Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281–97.
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.
Smith-Vikos T, Slack FJ. MicroRNAs and their roles in aging. J Cell Sci. 2012;125:7–17.
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.
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.
Boehm M, Slack F. A developmental timing microRNA and its target regulate life span in C. elegans. Science. 2005;310:1954–7.
Pincus Z, Smith-Vikos T, Slack FJ. MicroRNA predictors of longevity in caenorhabditis elegans. PLoS Genet. 2011;7(9):e1002306.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Rouault TA, Cooperman S. Brain iron metabolism. Semin Pediatr Neurol. 2006;13(3):142–8.
Dixon SJ, Stockwell BR. The role of iron and reactive oxygen species in cell death. Nat Chem Biol. 2014;10:9–17.
Massie HR, Aiello VR, Banziger V. Iron accumulation and lipid peroxidation in aging C57BL/6 J mice. Exp Gerontol. 1983;18:277–85.
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.
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.
Zecca L, Youdim MBH, Riederer P, Connor JR, Crichton RR. Iron, brain ageing and neurodegenerative disorders. Nat Rev Neurosci. 2004;5:863–73.
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.
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.
Massie HR, Aiello VR, Williams TR. Inhibition of iron absorption prolongs the life span of Drosophila. Mech Ageing Dev. 1993;67:227–37.
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.
Zhang D-L, Ghosh MC, Rouault TA. The physiological functions of iron regulatory proteins in iron homeostasis - an update. Front Pharmacol. 2014;5:124.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Platzer M, Englert C. Nothobranchius furzeri: a model for aging research and more. Trends Genet. 2016;32(9):543–52.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Rouault TA. The role of iron regulatory proteins in mammalian iron homeostasis and disease. Nat Chem Biol. 2006;2:406–14.
Rebouche CJ, Wilcox CL, Widness JA. Microanalysis of non-heme iron in animal tissues. J Biochem Biophys Methods. 2004;58:239–51.
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.
Brunk UT, Terman A. Lipofuscin: mechanisms of age-related accumulation and influence on cell function. Free Radic Biol Med. 2002;33(5):611–9.
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.
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.
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.
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.
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.
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.
Massie HR, Aiello VR, Williams TR. Iron accumulation during development and ageing of Drosophila. Mech Ageing Dev. 1985;29:215–20.
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.
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.
Moos T. Immunohistochemical localization of intraneuronal transferrin receptor immunoreactivity in the adult mouse central nervous system. J Comp Neurol. 1996;375:675–92.
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.
Radlowski EC, Johnson RW. Perinatal iron deficiency and neurocognitive development. Front Hum Neurosci. 2013;7:585.
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.
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.
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.
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.
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.
Xu Q. Microinjection into zebrafish embryos. Methods Mol Biol. 1999;127:125–32.
Thisse C, Thisse B. High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat Protoc. 2008;3:59–69.
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.
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.
Liao Y, Smyth GK, Shi W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009;26:139–40.
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.
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.
Kozomara A, Griffiths-Jones S. MiRBase: Annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42(Database issue):D68–73.
Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003;5:R1.