Longitudinal RNA-Seq Analysis of Vertebrate Aging Identifies Mitochondrial Complex I as a Small-Molecule-Sensitive Modifier of Lifespan

Anders, 2010, Differential expression analysis for sequence count data, Genome Biol., 11, R106, 10.1186/gb-2010-11-10-r106 Bartke, 2011, Single-gene mutations and healthy ageing in mammals, Philos. Trans. R. Soc. Lond. B Biol. Sci., 366, 28, 10.1098/rstb.2010.0281 Barzilai, 2012, The critical role of metabolic pathways in aging, Diabetes, 61, 1315, 10.2337/db11-1300 Baumgart, 2014, RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis, Aging Cell, 13, 965, 10.1111/acel.12257 Beekman, 2013, Genome-wide linkage analysis for human longevity: Genetics of Healthy Aging Study, Aging Cell, 12, 184, 10.1111/acel.12039 Bratic, 2013, The role of mitochondria in aging, J. Clin. Invest., 123, 951, 10.1172/JCI64125 Bridges, 2014, Effects of metformin and other biguanides on oxidative phosphorylation in mitochondria, Biochem. J., 462, 475, 10.1042/BJ20140620 Broer, 2015, GWAS of longevity in CHARGE consortium confirms APOE and FOXO3 candidacy, J. Gerontol. A Biol. Sci. Med. Sci., 70, 110, 10.1093/gerona/glu166 Casci, 2011, Development: Hourglass theory gets molecular approval, Nat. Rev. Genet., 12, 76, 10.1038/nrg2940 Cellerino, 2015, From the bush to the bench: the annual Nothobranchius fishes as a new model system in biology, Biol. Rev. Camb. Philos. Soc. Colantuoni, 2011, Temporal dynamics and genetic control of transcription in the human prefrontal cortex, Nature, 478, 519, 10.1038/nature10524 Copeland, 2009, Extension of Drosophila life span by RNAi of the mitochondrial respiratory chain, Curr. Biol., 19, 1591, 10.1016/j.cub.2009.08.016 de Cabo, 2014, The search for antiaging interventions: from elixirs to fasting regimens, Cell, 157, 1515, 10.1016/j.cell.2014.05.031 De Haes, 2014, Metformin promotes lifespan through mitohormesis via the peroxiredoxin PRDX-2, Proc. Natl. Acad. Sci. USA, 111, E2501, 10.1073/pnas.1321776111 de Magalhães, 2009, Meta-analysis of age-related gene expression profiles identifies common signatures of aging, Bioinformatics, 25, 875, 10.1093/bioinformatics/btp073 Deelen, 2014, Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age, Hum. Mol. Genet., 23, 4420, 10.1093/hmg/ddu139 Dillin, 2002, Timing requirements for insulin/IGF-1 signaling in C. elegans, Science, 298, 830, 10.1126/science.1074240 Dillin, 2002, Rates of behavior and aging specified by mitochondrial function during development, Science, 298, 2398, 10.1126/science.1077780 Fontana, 2010, Extending healthy life span--from yeast to humans, Science, 328, 321, 10.1126/science.1172539 Gems, 2013, Genetics of longevity in model organisms: debates and paradigm shifts, Annu. Rev. Physiol., 75, 621, 10.1146/annurev-physiol-030212-183712 Gerhard, 2003, Comparative aspects of zebrafish (Danio rerio) as a model for aging research, Exp. Gerontol., 38, 1333, 10.1016/j.exger.2003.10.022 Gerhard, 2002, Life spans and senescent phenotypes in two strains of Zebrafish (Danio rerio), Exp. Gerontol., 37, 1055, 10.1016/S0531-5565(02)00088-8 Guthke, 2005, Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection, Bioinformatics, 21, 1626, 10.1093/bioinformatics/bti226 Harel, 2015, A platform for rapid exploration of aging and diseases in a naturally short-lived vertebrate, Cell, 160, 1013, 10.1016/j.cell.2015.01.038 Hartmann, 2011, Mitochondrial DNA copy number and function decrease with age in the short-lived fish Nothobranchius furzeri, Aging Cell, 10, 824, 10.1111/j.1474-9726.2011.00723.x Herndon, 2002, Stochastic and genetic factors influence tissue-specific decline in ageing C. elegans, Nature, 419, 808, 10.1038/nature01135 Herrera, 2004, Annual fish as a genetic model for aging, J. Gerontol. A Biol. Sci. Med. Sci., 59, 101, 10.1093/gerona/59.2.B101 Houtkooper, 2013, Mitonuclear protein imbalance as a conserved longevity mechanism, Nature, 497, 451, 10.1038/nature12188 Huang, 2007, The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists, Genome Biol., 8, R183, 10.1186/gb-2007-8-9-r183 Huang, 2007, DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists, Nucleic Acids Res., 35, W169, 10.1093/nar/gkm415 Janssens, 2015, Protein biogenesis machinery is a driver of replicative aging in yeast, eLife, 4, 4, 10.7554/eLife.08527 Kim, 2007, Functional genomic approach to identify novel genes involved in the regulation of oxidative stress resistance and animal lifespan, Aging Cell, 6, 489, 10.1111/j.1474-9726.2007.00302.x Kim, 2013, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, R36, 10.1186/gb-2013-14-4-r36 Kirschner, 2012, Mapping of quantitative trait loci controlling lifespan in the short-lived fish Nothobranchius furzeri--a new vertebrate model for age research, Aging Cell, 11, 252, 10.1111/j.1474-9726.2011.00780.x Kishi, 2004, Functional aging and gradual senescence in zebrafish, Ann. N Y Acad. Sci., 1019, 521, 10.1196/annals.1297.097 Langfelder, 2008, WGCNA: an R package for weighted correlation network analysis, BMC Bioinformatics, 9, 559, 10.1186/1471-2105-9-559 Lee, 2003, A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity, Nat. Genet., 33, 40, 10.1038/ng1056 Liao, 2014, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, 30, 923, 10.1093/bioinformatics/btt656 López-Otín, 2013, The hallmarks of aging, Cell, 153, 1194, 10.1016/j.cell.2013.05.039 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8 Luo, 2009, GAGE: generally applicable gene set enrichment for pathway analysis, BMC Bioinformatics, 10, 161, 10.1186/1471-2105-10-161 Martin-Montalvo, 2013, Metformin improves healthspan and lifespan in mice, Nat. Commun., 4, 2192, 10.1038/ncomms3192 Miwa, 2014, Low abundance of the matrix arm of complex I in mitochondria predicts longevity in mice, Nat. Commun., 5, 3837, 10.1038/ncomms4837 Ori, 2015, Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats, Cell Syst., 1, 224, 10.1016/j.cels.2015.08.012 Pincus, 2011, MicroRNA predictors of longevity in Caenorhabditis elegans, PLoS Genet., 7, e1002306, 10.1371/journal.pgen.1002306 Pletikos, 2014, Temporal specification and bilaterality of human neocortical topographic gene expression, Neuron, 81, 321, 10.1016/j.neuron.2013.11.018 Rea, 2005, A stress-sensitive reporter predicts longevity in isogenic populations of Caenorhabditis elegans, Nat. Genet., 37, 894, 10.1038/ng1608 Reichwald, 2015, Insights into sex chromosome evolution and aging from the genome of a short-lived fish, Cell, 163, 1527, 10.1016/j.cell.2015.10.071 Ristow, 2014, Unraveling the truth about antioxidants: mitohormesis explains ROS-induced health benefits, Nat. Med., 20, 709, 10.1038/nm.3624 Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616 Schmeisser, 2013, Neuronal ROS signaling rather than AMPK/sirtuin-mediated energy sensing links dietary restriction to lifespan extension, Mol. Metab., 2, 92, 10.1016/j.molmet.2013.02.002 Schulz, 2007, Glucose restriction extends Caenorhabditis elegans life span by inducing mitochondrial respiration and increasing oxidative stress, Cell Metab., 6, 280, 10.1016/j.cmet.2007.08.011 Shen, 2014, Mitoflash frequency in early adulthood predicts lifespan in Caenorhabditis elegans, Nature, 508, 128, 10.1038/nature13012 Singer, 1994, The reaction sites of rotenone and ubiquinone with mitochondrial NADH dehydrogenase, Biochim. Biophys. Acta, 1187, 198, 10.1016/0005-2728(94)90110-4 Terzibasi, 2008, Large differences in aging phenotype between strains of the short-lived annual fish Nothobranchius furzeri, PLoS ONE, 3, e3866, 10.1371/journal.pone.0003866 Terzibasi, 2009, Effects of dietary restriction on mortality and age-related phenotypes in the short-lived fish Nothobranchius furzeri, Aging Cell, 8, 88, 10.1111/j.1474-9726.2009.00455.x Valdesalici, 2003, Extremely short lifespan in the annual fish Nothobranchius furzeri, Proc. Biol. Sci., 270, S189, 10.1098/rsbl.2003.0048 Valenzano, 2006, Temperature affects longevity and age-related locomotor and cognitive decay in the short-lived fish Nothobranchius furzeri, Aging Cell, 5, 275, 10.1111/j.1474-9726.2006.00212.x Valenzano, 2006, Resveratrol prolongs lifespan and retards the onset of age-related markers in a short-lived vertebrate, Curr. Biol., 16, 296, 10.1016/j.cub.2005.12.038 Valenzano, 2015, The African turquoise killifish genome provides insights into evolution and genetic architecture of lifespan, Cell, 163, 1539, 10.1016/j.cell.2015.11.008 Willcox, 2008, FOXO3A genotype is strongly associated with human longevity, Proc. Natl. Acad. Sci. USA, 105, 13987, 10.1073/pnas.0801030105 Zahn, 2007, Systems biology of aging in four species, Curr. Opin. Biotechnol., 18, 355, 10.1016/j.copbio.2007.07.004 Zahn, 2006, Transcriptional profiling of aging in human muscle reveals a common aging signature, PLoS Genet., 2, e115, 10.1371/journal.pgen.0020115 Zahn, 2007, AGEMAP: a gene expression database for aging in mice, PLoS Genet., 3, e201, 10.1371/journal.pgen.0030201 Zarse, 2012, Impaired insulin/IGF1 signaling extends life span by promoting mitochondrial L-proline catabolism to induce a transient ROS signal, Cell Metab., 15, 451, 10.1016/j.cmet.2012.02.013 Zhang, 2005, A general framework for weighted gene co-expression network analysis, Stat. Appl. Genet. Mol. Biol., 4, Article17, 10.2202/1544-6115.1128