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Supplementary Data Table 1. Genes Upregulated in N-Myc-Overexpressing Mouse Mac1+/Gr1+ BM Cells

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Supplementary Data Table 1. Genes upregulated in N-Myc-overexpressing mouse Mac1+/Gr1+ BM cells Probeset C-myc / N-myc / N-myc / C- Gene Title Representative 430v2 Vector Fold Vector Fold myc Fold Public ID Change Change Change 1435368_a_at 2.3 4.6 2.1 poly (ADP-ribose) polymerase family, member 1 BB767586 1455648_at 1.3 3.0 2.1 similar to reduced expression 2 /// similar to reduced expression 2 BG244780 1438973_x_at 2.5 9.8 4.0 gap junction membrane channel protein alpha 1 BB043407 1419915_at 2.0 3.0 2.1 DNA segment, Chr 10, ERATO Doi 438, expressed AW538011 1454842_a_at 1.6 4.0 2.3 UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, AI853240 polypeptide 2 1436704_x_at 2.1 9.2 3.2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent), AV215673 methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase 1423142_a_at 2.0 2.5 2.1 GTP binding protein 4 AI987834 1420043_s_at 2.5 5.7 2.8 THO complex 1 AW107924 1439444_x_at 1.5 4.3 2.5 transmembrane emp24-like trafficking protein 10 (yeast) /// similar to AV213456 transmembrane trafficking protein 1438610_a_at 1.9 4.9 2.3 Crystallin, zeta BB793369 1434291_a_at 2.5 4.3 2.8 small EDRK-rich factor 1 AA709993 1422716_a_at 2.8 6.5 2.6 acid phosphatase 1, soluble AW554436 1447895_x_at -1.3 2.3 2.6 PAN3 polyA specific ribonuclease subunit homolog (S. cerevisiae) AV368189 1434097_at 1.5 3.2 2.5 Transcribed locus BM218328 1420982_at 1.1 3.5 2.6 RNA-binding region (RNP1, RRM) containing 2 NM_133242 1433853_at 2.6 7.5 2.6 mindbomb homolog 1 (Drosophila) BG063791 1419824_a_at 1.6 4.0 2.1 RIKEN cDNA A230062G08 gene AI875121 1453797_at 7.5 14.9 2.1 phosphatase, orphan 2 AK010147 1440803_x_at 2.3 4.0 2.3 tachykinin receptor 3 BB498416 1455737_at -2.0 1.1 2.8 RIKEN cDNA C030002B11 gene AU040848 1450954_at -1.5 2.8 4.6 YME1-like 1 (S. cerevisiae) BB826168 1439047_s_at 1.3 2.3 2.1 RecQ protein-like BB258011 1423149_at -2.1 1.5 4.3 S-phase kinase-associated protein 1A AV347477 1456864_at -1.0 3.7 4.0 --- BB210733 1447150_at -1.3 2.3 2.5 pam, highwire, rpm 1 AW107633 1455930_at -1.4 3.0 7.0 hypothetical protein LOC673503 BI651113 1423140_at -1.1 2.5 2.3 lysosomal acid lipase 1 AI596237 1440924_at -1.6 2.1 3.5 M-phase phosphoprotein 1 BM239553 1457656_s_at -1.4 2.1 2.8 RIKEN cDNA C230085N15 gene BB235011 1420115_at -1.7 2.5 4.3 exosome component 8 C80158 1437162_at -1.9 2.1 3.5 GPI-anchored membrane protein 1 BM203355 1439302_at -1.1 2.6 3.7 ubiquitin-activating enzyme E1-like 2 AV266743 1425884_at -1.6 2.5 3.2 brix domain containing 1 BC025093 1441788_s_at -1.1 2.8 3.2 cDNA sequence BC068171 BB779105 1426906_at -1.0 2.6 3.2 interferon activated gene 203 M74124 1419484_a_at -1.2 2.5 2.5 glioblastoma amplified sequence NM_008095 1425922_a_at -2.3 17.1 73.5 v-myc myelocytomatosis viral related oncogene, neuroblastoma M36277 derived (avian) 1417695_a_at -1.4 2.3 3.2 sterol O-acyltransferase 1 BG064396 1457285_at -1.3 2.5 3.0 zinc finger protein 187 BB354728 1449217_at -1.2 2.1 2.6 caspase 8 associated protein 2 NM_011997 1436584_at -1.5 2.5 4.0 sprouty homolog 2 (Drosophila) BB529691 1439638_at -1.2 2.1 2.5 Erbb2 interacting protein BB336138 1437100_x_at -1.3 2.3 3.0 proviral integration site 3 BB206220 1416886_at 1.1 2.5 3.2 nuclear DNA binding protein NM_020558 1443771_x_at -1.4 2.8 4.3 MAD homolog 7 (Drosophila) BB241324 1443966_at -1.3 2.8 4.9 3 days neonate thymus cDNA, RIKEN full-length enriched library, BF466594 clone:A630040N16 product:unclassifiable, full insert sequence 1447813_x_at -1.1 2.5 2.8 src-like adaptor AV247013 1419926_at -1.1 2.1 2.6 Thioredoxin domain containing 10 AV259382 1440822_x_at -1.2 2.1 2.5 RalBP1 associated Eps domain containing protein BB333366 1458667_at -1.3 4.3 7.5 RIKEN cDNA 4930519N13 gene AV266695 1447757_x_at 1.3 3.2 2.6 inositol polyphosphate-5-phosphatase F AV033355 1443665_at -1.4 11.3 14.9 Expressed sequence AI852444 BE994639 1440179_x_at -1.2 2.1 2.6 IBR domain containing 1 BB268139 1441391_at -1.5 3.0 4.0 Guanine nucleotide binding protein (G protein), beta polypeptide 1- BG069873 like 1455855_x_at 1.1 2.1 2.5 heterogeneous nuclear ribonucleoprotein A/B BB168316 1434701_at -1.3 2.6 3.5 expressed sequence AW215868 BB795363 1450896_at -1.5 3.2 3.2 Rho GTPase activating protein 5 BM248774 1438908_at -1.2 3.7 4.6 mitogen activated protein kinase kinase kinase 12 BB370469 1418381_at -1.1 2.1 2.3 zinc finger protein 148 X98096 1437995_x_at 1.1 2.5 2.3 septin 7 AV219419 1459854_s_at -1.1 2.3 2.6 dynein light chain Tctex-type 3 AV059518 1439932_at 1.1 2.5 2.3 RIKEN cDNA 3110003A22 gene BQ174624 1433854_at -1.1 2.5 2.8 expressed sequence AW547186 BG064061 1416429_a_at -1.1 2.5 2.3 catalase NM_009804 1437288_at -1.5 2.1 3.0 inositol monophosphatase domain containing 1 BG797423 1435400_at 1.1 2.8 2.3 RIKEN cDNA 2900075B16 gene BF462791 1456573_x_at -1.1 2.1 2.3 nicotinamide nucleotide transhydrogenase BB205930 1459756_at -1.1 2.6 3.0 CCR4-NOT transcription complex, subunit 10 AV301999 1427229_at -1.3 2.3 4.0 3-hydroxy-3-methylglutaryl-Coenzyme A reductase BB123978 1454885_at 1.4 3.0 2.5 cDNA sequence BC063263 BM211194 1434820_s_at 1.5 3.2 2.3 protein kinase inhibitor, gamma AV209892 1437992_x_at 2.1 7.0 3.2 gap junction membrane channel protein alpha 1 BB039269 1430991_at 1.2 2.6 2.3 RIKEN cDNA 1810014B01 gene AK017634 1420083_at 1.2 3.7 2.6 expressed sequence AU016916 AU016916 1438962_s_at 1.6 3.2 2.5 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31 BB469965 1420042_at 1.7 8.0 4.3 THO complex 1 AW107924 1451313_a_at 1.5 4.0 2.8 RIKEN cDNA 1110067D22 gene BC019131 1427172_at 1.1 2.8 2.5 oral-facial-digital syndrome 1 gene homolog (human) AJ278702 1441733_s_at 1.7 3.2 2.1 nucleoporin 153 C88147 1438560_x_at 1.7 3.7 2.5 chaperonin subunit 4 (delta) AV103196 1433824_x_at 1.2 2.5 2.3 G-rich RNA sequence binding factor 1 BB314772 1439462_x_at 1.4 4.0 2.8 transmembrane emp24-like trafficking protein 10 (yeast) /// similar to AV060550 transmembrane trafficking protein 1440272_at 1.6 4.0 2.1 Eukaryotic translation initiation factor 2, subunit 1 alpha BB232473 1436032_at 1.4 4.3 3.7 Bone marrow macrophage cDNA, RIKEN full-length enriched library, BB201888 clone:I830083F22 product:unclassifiable, full insert sequence 1427152_at 1.3 3.5 2.1 glutamine and serine rich 1 BC021511 1433891_at 1.7 4.3 3.0 leucine-rich repeat-containing G protein-coupled receptor 4 /// BI107632 similar to Leucine-rich repeat-containing G-protein coupled receptor 4 precursor 1438941_x_at 1.4 3.0 2.1 adenosine monophosphate deaminase 2 (isoform L) AV330806 1456729_x_at 1.5 3.7 2.3 regulator of telomere elongation helicase 1 BB218661 1436737_a_at 2.3 9.2 3.0 sorbin and SH3 domain containing 1 BB737680 1439406_x_at 1.2 2.6 2.1 phenylalanine-tRNA synthetase 2 (mitochondrial) BB530332 1456057_x_at 1.5 4.3 2.8 transmembrane protein 109 BB117756 1434452_x_at 1.6 4.0 2.3 eukaryotic translation initiation factor 2a BG797460 1440816_x_at 1.6 4.0 2.3 DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 AV089443 1455496_at 1.6 4.3 2.5 phosphoribosylformylglycinamidine synthase (FGAR AV306055 amidotransferase) 1454688_x_at 1.4 3.7 2.5 transmembrane emp24-like trafficking protein 10 (yeast) /// similar to AV103299 transmembrane trafficking protein 1438786_a_at 1.7 4.6 2.5 RIKEN cDNA 2610021A01 gene /// similar to zinc finger protein 347 AV258879 1440284_at 1.1 3.0 2.3 Transcribed locus, weakly similar to XP_576460.1 PREDICTED: AI506066 similar to hypothetical protein PB402898.00.0 [Rattus norvegicus] 1437942_x_at 1.2 3.2 3.0 epsilon-tubulin 1 AV100095 1454149_a_at 1.4 3.0 2.3 cyclin L2 AK008585 1449641_at 1.1 2.5 2.1 --- AI508733 1438511_a_at 1.9 4.0 2.5 RIKEN cDNA 1190002H23 gene BB408123 1438931_s_at 1.3 3.7 3.0 sestrin 1 AV016566 1436113_a_at 1.2 2.8 2.1 --- BB770696 1457390_at 1.1 3.0 3.2 PRP3 pre-mRNA processing factor 3 homolog (yeast) BG069557 1438992_x_at 1.6 3.7 2.3 activating transcription factor 4 AV314773 1455816_a_at 2.0 4.6 2.5 potassium channel tetramerisation domain containing 3 BB321232 1441178_at 2.0 4.9 3.5 DTW domain containing 2 BB818617 1439419_at 2.1 5.3 2.3 RIKEN cDNA 2310057M21 gene BB189366 1433640_at 1.3 3.5 2.5 Far upstream element (FUSE) binding protein 1 BG070740 1437262_x_at 1.7 4.0 2.5 breast carcinoma amplified sequence 2 AA940256 1451967_x_at 1.9 4.3 2.3 karyopherin (importin) beta 1 BC004096 1455826_a_at 1.3 3.7 2.8 beta-site APP cleaving enzyme 1 BB114336 1459981_s_at 1.1 2.8 2.6 rosbin, round spermatid basic protein 1 AV240926 1437873_at -1.1 2.3 2.6 RIKEN cDNA 6030490I01 gene BB044772 1429332_at -1.0 2.5 2.3 RIKEN cDNA 4632427E13 gene AK019505 1437982_x_at 1.1 2.8 2.3 COX15 homolog, cytochrome c oxidase assembly protein (yeast) BB736240 1435493_at 1.1 3.2 2.6 desmoplakin AV297961 1423747_a_at 1.4 3.5 2.6 pyruvate dehydrogenase kinase, isoenzyme 1 BC027196 1452083_a_at 1.5 3.5 3.0 praja1, RING-H2 motif containing BM199789 1439263_at 1.2 3.7 2.6 fibroblast growth factor inducible 15 BB388301 1433568_at -1.0 3.0 3.0 PAP associated domain containing 4 AV301313 1436708_x_at 1.2 3.0 2.5 minichromosome maintenance deficient 4 homolog (S.
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  • Persistent Transcription-Blocking DNA Lesions Trigger Somatic Growth Attenuation Associated with Longevity

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    ARTICLES Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity George A. Garinis1,2, Lieneke M. Uittenboogaard1, Heike Stachelscheid3,4, Maria Fousteri5, Wilfred van Ijcken6, Timo M. Breit7, Harry van Steeg8, Leon H. F. Mullenders5, Gijsbertus T. J. van der Horst1, Jens C. Brüning4,9, Carien M. Niessen3,9,10, Jan H. J. Hoeijmakers1 and Björn Schumacher1,9,11 The accumulation of stochastic DNA damage throughout an organism’s lifespan is thought to contribute to ageing. Conversely, ageing seems to be phenotypically reproducible and regulated through genetic pathways such as the insulin-like growth factor-1 (IGF-1) and growth hormone (GH) receptors, which are central mediators of the somatic growth axis. Here we report that persistent DNA damage in primary cells from mice elicits changes in global gene expression similar to those occurring in various organs of naturally aged animals. We show that, as in ageing animals, the expression of IGF-1 receptor and GH receptor is attenuated, resulting in cellular resistance to IGF-1. This cell-autonomous attenuation is specifically induced by persistent lesions leading to stalling of RNA polymerase II in proliferating, quiescent and terminally differentiated cells; it is exacerbated and prolonged in cells from progeroid mice and confers resistance to oxidative stress. Our findings suggest that the accumulation of DNA damage in transcribed genes in most if not all tissues contributes to the ageing-associated shift from growth to somatic maintenance that triggers stress resistance and is thought to promote longevity. Ageing represents the progressive functional decline that is exempted levels as a result of pituitary dysfunction (Snell and Ames mice) — have an from evolutionary selection because it largely occurs after reproduc- extended lifespan17–20.
  • The Genetic Program of Pancreatic Beta-Cell Replication in Vivo

    The Genetic Program of Pancreatic Beta-Cell Replication in Vivo

    Page 1 of 65 Diabetes The genetic program of pancreatic beta-cell replication in vivo Agnes Klochendler1, Inbal Caspi2, Noa Corem1, Maya Moran3, Oriel Friedlich1, Sharona Elgavish4, Yuval Nevo4, Aharon Helman1, Benjamin Glaser5, Amir Eden3, Shalev Itzkovitz2, Yuval Dor1,* 1Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. 3Department of Cell and Developmental Biology, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel 4Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University and Hadassah, The Institute for Medical Research Israel- Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel 5Endocrinology and Metabolism Service, Department of Internal Medicine, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel *Correspondence: [email protected] Running title: The genetic program of pancreatic β-cell replication 1 Diabetes Publish Ahead of Print, published online March 18, 2016 Diabetes Page 2 of 65 Abstract The molecular program underlying infrequent replication of pancreatic beta- cells remains largely inaccessible. Using transgenic mice expressing GFP in cycling cells we sorted live, replicating beta-cells and determined their transcriptome. Replicating beta-cells upregulate hundreds of proliferation- related genes, along with many novel putative cell cycle components. Strikingly, genes involved in beta-cell functions, namely glucose sensing and insulin secretion were repressed. Further studies using single molecule RNA in situ hybridization revealed that in fact, replicating beta-cells double the amount of RNA for most genes, but this upregulation excludes genes involved in beta-cell function.
  • Regulation of COX Assembly and Function by Twin CX9C Proteins—Implications for Human Disease

    Regulation of COX Assembly and Function by Twin CX9C Proteins—Implications for Human Disease

    cells Review Regulation of COX Assembly and Function by Twin CX9C Proteins—Implications for Human Disease Stephanie Gladyck 1, Siddhesh Aras 1,2, Maik Hüttemann 1 and Lawrence I. Grossman 1,2,* 1 Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA; [email protected] (S.G.); [email protected] (S.A.); [email protected] (M.H.) 2 Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland and Detroit, MI 48201, USA * Correspondence: [email protected] Abstract: Oxidative phosphorylation is a tightly regulated process in mammals that takes place in and across the inner mitochondrial membrane and consists of the electron transport chain and ATP synthase. Complex IV, or cytochrome c oxidase (COX), is the terminal enzyme of the electron transport chain, responsible for accepting electrons from cytochrome c, pumping protons to contribute to the gradient utilized by ATP synthase to produce ATP, and reducing oxygen to water. As such, COX is tightly regulated through numerous mechanisms including protein–protein interactions. The twin CX9C family of proteins has recently been shown to be involved in COX regulation by assisting with complex assembly, biogenesis, and activity. The twin CX9C motif allows for the import of these proteins into the intermembrane space of the mitochondria using the redox import machinery of Mia40/CHCHD4. Studies have shown that knockdown of the proteins discussed in this review results in decreased or completely deficient aerobic respiration in experimental models ranging from yeast to human cells, as the proteins are conserved across species.