone to promote PP activity in vitro. We show that this regulation is mediated primarily by the N-terminal OB fold of STN1, but does not require the DNA-binding activity of this domain. Rather, we observed a strong correlation between the PP-stimulatory activity of STN1 variants and their abilities to bind POLA2. Remarkably, the main binding target of STN1 in POLA2 is the latter's central OB fold domain. In the substrate-free structure of PP, this domain is positioned so as to block nucleic acid entry to the Pol α active site. Thus the STN1–POLA2 interaction may promote the necessary conformational change for nucleic acid delivery to Pol α and subsequent DNA synthesis. A disease-causing mutation in human STN1 engenders a selective defect in POLA2-binding and PP stimulation, indicating that these activities are critical for the in vivo function of STN1. Our findings have implications for the molecular mechanisms of PP, STN1 and STN1-related molecular pathology.

    更新日期:2017-09-21
  • Systematic analysis of DNA crosslink repair pathways during development and aging in Caenorhabditis elegans
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-29
    David M. Wilson, Matthias Rieckher, Ashley B. Williams, Björn Schumacher

    DNA interstrand crosslinks (ICLs) are generated by endogenous sources and chemotherapeutics, and pose a threat to genome stability and cell survival. Using Caenorhabditis elegans mutants, we identify DNA repair factors that protect against the genotoxicity of ICLs generated by trioxsalen/ultraviolet A (TMP/UVA) during development and aging. Mutations in nucleotide excision repair (NER) components (e.g. XPA-1 and XPF-1) imparted extreme sensitivity to TMP/UVA relative to wild-type animals, manifested as developmental arrest, defects in adult tissue morphology and functionality, and shortened lifespan. Compensatory roles for global-genome (XPC-1) and transcription-coupled (CSB-1) NER in ICL sensing were exposed. The analysis also revealed contributions of homologous recombination (BRC-1/BRCA1), the MUS-81, EXO-1, SLX-1 and FAN-1 nucleases, and the DOG-1 (FANCJ) helicase in ICL resolution, influenced by the replicative-status of the cell/tissue. No obvious or critical role in ICL repair was seen for non-homologous end-joining (cku-80) or base excision repair (nth-1, exo-3), the Fanconi-related proteins BRC-2 (BRCA2/FANCD1) and FCD-2 (FANCD2), the WRN-1 or HIM-6 (BLM) helicases, or the GEN-1 or MRT-1 (SNM1) nucleases. Our efforts uncover replication-dependent and -independent ICL repair networks, and establish nematodes as a model for investigating the repair and consequences of DNA crosslinks in metazoan development and in adult post-mitotic and proliferative germ cells.

    更新日期:2017-09-21
  • A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-26
    Lifang Feng, Guangying Wang, Eileen P. Hamilton, Jie Xiong, Guanxiong Yan, Kai Chen, Xiao Chen, Wen Dui, Amber Plemens, Lara Khadr, Arjune Dhanekula, Mina Juma, Hung Quang Dang, Geoffrey M. Kapler, Eduardo Orias, Wei Miao, Yifan Liu

    Developmentally programmed genome rearrangement accompanies differentiation of the silent germline micronucleus into the transcriptionally active somatic macronucleus in the ciliated protozoan Tetrahymena thermophila. Internal eliminated sequences (IES) are excised, followed by rejoining of MAC-destined sequences, while fragmentation occurs at conserved chromosome breakage sequences, generating macronuclear chromosomes. Some macronuclear chromosomes, referred to as non-maintained chromosomes (NMC), are lost soon after differentiation. Large NMC contain genes implicated in development-specific roles. One such gene encodes the domesticated piggyBac transposase TPB6, required for heterochromatin-dependent precise excision of IES residing within exons of functionally important genes. These conserved exonic IES determine alternative transcription products in the developing macronucleus; some even contain free-standing genes. Examples of precise loss of some exonic IES in the micronucleus and retention of others in the macronucleus of related species suggest an evolutionary analogy to introns. Our results reveal that germline-limited sequences can encode genes with specific expression patterns and development-related functions, which may be a recurring theme in eukaryotic organisms experiencing programmed genome rearrangement during germline to soma differentiation.

    更新日期:2017-09-21
  • Widespread intra-dependencies in the removal of introns from human transcripts
    Nucleic Acids Res. (IF 10.162) Pub Date : 2017-07-29
    Seong Won Kim, Allison J. Taggart, Claire Heintzelman, Kamil J. Cygan, Caitlin G. Hull, Jing Wang, Barsha Shrestha, William G. Fairbrother

    Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough information to explain the observed fidelity of splicing. Here, we conclude that introns do not necessarily contain ‘missing’ information but rather may require definition from neighboring processing events. For example, there are known cases where an intronic mutation disrupts the splicing of not only the local intron but also adjacent introns. We present a genome-wide measurement of the order of splicing within human transcripts. The observed order of splicing cannot be explained by a simple kinetic model. Simulations reveal a bias toward a particular, transcript-specific order of intron removal in human genes. We validate an extreme class of intron that can only splice in a multi-intron context. Special categories of splicing such as exon circularization, first and last intron processing, alternative 5 and 3′ss usage and exon skipping are marked by distinct patterns of ordered intron removal. Excessive intronic length and silencer density tend to delay splicing. Shorter introns that contain enhancers splice early.

    更新日期:2017-09-21
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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