Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281–97.
Article
CAS
PubMed
Google Scholar
Baroudi M, Corà D, Bosia C, Osella M, Caselle M. A curated database of miRNA mediated feed-forward loops involving MYC as master regulator. PLoS One. 2011;6:17–8.
Article
Google Scholar
Smith-Vikos T, Slack FJ. MicroRNAs and their roles in aging. J Cell Sci. 2012;125:7–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ibáñez-Ventoso C, Yang M, Guo S, Robins H, Padgett RW, Driscoll M. Modulated microRNA expression during adult lifespan in Caenorhabditis elegans. Aging Cell. 2006;5:235–46.
Article
PubMed
Google Scholar
Somel M, Guo S, Fu N, Yan Z, Hu HY, Xu Y, et al. MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res. 2010;20:1207–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boehm M, Slack F. A developmental timing microRNA and its target regulate life span in C. elegans. Science. 2005;310:1954–7.
Article
CAS
PubMed
Google Scholar
Pincus Z, Smith-Vikos T, Slack FJ. MicroRNA predictors of longevity in caenorhabditis elegans. PLoS Genet. 2011;7(9):e1002306.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen Y, Wollam J, Magner D, Karalay O, Antebi A. A steroid receptor-microRNA switch regulates life span in response to signals from the gonad. Science. 2012;338:1472–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu N, Landreh M, Cao K, Abe M, Hendriks G-J, Kennerdell JR, et al. The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila. Nature. 2012;482:519–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boon RA, Iekushi K, Lechner S, Seeger T, Fischer A, Heydt S, et al. MicroRNA-34a regulates cardiac ageing and function. Nature. 2013;495:107–10.
Article
CAS
PubMed
Google Scholar
Baumgart M, Groth M, Priebe S, Appelt J, Guthke R, Platzer M, et al. Age-dependent regulation of tumor-related microRNAs in the brain of the annual fish Nothobranchius furzeri. Mech Ageing Dev. 2012;133:226–33.
Article
CAS
PubMed
Google Scholar
Takahashi M, Eda A, Fukushima T, Hohjoh H. Reduction of type IV collagen by upregulated miR-29 in normal elderly mouse and klotho-deficient, senescence-model mouse. PLoS One. 2012;11:e48974.
Article
Google Scholar
Nolan K, Mitchem MR, Jimenez-Mateos EM, Henshall DC, Concannon CG, Prehn JHM. Increased expression of MicroRNA-29a in ALS mice: Functional analysis of its inhibition. J Mol Neurosci. 2014;53:231–41.
Article
CAS
PubMed
Google Scholar
Ugalde AP, Ramsay AJ, de la Rosa J, Varela I, Mariño G, Cadiñanos J, et al. Aging and chronic DNA damage response activate a regulatory pathway involving miR-29 and p53. EMBO J. 2011;30:2219–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fenn AM, Smith KM, Lovett-Racke AE, Guerau-de-Arellano M, Whitacre CC, Godbout JP. Increased micro-RNA 29b in the aged brain correlates with the reduction of insulin-like growth factor-1 and fractalkine ligand. Neurobiol Aging. 2013;34:2748–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Mao S, Wang H, Zen K, Zhang C, Li L. MicroRNA-29a modulates axon branching by targeting doublecortin in primary neurons. Protein Cell. 2014;5:160–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cushing L, Costinean S, Xu W, Jiang Z, Madden L, Kuang P, et al. Disruption of miR-29 leads to aberrant differentiation of smooth muscle cells selectively associated with distal lung vasculature. PLoS Genet. 2015;11(5):e1005238.
Article
PubMed
PubMed Central
Google Scholar
Papadopoulou AS, Serneels L, Achsel T, Mandemakers W, Callaerts-Vegh Z, Dooley J, et al. Deficiency of the miR-29a/b-1 cluster leads to ataxic features and cerebellar alterations in mice. Neurobiol Dis. 2015;73:275–88.
Article
CAS
PubMed
Google Scholar
Roshan R, Shridhar S, Sarangdhar MA, Banik A, Chawla M, Garg M, et al. Brain-specific knockdown of miR-29 results in neuronal cell death and ataxia in mice. RNA. 2014;20:1287–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Khanna S, Rink C, Ghoorkhanian R, Gnyawali S, Heigel M, Wijesinghe DS, et al. Loss of miR-29b following acute ischemic stroke contributes to neural cell death and infarct size. J Cereb Blood Flow Metab. 2013;33:1197–206.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ouyang YB, Xu L, Lu Y, Sun X, Yue S, Xiong XX, et al. Astrocyte-enriched miR-29a targets PUMA and reduces neuronal vulnerability to forebrain ischemia. Glia. 2013;61:1784–94.
Article
PubMed
Google Scholar
Kole AJ, Swahari V, Hammond SM, Deshmukh M. miR-29b is activated during neuronal maturation and targets BH3-only genes to restrict apoptosis. Genes Dev. 2011;25:125–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hébert SS, Horré K, Nicolaï L, Papadopoulou AS, Mandemakers W, Silahtaroglu AN, et al. Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer’s disease correlates with increased BACE1/beta-secretase expression. Proc Natl Acad Sci U S A. 2008;105:6415–20.
Article
PubMed
PubMed Central
Google Scholar
Rouault TA, Cooperman S. Brain iron metabolism. Semin Pediatr Neurol. 2006;13(3):142–8.
Article
PubMed
Google Scholar
Dixon SJ, Stockwell BR. The role of iron and reactive oxygen species in cell death. Nat Chem Biol. 2014;10:9–17.
Article
CAS
PubMed
Google Scholar
Massie HR, Aiello VR, Banziger V. Iron accumulation and lipid peroxidation in aging C57BL/6 J mice. Exp Gerontol. 1983;18:277–85.
Article
CAS
PubMed
Google Scholar
Hahn P, Song Y, Ying GS, He X, Beard J, Dunaief JL. Age-dependent and gender-specific changes in mouse tissue iron by strain. Exp Gerontol. 2009;44:594–600.
Article
CAS
PubMed
PubMed Central
Google Scholar
Acosta-Cabronero J, Betts MJ, Cardenas-Blanco A, Yang S, Nestor PJ. In vivo MRI mapping of brain iron deposition across the adult lifespan. J Neurosci. 2016;36:364–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zecca L, Youdim MBH, Riederer P, Connor JR, Crichton RR. Iron, brain ageing and neurodegenerative disorders. Nat Rev Neurosci. 2004;5:863–73.
Article
CAS
PubMed
Google Scholar
Seo AY, Xu J, Servais S, Hofer T, Marzetti E, Wohlgemuth SE, et al. Mitochondrial iron accumulation with age and functional consequences. Aging Cell. 2008;7:706–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Klang IM, Schilling B, Sorensen DJ, Sahu AK, Kapahi P, Andersen JK, et al. Iron promotes protein insolubility and aging in C. elegans. Aging (Albany NY). 2014;6:975–91.
Article
Google Scholar
Massie HR, Aiello VR, Williams TR. Inhibition of iron absorption prolongs the life span of Drosophila. Mech Ageing Dev. 1993;67:227–37.
Article
CAS
PubMed
Google Scholar
Valentini S, Cabreiro F, Ackerman D, Alam MM, Kunze MBA, Kay CWM, et al. Manipulation of in vivo iron levels can alter resistance to oxidative stress without affecting ageing in the nematode C. elegans. Mech Ageing Dev. 2012;133:282–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang D-L, Ghosh MC, Rouault TA. The physiological functions of iron regulatory proteins in iron homeostasis - an update. Front Pharmacol. 2014;5:124.
PubMed
PubMed Central
Google Scholar
Meyron-Holtz EG, Ghosh MC, Iwai K, LaVaute T, Brazzolotto X, Berger UV, et al. Genetic ablations of iron regulatory proteins 1 and 2 reveal why iron regulatory protein 2 dominates iron homeostasis. EMBO J. 2004;23:386–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
LaVaute T, Smith S, Cooperman S, Iwai K, Land W, Meyron-Holtz E, et al. Targeted deletion of the gene encoding iron regulatory protein-2 causes misregulation of iron metabolism and neurodegenerative disease in mice. Nat Genet. 2001;27:209–14.
Article
CAS
PubMed
Google Scholar
de Magalhães JP, Curado J, Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics. 2009;25:875–81.
Article
PubMed
PubMed Central
Google Scholar
Valenzano DR, Terzibasi E, Cattaneo A, Domenici L, Cellerino A. Temperature affects longevity and age-related locomotor and cognitive decay in the short-lived fish: Nothobranchius furzeri. Aging Cell. 2006;5:275–8.
Article
CAS
PubMed
Google Scholar
Valenzano DR, Terzibasi E, Genade T, Cattaneo A, Domenici L, Cellerino A. Resveratrol prolongs lifespan and retards the onset of age-related markers in a short-lived vertebrate. Curr Biol. 2006;16:296–300.
Article
CAS
PubMed
Google Scholar
Di Cicco E, Tozzini ET, Rossi G, Cellerino A. The short-lived annual fish Nothobranchius furzeri shows a typical teleost aging process reinforced by high incidence of age-dependent neoplasias. Exp Gerontol. 2011;46:249–56.
Article
PubMed
Google Scholar
Terzibasi E, Lefrançois C, Domenici P, Hartmann N, Graf M, Cellerino A. Effects of dietary restriction on mortality and age-related phenotypes in the short-lived fish Nothobranchius furzeri. Aging Cell. 2009;8:88–99.
Article
CAS
PubMed
Google Scholar
Tozzini ET, Baumgart M, Battistoni G, Cellerino A. Adult neurogenesis in the short-lived teleost Nothobranchius furzeri: Localization of neurogenic niches, molecular characterization and effects of aging. Aging Cell. 2012;11:241–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wendler S, Hartmann N, Hoppe B, Englert C. Age-dependent decline in fin regenerative capacity in the short-lived fish Nothobranchius furzeri. Aging Cell. 2015;14:857–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harel I, Benayoun BA, Machado B, Singh PP, Hu CK, Pech MF, et al. A platform for rapid exploration of aging and diseases in a naturally short-lived vertebrate. Cell. 2015;160:1013–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Platzer M, Englert C. Nothobranchius furzeri: a model for aging research and more. Trends Genet. 2016;32(9):543–52.
Article
CAS
PubMed
Google Scholar
Baumgart M, Groth M, Priebe S, Savino A, Testa G, Dix A, et al. RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis. Aging Cell. 2014;13:965–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reichwald K, Petzold A, Koch P, Downie BR, Hartmann N, Pietsch S, et al. Insights into sex chromosome evolution and aging from the genome of a short-lived fish. Cell. 2015;163:1527–38.
Article
CAS
PubMed
Google Scholar
Gallardo VE, Behra M. Fluorescent activated cell sorting (FACS) combined with gene expression microarrays for transcription enrichment profiling of zebrafish lateral line cells. Methods. 2013;62:226–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, et al. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev. 2005;19:1288–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gerhard GS, Kauffman EJ, Wang X, Stewart R, Moore JL, Kasales CJ, et al. Life spans and senescent phenotypes in two strains of Zebrafish (Danio rerio). Exp Gerontol. 2002;37:1055–68.
Article
PubMed
Google Scholar
Terzibasi E, Valenzano DR, Benedetti M, Roncaglia P, Cattaneo A, Domenici L, et al. Large differences in aging phenotype between strains of the short-lived annual fish Nothobranchius furzeri. PLoS One. 2008;3(12):e3866.
Article
PubMed
PubMed Central
Google Scholar
Baumgart M, Priebe S, Groth M, Hartmann N, Menzel U, Pandolfini L, et al. Longitudinal RNA-seq analysis of vertebrate aging identifies mitochondrial complex i as a small-molecule-sensitive modifier of lifespan. Cell Syst. 2016;2:122–32.
Article
CAS
PubMed
Google Scholar
Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell GW, et al. Extensive alternative polyadenylation during zebrafish development. Genome Res. 2012;22:2054–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Penke L, Vald Hernand MC, Maniega SM, Gow AJ, Murray C, Starr JM, et al. Brain iron deposits are associated with general cognitive ability and cognitive aging. Neurobiol Aging. 2012;33(3):510–7. e2.
Article
CAS
PubMed
Google Scholar
Gakh O, Park S, Liu G, Macomber L, Imlay JA, Ferreira GC, et al. Mitochondrial iron detoxification is a primary function of frataxin that limits oxidative damage and preserves cell longevity. Hum Mol Genet. 2006;15:467–79.
Article
CAS
PubMed
Google Scholar
Betel D, Koppal A, Agius P, Sander C, Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. 2010;11:R90.
Article
PubMed
PubMed Central
Google Scholar
Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4. doi:10.7554/eLife.05005.
Li JH, Liu S, Zhou H, Qu LH, Yang JH. StarBase v2.0: Decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42(Database issue):D92–7.
Article
CAS
PubMed
Google Scholar
Rouault TA. The role of iron regulatory proteins in mammalian iron homeostasis and disease. Nat Chem Biol. 2006;2:406–14.
Article
CAS
PubMed
Google Scholar
Rebouche CJ, Wilcox CL, Widness JA. Microanalysis of non-heme iron in animal tissues. J Biochem Biophys Methods. 2004;58:239–51.
Article
CAS
PubMed
Google Scholar
Asano T, Koike M, Sakata S, Takeda Y, Nakagawa T, Hatano T, et al. Possible involvement of iron-induced oxidative insults in neurodegeneration. Neurosci Lett. 2015;588:29–35.
Article
CAS
PubMed
Google Scholar
Brunk UT, Terman A. Lipofuscin: mechanisms of age-related accumulation and influence on cell function. Free Radic Biol Med. 2002;33(5):611–9.
Article
CAS
PubMed
Google Scholar
Bertacchi M, Pandolfini L, Murenu E, Viegi A, Capsoni S, Cellerino A, et al. The positional identity of mouse ES cell-generated neurons is affected by BMP signaling. Cell Mol Life Sci. 2013;70:1095–111.
Article
CAS
PubMed
Google Scholar
Schmitt MJ, Margue C, Behrmann I, Kreis S. MiRNA-29: a microRNA family with tumor-suppressing and immune-modulating properties. Curr Mol Med. 2013;13:572–85.
Article
CAS
PubMed
Google Scholar
Papadopoulou AS, Dooley J, Linterman MA, Pierson W, Ucar O, Kyewski B, et al. The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nat Immunol. 2012;13:181–7.
Article
CAS
Google Scholar
Ma F, Xu S, Liu X, Zhang Q, Xu X, Liu M, et al. The microRNA miR-29 controls innate and adaptive immune responses to intracellular bacterial infection by targeting interferon-gamma. Nat Immunol. 2011;12(9):861–9.
Article
CAS
PubMed
Google Scholar
Liston A, Papadopoulou AS, Danso-Abeam D, Dooley J. MicroRNA-29 in the adaptive immune system: Setting the threshold. Cell Mol Life Sci. 2012;69(21):3533–41.
Article
CAS
PubMed
Google Scholar
Mansfeld J, Urban N, Priebe S, Groth M, Frahm C, Hartmann N, et al. Branched-chain amino acid catabolism is a conserved regulator of physiological ageing. Nat Commun. 2015;6:10043.
Article
CAS
PubMed
PubMed Central
Google Scholar
Massie HR, Aiello VR, Williams TR. Iron accumulation during development and ageing of Drosophila. Mech Ageing Dev. 1985;29:215–20.
Article
CAS
PubMed
Google Scholar
Cass WA, Grondin R, Andersen AH, Zhang Z, Hardy PA, Hussey-Andersen LK, et al. Iron accumulation in the striatum predicts aging-related decline in motor function in rhesus monkeys. Neurobiol Aging. 2007;28:258–71.
Article
CAS
PubMed
Google Scholar
Kastman EK, Willette AA, Coe CL, Bendlin BB, Kosmatka KJ, McLaren DG, et al. A calorie-restricted diet decreases brain iron accumulation and preserves motor performance in old rhesus monkeys. J Neurosci. 2010;30:7940–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moos T. Immunohistochemical localization of intraneuronal transferrin receptor immunoreactivity in the adult mouse central nervous system. J Comp Neurol. 1996;375:675–92.
Article
CAS
PubMed
Google Scholar
Snyder AM, Neely EB, Levi S, Arosio P, Connor JR. Regional and cellular distribution of mitochondrial ferritin in the mouse brain. J Neurosci Res. 2010;88:3133–43.
Article
CAS
PubMed
Google Scholar
Radlowski EC, Johnson RW. Perinatal iron deficiency and neurocognitive development. Front Hum Neurosci. 2013;7:585.
Article
PubMed
PubMed Central
Google Scholar
Siddappa AJ, Rao RB, Wobken JD, Leibold EA, Connor JR, Georgieff MK. Developmental changes in the expression of iron regulatory proteins and iron transport proteins in the perinatal rat brain. J Neurosci Res. 2002;68:761–75.
Article
CAS
PubMed
Google Scholar
Cloonan SM, Glass K, Laucho-Contreras ME, Bhashyam AR, Cervo M, Pabón MA, et al. Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. Nat Med. 2016;22:163–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jeong SY, Crooks DR, Wilson-Ollivierre H, Ghosh MC, Sougrat R, Lee J, et al. Iron insufficiency compromises motor neurons and their mitochondrial function in Irp2-null mice. PLoS One. 2011;6(10):e25404.
Article
CAS
PubMed
PubMed Central
Google Scholar
Galy B, Ferring-Appel D, Sauer SW, Kaden S, Lyoumi S, Puy H, et al. Iron regulatory proteins secure mitochondrial iron sufficiency and function. Cell Metab. 2010;12:194–201.
Article
CAS
PubMed
Google Scholar
Valenzano DR, Sharp S, Brunet A. Transposon-mediated transgenesis in the short-lived african killifish Nothobranchius furzeri, a vertebrate model for aging. G3 (Bethesda). 2011;1:531–8.
Article
CAS
Google Scholar
Xu Q. Microinjection into zebrafish embryos. Methods Mol Biol. 1999;127:125–32.
Article
CAS
PubMed
Google Scholar
Thisse C, Thisse B. High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat Protoc. 2008;3:59–69.
Article
CAS
PubMed
Google Scholar
Meguro R, Asano Y, Odagiri S, Li C, Iwatsuki H, Shoumura K. Nonheme-iron histochemistry for light and electron microscopy: a historical, theoretical and technical review. Arch Histol Cytol. 2007;70(1):1–19.
Article
CAS
PubMed
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
PubMed
PubMed Central
Google Scholar
Liao Y, Smyth GK, Shi W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.
Article
CAS
PubMed
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009;26:139–40.
Article
PubMed
PubMed Central
Google Scholar
Zhang B, Kirov S, Snoddy J. WebGestalt: An integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005;33(Web Server issue):W741–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R. ShortRead: A bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics. 2009;25:2607–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kozomara A, Griffiths-Jones S. MiRBase: Annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42(Database issue):D68–73.
Article
CAS
PubMed
Google Scholar
Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003;5:R1.
Article
PubMed
PubMed Central
Google Scholar