DOCSLIB.ORG

Mtor Regulates Endocytosis and Nutrient Transport in Proximal Tubular Cells

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mtor Regulates Endocytosis and Nutrient Transport in Proximal Tubular Cells BASIC RESEARCH www.jasn.org mTOR Regulates Endocytosis and Nutrient Transport in Proximal Tubular Cells † ‡ † Florian Grahammer,* Suresh K. Ramakrishnan, Markus M. Rinschen, Alexey A. Larionov, † | Maryam Syed, Hazim Khatib,§ Malte Roerden,§ Jörn Oliver Sass, ¶ Martin Helmstaedter,* Dorothea Osenberg,* Lucas Kühne,* Oliver Kretz,* Nicola Wanner,* Francois Jouret,** ‡ ††‡‡ † Thomas Benzing, Ferruh Artunc,§ Tobias B. Huber,* and Franziska Theilig *Department of Medicine IV, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; †Institute of Anatomy, Department of Medicine, University of Fribourg, Fribourg, Switzerland; ‡Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; §Department of Medical IV, Sektion Nieren- und Hochdruckkrankheiten, University of Tübingen, Tübingen, Germany; |Bioanalytics and Biochemistry, Department of Natural Sciences, Bonn Rhein Sieg University of Applied Sciences, Rheinbach, Germany; ¶Division of Clinical Chemistry and Biochemistry and Children’s Research Centre, University Children’s Hospital Zürich, Zurich, Switzerland; **Groupe Interdisciplinaire de Génoprotéomique Appliquée, Cardiovascular Sciences, University of Liège, Liege, Belgium; and ††BIOSS, Centre for Biological Signalling Studies and ‡‡FRIAS, Freiburg Institute for Advanced Studies and ZBSA, Center for Biological System Analysis, Albert Ludwigs University of Freiburg, Freiburg, Germany ABSTRACT Renal proximal tubular cells constantly recycle nutrients to ensure minimal loss of vital substrates into the urine. Although most of the transport mechanisms have been discovered at the molecular level, little is known about the factors regulating these processes. Here, we show that mTORC1 and mTORC2 specifically and synergistically regulate PTC endocytosis and transport processes. Using a conditional mouse genetic ap- proach to disable nonredundant subunits of mTORC1, mTORC2, or both, we showed that mice lacking mTORC1 or mTORC1/mTORC2 but not mTORC2 alone develop a Fanconi-like syndrome of glucosuria, phosphaturia, aminoaciduria, low molecular weight proteinuria, and albuminuria. Interestingly, proteomics and phosphoproteomics of freshly isolated kidney cortex identified either reduced expression or loss of phosphorylation at critical residues of different classes of specific transport proteins. Functionally, this resul- ted in reduced nutrient transport and a profound perturbation of the endocytic machinery, despite preserved absolute expression of the main scavenger receptors, MEGALIN and CUBILIN. Our findings highlight a novel mTOR–dependent regulatory network for nutrient transport in renal proximal tubular cells. J Am Soc Nephrol 28: ccc–ccc, 2016. doi: 10.1681/ASN.2015111224 With the transition from water to land, mammalian affect several transport systems, leading to a Fanconi kidneys developed into a high–pressure filtration syndrome.5,6 In addition to aminoaciduria, system combining excess ultrafiltration with highly Received November 12, 2015. Accepted May 14, 2016. efficient tubular reabsorption to minimize nutrient and protein loss.1 The vast amount of the ultrafil- T.B.H. and F.T. contributed equally to this work. trate (approximately 60%–70%), including virtu- Published online ahead of print. Publication date available at ally all nutrients, is already being reabsorbed by the www.jasn.org. 2 first nephron segment, the proximal tubule (PT). Correspondence: Dr. Franziska Theilig, Department of Medi- Specific loss of PT amino acid or phosphate trans- cine, University of Fribourg, Route Albert-Gockel 1, 1700 Fri- fi bourg, Switzerland or Dr. Tobias B. Huber, Medical Center, port function is associated with genetically de ned University of Freiburg, Center of Medicine, Renal Division, disease entities, such as Hartnup disorder or hypo- Breisacherstrasse 66, 79106 Freiburg, Germany. Email: franziska. phosphatemic rickets.3,4 In contrast, disrupted en- [email protected] or [email protected] ergy metabolism or toxic injury can simultaneously Copyright © 2016 by the American Society of Nephrology J Am Soc Nephrol 28: ccc–ccc, 2016 ISSN : 1046-6673/2801-ccc 1 BASIC RESEARCH www.jasn.org glucosuria, and phosphaturia, Fanconi syndrome is charac- genes (Raptorfl/fl 3 Rictorfl/fl 3 Pax8rtTA 3 TetOCre;subse- D terized by low molecular weight proteinuria.7 This is caused quently termed RapRic Tubule)(Figure1,A–C). Protein abun- by dysfunction of receptor-mediated endocytosis, which is dance or reduced phosphorylation of known downstream targets mediated by the two scavenger receptors, MEGALIN and was used to assess efficiency of our knockout approach (Figure 1, CUBILIN, followed by clathrin-mediated internalization of D–F). In comparison with the respective control group, all exam- D the ligand-receptor complex.8 Fusion with early endosomes ined parameters were at least reduced by 70% (Rap Tubule: delivers the complex to the endosomal-lysosomal com- RAPTOR, 274.6%64.6%; p-S6P/S6P, 278.9%66.4%; P,0.05; D partment, leading to recycling or degradation of retrieved n=6; Ric Tubule:RICTOR,284.5%68.4%; p-NDRG1/ D proteins.8 The prominent endocytotic activity of the PT is NDRG1, 271.1%63.7%; P,0.05; n=6; RapRic Tubule:RAPTOR, important to retrieve vital plasma proteins and maintain 278.3%66.2%; RICTOR, 269.1%65.3%; p-S6P/S6P, 289.2% body homeostasis.9 Although individual components of this 64.7%; p-NDRG1/NDRG1, 271.7%69.8%; P,0.05; n=6) (Fig- system have been recently described, little is known on the ure 1, D–F). organ-specific regulation of these transport processes. Measurement of urinary glucose and phosphate excretion D The mammalian homolog of TOR1 (mTORC1) and in RapRic Tubule mice revealed 3.3- and fivefold increases in mTORC2 are intracellular multiprotein complexes regulating urinary losses of glucose and phosphate, respectively, in- tissue–specific cellular functions.10 The regulatory associated dicating impaired nutrient reabsorption (Figure 1H). In protein of mammalian target of rapamycin (RAPTOR) is im- addition, SDS-PAGE of urinary samples revealed a slight D portant to assemble mammalian target of rapamycin (mTOR) increase in albuminuria in Rap Tubule,whichwassignificant D complex 1, and its function can be blocked by rapamycin. In in RapRic Tubule (Figure 1, I and K). This observation was contrast, mTORC2, containing the rapamycin-insensitive confirmed by direct measurement of mouse albumin in uri- companion of mammalian target of rapamycin (RICTOR) nary samples (Figure 1L). Furthermore, an increase in low as a scaffolding protein, seems to be insensitive to short– molecular mass (LMW) proteinuria between 25 and 68 kD D term rapamycin treatment.11 mTORC1 integrates a wide va- could be detected in RapRic Tubule (+126%637%; P,0.05; riety of signals, including growth factors, amino acids, cellular n=5)aswellasasignificant increase in proteinuria at ap- D D energy content, and cellular stress, to regulate cellular growth proximately25kDinRap Tubule and RapRic Tubule animals D D and division as well as lipid and mitochondrial biogenesis.12,13 (Rap Tubule:+70%613%; RapRic Tubule:+44%66%; The wide range of mTORC1 phosphorylation targets is still P,0.05; n=5). In addition, a pronounced increase in urinary D incompletely defined but seems to vary in a cell-specific man- amino acid excretion was observed in Rap Tubule animals, and D ner. Conversely, mTORC2 seems to be activated by insulin and an even more pronounced increase was in RapRic Tubule an- D related pathways and controls several downstream AGC ki- imals but not in Ric Tubule mice (Figure 1M, Supplemental nases by phosphorylating their hydrophobic motif.14,15 Figure 2A). Amino acid plasma concentrations were similar Thereby, mTORC2 could play an important role in cell sur- in all experimental groups (Supplemental Figure 2B), vival and organization of the cytoskeleton. confirming a renal amino acid transport defect rather than Toinvestigate the effect of mTOR-controlled signaling in PT defects in hepatic or muscular metabolism. D D function, we generated inducible conditional Raptor, Rictor,or Compared with control mice, Rap Tubule and RapRic Tubule double-knockout mice in renal tubular cells along the nephron. animals showed significantly higher food and fluid intakes, which were associated with increased urinary volume and sodium excretion (Supplemental Table 1). No alterations D RESULTS were found in Ric Tubule animals. Together, these data show a significant mTORC1–dependent defect in tubular Loss of mTOR in PT Cells Results in a Fanconi-Like reabsorption of glucose, phosphate, amino acids, LMW pro- Phenotype teins, and albumin. Expression of the mTORC1 and mTORC2 complexes in the PT was verified by staining for mTOR, RAPTOR, S6K1, ribosomal mTOR Regulates PTC Endocytosis and Intracellular S6 protein (S6P), and N-Myc Downstream Regulated 1 Trafficking In Vivo (NDRG1) (Supplemental Figure 1). All components were Togain additional insights into the effects of gene knockout on strongly expressed in the S1 and S2 segments of the PT in either PT endocytosis, mice were injected with horseradish perox- overlay or close vicinity to MEGALIN. The proximal tubular S3 idase (taken up by fluid-phase endocytosis) and Alexa555- segment only showed minor signal intensity for mTOR, S6K1, coupled lactoglobulin (reabsorbed by receptor-mediated and S6P and was devoid of signals for RAPTOR and NDRG1. endocytosis) before perfusion fixation.16 Morphologic anal- To examine the effects of mTORC deletion
Load more

Recommended publications
  • Myopia in African Americans Is Significantly Linked to Chromosome 7P15.2-14.2
    Genetics Myopia in African Americans Is Significantly Linked to Chromosome 7p15.2-14.2 Claire L. Simpson,1,2,* Anthony M. Musolf,2,* Roberto Y. Cordero,1 Jennifer B. Cordero,1 Laura Portas,2 Federico Murgia,2 Deyana D. Lewis,2 Candace D. Middlebrooks,2 Elise B. Ciner,3 Joan E. Bailey-Wilson,1,† and Dwight Stambolian4,† 1Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States 2Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States 3The Pennsylvania College of Optometry at Salus University, Elkins Park, Pennsylvania, United States 4Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States Correspondence: Joan E. PURPOSE. The purpose of this study was to perform genetic linkage analysis and associ- Bailey-Wilson, NIH/NHGRI, 333 ation analysis on exome genotyping from highly aggregated African American families Cassell Drive, Suite 1200, Baltimore, with nonpathogenic myopia. African Americans are a particularly understudied popula- MD 21131, USA; tion with respect to myopia. [email protected]. METHODS. One hundred six African American families from the Philadelphia area with a CLS and AMM contributed equally to family history of myopia were genotyped using an Illumina ExomePlus array and merged this work and should be considered co-first authors. with previous microsatellite data. Myopia was initially measured in mean spherical equiv- JEB-W and DS contributed equally alent (MSE) and converted to a binary phenotype where individuals were identified as to this work and should be affected, unaffected, or unknown.
    [Show full text]
  • Original Article a Database and Functional Annotation of NF-Κb Target Genes
    Int J Clin Exp Med 2016;9(5):7986-7995 www.ijcem.com /ISSN:1940-5901/IJCEM0019172 Original Article A database and functional annotation of NF-κB target genes Yang Yang, Jian Wu, Jinke Wang The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People’s Republic of China Received November 4, 2015; Accepted February 10, 2016; Epub May 15, 2016; Published May 30, 2016 Abstract: Backgrounds: The previous studies show that the transcription factor NF-κB always be induced by many inducers, and can regulate the expressions of many genes. The aim of the present study is to explore the database and functional annotation of NF-κB target genes. Methods: In this study, we manually collected the most complete listing of all NF-κB target genes identified to date, including the NF-κB microRNA target genes and built the database of NF-κB target genes with the detailed information of each target gene and annotated it by DAVID tools. Results: The NF-κB target genes database was established (http://tfdb.seu.edu.cn/nfkb/). The collected data confirmed that NF-κB maintains multitudinous biological functions and possesses the considerable complexity and diversity in regulation the expression of corresponding target genes set. The data showed that the NF-κB was a central regula- tor of the stress response, immune response and cellular metabolic processes. NF-κB involved in bone disease, immunological disease and cardiovascular disease, various cancers and nervous disease. NF-κB can modulate the expression activity of other transcriptional factors. Inhibition of IKK and IκBα phosphorylation, the decrease of nuclear translocation of p65 and the reduction of intracellular glutathione level determined the up-regulation or down-regulation of expression of NF-κB target genes.
    [Show full text]
  • Combinatorial Strategies Using CRISPR/Cas9 for Gene Mutagenesis in Adult Mice
    Combinatorial strategies using CRISPR/Cas9 for gene mutagenesis in adult mice Avery C. Hunker A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2019 Reading Committee: Larry S. Zweifel, Chair Sheri J. Mizumori G. Stanley McKnight Program Authorized to Offer Degree: Pharmacology 2 © Copyright 2019 Avery C. Hunker 3 University of Washington ABSTRACT Combinatorial strategies using CRISPR/Cas9 for gene mutagenesis in adult mice Avery C. Hunker Chair of the Supervisory Committee: Larry Zweifel Department of Pharmacology A major challenge to understanding how genes modulate complex behaviors is the inability to restrict genetic manipulations to defined cell populations or circuits. To circumvent this, we created a simple strategy for limiting gene knockout to specific cell populations using a viral-mediated, conditional CRISPR/SaCas9 system in combination with intersectional genetic strategies. A small single guide RNA (sgRNA) directs Staphylococcus aureus CRISPR-associated protein (SaCas9) to unique sites on DNA in a Cre-dependent manner resulting in double strand breaks and gene mutagenesis in vivo. To validate this technique we targeted nine different genes of diverse function in distinct cell types in mice and performed an array of analyses to confirm gene mutagenesis and subsequent protein loss, including IHC, cell-type specific DNA sequencing, electrophysiology, Western blots, and behavior. We show that these vectors are as efficient as conventional conditional gene knockout and provide a viable alternative to complex genetic crosses. This strategy provides additional benefits of 4 targeting gene mutagenesis to cell types previously difficult to isolate, and the ability to target genes in specific neural projections for gene inactivation.
    [Show full text]
  • A Role for Alternative Splicing in Circadian Control of Exocytosis and Glucose Homeostasis
    Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press A role for alternative splicing in circadian control of exocytosis and glucose homeostasis Biliana Marcheva,1,5 Mark Perelis,1,2,5 Benjamin J. Weidemann,1,5 Akihiko Taguchi,1 Haopeng Lin,3 Chiaki Omura,1 Yumiko Kobayashi,1 Marsha V. Newman,1 Eugene J. Wyatt,4 Elizabeth M. McNally,4 Jocelyn E. Manning Fox,3 Heekyung Hong,1 Archana Shankar,2 Emily C. Wheeler,2 Kathryn Moynihan Ramsey,1 Patrick E. MacDonald,3 Gene W. Yeo,2 and Joseph Bass1 1Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA; 2Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; 3Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada; 4Center for Genetic Medicine, Northwestern University, Chicago, Illinois 60611, USA The circadian clock is encoded by a negative transcriptional feedback loop that coordinates physiology and behavior through molecular programs that remain incompletely understood. Here, we reveal rhythmic genome-wide alter- native splicing (AS) of pre-mRNAs encoding regulators of peptidergic secretion within pancreatic β cells that are − − − − perturbed in Clock / and Bmal1 / β-cell lines. We show that the RNA-binding protein THRAP3 (thyroid hormone receptor-associated protein 3) regulates circadian clock-dependent AS by binding to exons at coding sequences flanking exons that are more frequently skipped in clock mutant β cells, including transcripts encoding Cask (calcium/calmodulin-dependent serine protein kinase) and Madd (MAP kinase-activating death domain).
    [Show full text]
  • Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
    Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ......................................................
    [Show full text]
  • Proteomic Profiling and Genome-Wide Mapping of O-Glcnac Chromatin
    ARTICLE https://doi.org/10.1038/s41467-020-19579-y OPEN Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response Yubo Liu 1,3, Qiushi Chen 2,3, Nana Zhang1, Keren Zhang2, Tongyi Dou1, Yu Cao1, Yimin Liu1, Kun Li1, ✉ ✉ Xinya Hao1, Xueqin Xie1, Wenli Li1, Yan Ren 2 & Jianing Zhang 1 fi 1234567890():,; O-GlcNAc modi cation plays critical roles in regulating the stress response program and cellular homeostasis. However, systematic and multi-omics studies on the O-GlcNAc regu- lated mechanism have been limited. Here, comprehensive data are obtained by a chemical reporter-based method to survey O-GlcNAc function in human breast cancer cells stimulated with the genotoxic agent adriamycin. We identify 875 genotoxic stress-induced O-GlcNAc chromatin-associated proteins (OCPs), including 88 O-GlcNAc chromatin-associated tran- scription factors and cofactors (OCTFs), subsequently map their genomic loci, and construct a comprehensive transcriptional reprogramming network. Notably, genotoxicity-induced O- GlcNAc enhances the genome-wide interactions of OCPs with chromatin. The dynamic binding switch of hundreds of OCPs from enhancers to promoters is identified as a crucial feature in the specific transcriptional activation of genes involved in the adaptation of cancer cells to genotoxic stress. The OCTF nuclear factor erythroid 2-related factor-1 (NRF1) is found to be a key response regulator in O-GlcNAc-modulated cellular homeostasis. These results provide a valuable clue suggesting that OCPs act as stress sensors by regulating the expression of various genes to protect cancer cells from genotoxic stress.
    [Show full text]
  • Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
    Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons.
    [Show full text]
  • The Neurodegenerative Diseases ALS and SMA Are Linked at The
    Nucleic Acids Research, 2019 1 doi: 10.1093/nar/gky1093 The neurodegenerative diseases ALS and SMA are linked at the molecular level via the ASC-1 complex Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gky1093/5162471 by [email protected] on 06 November 2018 Binkai Chi, Jeremy D. O’Connell, Alexander D. Iocolano, Jordan A. Coady, Yong Yu, Jaya Gangopadhyay, Steven P. Gygi and Robin Reed* Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA Received July 17, 2018; Revised October 16, 2018; Editorial Decision October 18, 2018; Accepted October 19, 2018 ABSTRACT Fused in Sarcoma (FUS) and TAR DNA Binding Protein (TARDBP) (9–13). FUS is one of the three members of Understanding the molecular pathways disrupted in the structurally related FET (FUS, EWSR1 and TAF15) motor neuron diseases is urgently needed. Here, we family of RNA/DNA binding proteins (14). In addition to employed CRISPR knockout (KO) to investigate the the RNA/DNA binding domains, the FET proteins also functions of four ALS-causative RNA/DNA binding contain low-complexity domains, and these domains are proteins (FUS, EWSR1, TAF15 and MATR3) within the thought to be involved in ALS pathogenesis (5,15). In light RNAP II/U1 snRNP machinery. We found that each of of the discovery that mutations in FUS are ALS-causative, these structurally related proteins has distinct roles several groups carried out studies to determine whether the with FUS KO resulting in loss of U1 snRNP and the other two members of the FET family, TATA-Box Bind- SMN complex, EWSR1 KO causing dissociation of ing Protein Associated Factor 15 (TAF15) and EWS RNA the tRNA ligase complex, and TAF15 KO resulting in Binding Protein 1 (EWSR1), have a role in ALS.
    [Show full text]
  • The RNA Processing Factors THRAP3 and BCLAF1 Promote the DNA Damage Response Through Selective Mrna Splicing and Nuclear Export Vohhodina, J., Barros, E
    The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export Vohhodina, J., Barros, E. M., Savage, A. L., Liberante, F. G., Manti, L., Bankhead, P., Cosgrove, N., Madden, A. F., Harkin, D. P., & Savage, K. I. (2017). The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export. Nucleic Acids Research, 45(22), 1-18. [gkx1046]. https://doi.org/10.1093/nar/gkx1046 Published in: Nucleic Acids Research Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2017 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected].
    [Show full text]
  • Tam Et Al., Genome Instability in Splicing Mutants 1 the Yeast Core
    bioRxiv preprint doi: https://doi.org/10.1101/272807; this version posted February 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Tam et al., Genome instability in splicing mutants The yeast core spliceosome maintains genome integrity through R-loop prevention and α-tubulin expression Annie S. Tam1,2, Veena Mathew1, Tianna S. Sihota1, Anni Zhang1, Peter C. Stirling1,2 1 Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver Canada 2 Department of Medical Genetics, University of British Columbia, Vancouver Canada Correspondence to P.C.S. [email protected] KEYWORDS: Splicing, Genome Instability, R-loops, Microtubules, Mitosis, Yeast To achieve genome stability cells must coordinate the action of various DNA transactions including DNA replication, repair, transcription and chromosome segregation. How transcription and RNA processing enable genome stability is only partly understood. Two predominant models have emerged: one involving changes in gene expression that perturb other genome maintenance factors, and another in which genotoxic DNA:RNA hybrids, called R-loops, impair DNA replication. Here we characterize genome instability phenotypes in a panel yeast splicing factor mutants and find that mitotic defects, and in some cases R-loop accumulation, are causes of genome instability. Genome instability in splicing mutants is exacerbated by loss of the spindle-assembly checkpoint protein Mad1. Moreover, removal of the intron from the α-tubulin gene TUB1 restores genome integrity. Thus, while R-loops contribute in some settings, defects in yeast splicing predominantly lead to genome instability through effects on gene expression.
    [Show full text]
  • Zbtb7b Engages the Long Noncoding RNA Blnc1 to Drive Brown
    Zbtb7b engages the long noncoding RNA Blnc1 to drive PNAS PLUS brown and beige fat development and thermogenesis Siming Lia,b,1, Lin Mia,b, Lei Yua,b,QiYua,b, Tongyu Liua,b, Guo-Xiao Wanga,b, Xu-Yun Zhaoa,b, Jun Wua,c, and Jiandie D. Lina,b,1 aLife Sciences Institute, University of Michigan, Ann Arbor, MI 48109; bDepartment of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI 48109; and cDepartment of Molecular & Integrated Physiology, University of Michigan Medical Center, Ann Arbor, MI 48109 Edited by Steven A. Kliewer, The University of Texas Southwestern Medical Center, Dallas, TX, and approved July 12, 2017 (received for review March 1, 2017) Brown and beige adipocytes convert chemical energy into heat number of transcription factors and cofactors have been identified throughuncoupledrespirationtodefendagainstcoldstress. that regulate the determination, differentiation, maturation, and Beyond thermogenesis, brown and beige fats engage other maintenance of thermogenic adipocytes (3, 24). Among these, metabolic tissues via secreted factors to influence systemic energy Prdm16 and EBF2 are emerging as key factors that stimulate ther- metabolism. How the protein and long noncoding RNA (lncRNA) mogenic gene programs during brown and beige adipocyte differ- regulatory networks act in concert to regulate key aspects of entiation. Interestingly, while Prdm16 is largely dispensable for thermogenic adipocyte biology remains largely unknown. Here we brown fat development, it is required for cold-induced browning of developed a genome-wide functional screen to interrogate the s.c. fat and maintaining the thermogenic capacity of brown fat during transcription factors and cofactors in thermogenic gene activation aging (25, 26).
    [Show full text]
  • Developing a Network View of Type 2 Diabetes Risk Pathways Through Integration of Genetic, Genomic and Functional Data Juan Fernández-Tajes1†, Kyle J
    Fernández-Tajes et al. Genome Medicine (2019) 11:19 https://doi.org/10.1186/s13073-019-0628-8 RESEARCH Open Access Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data Juan Fernández-Tajes1†, Kyle J. Gaulton2†, Martijn van de Bunt1,3,8, Jason Torres1,3, Matthias Thurner1,3, Anubha Mahajan1, Anna L. Gloyn1,3,4, Kasper Lage5,6,7 and Mark I. McCarthy1,3,4* Abstract Background: Genome-wide association studies (GWAS) have identified several hundred susceptibility loci for type 2 diabetes (T2D). One critical, but unresolved, issue concerns the extent to which the mechanisms through which these diverse signals influencing T2D predisposition converge on a limited set of biological processes. However, the causal variants identified by GWAS mostly fall into a non-coding sequence, complicating the task of defining the effector transcripts through which they operate. Methods: Here, we describe implementation of an analytical pipeline to address this question. First, we integrate multiple sources of genetic, genomic and biological data to assign positional candidacy scores to the genes that map to T2D GWAS signals. Second, we introduce genes with high scores as seeds within a network optimization algorithm (the asymmetric prize-collecting Steiner tree approach) which uses external, experimentally confirmed protein-protein interaction (PPI) data to generate high-confidence sub-networks. Third, we use GWAS data to test the T2D association enrichment of the “non-seed” proteins introduced
    [Show full text]