López-Otín C, Blasco MA, Partridge L, Serrano M, Kroemer G. The hallmarks of aging. Cell. 2013;153:1194–217.
Article
PubMed
PubMed Central
CAS
Google Scholar
Longo VD, Antebi A, Bartke A, Barzilai N, Brown-Borg HM, Caruso C, et al. Interventions to slow aging in humans: are we ready? Aging Cell. 2015;14:497–510.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weindruch R, Walford RL, Fligiel S, Guthrie D. The retardation of aging in mice by dietary restriction: longevity, cancer, immunity and lifetime energy intake. J Nutr. 1986;116(4):641–54.
López-Otín C, Galluzzi L, Freije JMP, Madeo F, Kroemer G. Metabolic control of longevity. Cell. 2016;166:802–21.
Article
PubMed
CAS
Google Scholar
Fontana L, Partridge L, Longo VD. Extending healthy life span--from yeast to humans. Science. 2010;328:321–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fontana L, Partridge L. Promoting health and longevity through diet: from model organisms to humans. Cell. 2015;161:106–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Colman RJ, Beasley TM, Kemnitz JW, Johnson SC, Weindruch R, Anderson RM. Caloric restriction reduces age-related and all-cause mortality in rhesus monkeys. Nat Commun. 2014;5:3557.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cava E, Fontana L. Will calorie restriction work in humans? Aging. 2013;5(7):507–14.
Garcia AM, Busuttil RA, Calder RB, Dollé MET, Diaz V, McMahan CA, et al. Effect of Ames dwarfism and caloric restriction on spontaneous DNA mutation frequency in different mouse tissues. Mech Ageing Dev. 2008;129:528–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Clancy DJ, Gems D, Hafen E, Leevers SJ. Dietary restriction in long-lived dwarf flies. Science. 2002;296(5566):319.
Kapahi P, Zid BM, Harper T, Koslover D, Sapin V, Benzer S. Regulation of lifespan in Drosophila by modulation of genes in the TOR signaling pathway. Curr Biol. 2004;14:885–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bartke A, Westbrook R. Metabolic characteristics of long-lived mice. Front Genet. 2012;3:288.
Article
PubMed
PubMed Central
Google Scholar
Singh R, Cuervo AM. Autophagy in the cellular energetic balance. Cell Metabolism. 2011;13(5):495–504.
Pamplona R, Barja G. Mitochondrial oxidative stress, aging and caloric restriction: the protein and methionine connection. Biochim Biophys Acta. 2006;1757:496–508.
Article
CAS
PubMed
Google Scholar
Hine C, Harputlugil E, Zhang Y, Ruckenstuhl C, Lee BC, Brace L, et al. Endogenous hydrogen sulfide production is essential for dietary restriction benefits. Cell. 2015;160:132–44.
Article
CAS
PubMed
Google Scholar
Anderson RM, Weindruch R. Metabolic reprogramming, caloric restriction and aging. Trends Endocrinol Metab. 2010;21:134–41.
Article
CAS
PubMed
Google Scholar
Anderson RM, Weindruch R. Metabolic reprogramming in dietary restriction. Interdiscip Top Gerontol. 2007;35:18–38.
CAS
PubMed
Google Scholar
Plank M, Wuttke D, van Dam S, Clarke SA, de Magalhães JP. A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms. Mol Biosyst. 2012;8:1339–49.
Article
CAS
PubMed
Google Scholar
Swindell WR. Genes and gene expression modules associated with caloric restriction and aging in the laboratory mouse. BMC Genomics. 2009;10:585.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wood SH, van Dam S, Craig T, Tacutu R, O’Toole A, Merry BJ, et al. Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging. Genome Biol. 2015;16:285.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gillespie ZE, Pickering J, Eskiw CH. Better living through chemistry: caloric restriction (CR) and CR mimetics alter genome function to promote increased health and lifespan. Front Genet. 2016;7:142.
Article
PubMed
PubMed Central
Google Scholar
Jiang T, Liebman SE, Lucia MS, Phillips CL, Levi M. Calorie restriction modulates renal expression of sterol regulatory element binding proteins, lipid accumulation, and age-related renal disease. J Am Soc Nephrol. 2005;16:2385–94.
Article
CAS
PubMed
Google Scholar
Kuhla A, Hahn S, Butschkau A, Lange S, Wree A, Vollmar B. Lifelong caloric restriction reprograms hepatic fat metabolism in mice. J Gerontol A Biol Sci Med Sci. 2014;69:915–22.
Article
CAS
PubMed
Google Scholar
Katewa SD, Demontis F, Kolipinski M, Hubbard A, Gill MS, Perrimon N, et al. Intramyocellular fatty-acid metabolism plays a critical role in mediating responses to dietary restriction in Drosophila melanogaster. Cell Metab. 2012;16:97–103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Booth LN, Brunet A. The aging epigenome. Mol Cell. 2016;62:728–44.
Article
CAS
PubMed
Google Scholar
Zhang N. Epigenetic modulation of DNA methylation by nutrition and its mechanisms in animals. Anim Nutr. 2015;1(3):144–51.
Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res. 2011;21:381–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Benayoun BA, Pollina EA, Brunet A. Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nat Rev Mol Cell Biol. 2015;16:593–610.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maegawa S, Hinkal G, Kim HS, Shen L, Zhang L, Zhang J, et al. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res. 2010;20(3):332–40.
Day K, Waite LL, Thalacker-Mercer A, West A, Bamman MM, Brooks JD, et al. Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. Genome Biol. 2013;14:R102.
Article
PubMed
PubMed Central
CAS
Google Scholar
Deaton AM, Bird A. CpG islands and the regulation of transcription. Genes Dev. 2011;25:1010–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Issa J-P. Aging and epigenetic drift: a vicious cycle. J Clin Invest. 2014;124:24–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Voigt P, Tee WW, Reinberg D. A double take on bivalent promoters. Genes Dev. 2013;27:1318–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Beerman I, Bock C, Garrison BS, Smith ZD, Gu H, Meissner A, et al. Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging. Cell Stem Cell. 2013;12:413–25.
Article
CAS
PubMed
Google Scholar
Bormann F, Rodríguez-Paredes M, Hagemann S, Manchanda H, Kristof B, Gutekunst J, et al. Reduced DNA methylation patterning and transcriptional connectivity define human skin aging. Aging Cell. 2016;15:563–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sun D, Luo M, Jeong M, Rodriguez B, Xia Z, Hannah R, et al. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell. 2014;14:673–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013;49:359–67.
Article
CAS
PubMed
Google Scholar
Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14:R115.
Article
PubMed
PubMed Central
Google Scholar
Horvath S, Gurven M, Levine ME, Trumble BC, Kaplan H, Allayee H, et al. An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biol. 2016;17:171.
Article
PubMed
PubMed Central
CAS
Google Scholar
Horvath S, Levine AJ. HIV-1 Infection accelerates age according to the epigenetic clock. J Infect Dis. 2015;212:1563–73.
Article
PubMed
PubMed Central
Google Scholar
Horvath S, Ritz BR. Increased epigenetic age and granulocyte counts in the blood of Parkinson’s disease patients. Aging (Albany NY). 2015;7:1130–42.
Article
Google Scholar
Kim CH, Lee EK, Choi YJ, An HJ, Chung HO, Park DE, et al. Short-term calorie restriction ameliorates genomewide, age-related alterations in DNA methylation. Aging Cell. 2016:15(6):1074–81.
Zampieri M, Ciccarone F, Calabrese R. Reconfiguration of DNA methylation in aging. Mech Ageing Dev. 2015;151:60–70.
Radford EJ, Ito M, Shi H, Corish JA, Yamazawa K, Isganaitis E, et al. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism. Science. 2014;345:1255903.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu H, Zhang Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell. 2014;156:45–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fazzari MJ, Greally JM. Epigenomics: beyond CpG islands. Nat Rev Genet. 2004;5:446–55.
Article
CAS
PubMed
Google Scholar
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921.
Article
CAS
PubMed
Google Scholar
von Meyenn F, Berrens RV, Andrews S, Santos F, Collier AJ, Krueger F, et al. Comparative principles of DNA methylation reprogramming during human and mouse in vitro primordial germ cell specification. Dev Cell. 2016;39:104–15.
Article
CAS
Google Scholar
Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484–92.
Article
CAS
PubMed
Google Scholar
Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011;480(7378):490–5.
Spiers H, Hannon E, Wells S, Williams B, Fernandes C, Mill J. Age-associated changes in DNA methylation across multiple tissues in an inbred mouse model. Mech Ageing Dev. 2016;154:20–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Florath I, Butterbach K, Müller H, Bewerunge-Hudler M, Brenner H. Cross-sectional and longitudinal changes in DNA methylation with age: an epigenome-wide analysis revealing over 60 novel age-associated CpG sites. Hum Mol Genet. 2014;23:1186–201.
Article
CAS
PubMed
Google Scholar
Bacalini MG, Deelen J, Pirazzini C, De Cecco M, Giuliani C, Lanzarini C, et al. Systemic age-associated DNA hypermethylation of ELOVL2 gene: in vivo and in vitro evidences of a cell replication process. J Gerontol A Biol Sci Med Sci. 2016. glw185. doi:10.1093/gerona/glw185.
Garagnani P, Bacalini MG, Pirazzini C, Gori D, Giuliani C, Mari D, et al. Methylation of ELOVL2 gene as a new epigenetic marker of age. Aging Cell. 2012;11:1132–4.
Article
CAS
PubMed
Google Scholar
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, et al. The accessible chromatin landscape of the human genome. Nature. 2012;489:75–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jjingo D, Conley AB, Yi SV, Lunyak VV, Jordan IK. On the presence and role of human gene-body DNA methylation. Oncotarget. 2012;3:462–74.
Article
PubMed
PubMed Central
Google Scholar
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.
Article
CAS
Google Scholar
Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, et al. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 2011;12:R83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mei S, Qin Q, Wu Q, Sun H, Zheng R, Zang C, et al. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res. 2016;45(D1):D658-D662.
Rakyan VK, Down TA, Maslau S, Andrew T, Yang T-P, Beyan H, et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res. 2010;20:434–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weiner A, Lara-Astiaso D, Krupalnik V, Gafni O, David E, Winter DR, et al. Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution. Nat Biotechnol. 2016;34:953–61.
Article
CAS
PubMed
Google Scholar
De Cecco M, Criscione SW, Peckham EJ, Hillenmeyer S, Hamm EA, Manivannan J, et al. Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements. Aging Cell. 2013;12:247–56.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shenker N, Flanagan JM. Intragenic DNA methylation: implications of this epigenetic mechanism for cancer research. Br J Cancer. 2011;106:248–53.
Article
PubMed
PubMed Central
CAS
Google Scholar
Singer M, Kosti I, Pachter L, Mandel-Gutfreund Y. A diverse epigenetic landscape at human exons with implication for expression. Nucleic Acids Res. 2015;43:3498–508.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yuan T, Jiao Y, de Jong S, Ophoff RA, Beck S, Teschendorff AE. An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet. 2015;11:e1004996.
Article
PubMed
PubMed Central
CAS
Google Scholar
Avrahami D, Li C, Zhang J, Schug J, Avrahami R, Rao S, et al. Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved B cell function. Cell Metab. 2015;22:619–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma L, Robinson LN, Towle HC. ChREBP*Mlx is the principal mediator of glucose-induced gene expression in the liver. J Biol Chem. 2006;281:28721–30.
Article
CAS
PubMed
Google Scholar
Horton JD, Shah NA, Warrington JA, Anderson NN, Park SW, Brown MS, et al. Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes. Proc Natl Acad Sci U S A. 2003;100:12027–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yamashita H, Takenoshita M, Sakurai M, Bruick RK, Henzel WJ, Shillinglaw W, et al. A glucose-responsive transcription factor that regulates carbohydrate metabolism in the liver. Proc Natl Acad Sci U S A. 2001;98:9116–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harada N, Fujimoto E, Okuyama M, Sakaue H, Nakaya Y. Identification and functional characterization of human glycerol-3-phosphate acyltransferase 1 gene promoters. Biochem Biophys Res Commun. 2012;423:128–33.
Article
CAS
PubMed
Google Scholar
Matsuzaka T, Shimano H, Yahagi N, Kato T, Atsumi A, Yamamoto T, et al. Crucial role of a long-chain fatty acid elongase, Elovl6, in obesity-induced insulin resistance. Nat Med. 2007;13:1193–202.
Article
CAS
PubMed
Google Scholar
Rome S, Lecomte V, Meugnier E, Rieusset J, Debard C, Euthine V, et al. Microarray analyses of SREBP-1a and SREBP-1c target genes identify new regulatory pathways in muscle. Physiol Genomics. 2008;34:327–37.
Article
CAS
PubMed
Google Scholar
Poupeau A, Postic C. Cross-regulation of hepatic glucose metabolism via ChREBP and nuclear receptors. Biochim Biophys Acta. 2011;1812:995–1006.
Article
CAS
PubMed
Google Scholar
Xu X, So J-S, Park J-G, Lee A-H. Transcriptional control of hepatic lipid metabolism by SREBP and ChREBP. Semin Liver Dis. 2013;33:301–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Taguchi A, Wartschow LM, White MF. Brain IRS2 signaling coordinates life span and nutrient homeostasis. Science. 2007;317:369–72.
Article
CAS
PubMed
Google Scholar
Kudo T, Ikeda M, Nishikawa M, Yang Z, Ohno K. The RASSF3 candidate tumor suppressor induces apoptosis and G1–S cell-cycle arrest via p53. Cancer Res. 2012;72(11)2901–11.
Peng H, Liu H, Zhao S, Wu J, Fan J, Liao J. Silencing of RASSF3 by DNA hypermethylation is associated with tumorigenesis in somatotroph adenomas. PLoS One. 2013;8:e59024.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wendel AA, Lewin TM, Coleman RA. Biochim Biophys Acta. Glycerol-3-phosphate acyltransferases: rate limiting enzymes of triacylglycerol biosynthesis. 2009;1791(6):501–6.
Chypre M, Zaidi N, Smans K. ATP-citrate lyase: a mini-review. Biochem Biophys Res Commun. 2012;422:1–4.
Article
CAS
PubMed
Google Scholar
Jakobsson A, Westerberg R, Jacobsson A. Fatty acid elongases in mammals: their regulation and roles in metabolism. Prog Lipid Res. 2006;45:237–49.
Article
CAS
PubMed
Google Scholar
Li Y, Daniel M, Tollefsbol TO. Epigenetic regulation of caloric restriction in aging. BMC Med. 2011;9:98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bacalini MG, Friso S, Olivieri F, Pirazzini C, Giuliani C, Capri M, et al. Present and future of anti-ageing epigenetic diets. Mech Ageing Dev. 2014;136-137:101–15.
Feil R, Fraga MF. Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet. 2012;13:97–109.
CAS
PubMed
Google Scholar
Iurlaro M, Meyenn von F, Reik W. DNA methylation homeostasis in human and mouse development. Curr Op Genet Dev. 2017;43:101–109.
Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, et al. FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell. 2013;13:351–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hore TA, von Meyenn F, Ravichandran M, Bachman M, Ficz G, Oxley D, et al. Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms. Proc Natl Acad Sci. 2016;113:12202–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simons K, Sampaio JL. Membrane organization and lipid rafts. Cold Spring Harb Perspect Biol. 2011;3:a004697–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hancock JF. Ras proteins: different signals from different locations. Nat Rev Mol Cell Biol. 2003;4:373–84.
Article
CAS
PubMed
Google Scholar
Porstmann T, Santos CR, Griffiths B, Cully M, Wu M, Leevers S, et al. SREBP activity is regulated by mTORC1 and contributes to Akt-dependent cell growth. Cell Metab. 2008;8:224–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Taniguchi CM, Emanuelli B, Kahn CR. Critical nodes in signalling pathways: insights into insulin action. Nat Rev Mol Cell Biol. 2006;7:85–96.
Article
CAS
PubMed
Google Scholar
Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res. 2010;20:440–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Raddatz G, Hagemann S, Aran D, Söhle J, Kulkarni PP, Kaderali L, et al. Aging is associated with highly defined epigenetic changes in the human epidermis. Epigenetics Chromatin. 2013;6:36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ziller MJ, Hansen KD, Meissner A, Aryee MJ. Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nat Meth. 2015;12:230–2.
Article
CAS
Google Scholar
Current ENCODE Experiment Guidelines – ENCODE [Internet]. encodeproject.org. https://www.encodeproject.org/about/experiment-guidelines/. Accessed 9 Feb 2017.
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016;17:13.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kulis M, Heath S, Bibikova M, Queirós AC, Navarro A, Clot G, et al. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet. 2012;44:1236–42.
Article
CAS
PubMed
Google Scholar
Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466(7303):253–57.
Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013;23:555–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
Veloso A, Kirkconnell KS, Magnuson B, Biewen B, Paulsen MT, Wilson TE, et al. Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res. 2014;24:896–905.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jonkers I, Kwak H, Lis JT. Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. elife. 2014;3:e02407.
Article
PubMed
PubMed Central
CAS
Google Scholar
Finkel T. The metabolic regulation of aging. Nat Med. 2015;21:1416–23.
Article
CAS
PubMed
Google Scholar
Ide T, Shimano H, Yahagi N, Matsuzaka T, Nakakuki M, Yamamoto T, et al. SREBPs suppress IRS-2-mediated insulin signalling in the liver. Nat Cell Biol. 2004;6:351–7.
Article
CAS
PubMed
Google Scholar
Shikama A, Shinozaki H, Takeuchi Y, Matsuzaka T, Aita Y, Murayama T, et al. Identification of human ELOVL5 enhancer regions controlled by SREBP. Biochem Biophys Res Commun. 2015;465:857–63.
Article
CAS
PubMed
Google Scholar
Wang Y, Viscarra J, Kim SJ, Sul HS. Transcriptional regulation of hepatic lipogenesis. Nat Rev Mol Cell Biol. 2015;16:678–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dong X, Park S, Lin X, Copps K, Yi X, White MF. Irs1 and Irs2 signaling is essential for hepatic glucose homeostasis and systemic growth. J Clin Invest. 2006;116:101–14.
Article
CAS
PubMed
Google Scholar
Geng S, Zhu W, Xie C, Li X, Wu J, Liang Z, et al. Medium-chain triglyceride ameliorates insulin resistance and inflammation in high fat diet-induced obese mice. Eur J Nutr. 2016;55:931–40.
Article
CAS
PubMed
Google Scholar
Ronis MJJ, Baumgardner JN, Sharma N, Vantrease J, Ferguson M, Tong Y, et al. Medium chain triglycerides dose-dependently prevent liver pathology in a rat model of non-alcoholic fatty liver disease. Exp Biol Med (Maywood). 2013;238:151–62.
Article
CAS
Google Scholar
Chang P, Terbach N, Plant N, Chen PE, Walker MC, Williams RSB. Seizure control by ketogenic diet-associated medium chain fatty acids. Neuropharmacology. 2013;69:105–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Greene AE, Todorova MT, McGowan R, Seyfried TN. Caloric restriction inhibits seizure susceptibility in epileptic EL mice by reducing blood glucose. Epilepsia. 2001;42:1371–8.
Article
CAS
PubMed
Google Scholar
Yuen AWC, Sander JW. Rationale for using intermittent calorie restriction as a dietary treatment for drug resistant epilepsy. Epilepsy Behav. 2014;33:110–4.
Article
PubMed
Google Scholar
Ong KT, Mashek MT, Bu SY, Greenberg AS, Mashek DG. Adipose triglyceride lipase is a major hepatic lipase that regulates triacylglycerol turnover and fatty acid signaling and partitioning. Hepatology. 2011;53:116–26.
Article
CAS
PubMed
Google Scholar
Finck BN, Hall AM. Does diacylglycerol accumulation in fatty liver disease cause hepatic insulin resistance? Biomed Res Int. 2015;2015:104132.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sultan M, Sultan M, Dökel S, Dökel S, Amstislavskiy V, Amstislavskiy V, et al. A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods. Biochem Biophys Res Commun. 2012;422:643–6.
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
CAS
Google Scholar
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22:1760–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25:1091–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
PubMed
PubMed Central
CAS
Google Scholar
Alexa A, Rahnenfuhrer J. Bioconductor - topGO. R package version. 2010
Seisenberger S, Andrews S, Krueger F, Arand J, Walter J, Santos F, et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell. 2012;48:849–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30:207–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics. 2011;27:1571–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Meth. 2012;9:357–9.
Article
CAS
Google Scholar
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137.
Article
PubMed
PubMed Central
CAS
Google Scholar
Morales-Rios E, Watt IN, Zhang Q, Ding S, Fearnley IM, Montgomery MG, et al. Purification, characterization and crystallization of the F-ATPase from Paracoccus denitrificans. Open Biol. 2015;5:150119.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 2015;43:D670–81.
Article
PubMed
Google Scholar
Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr ARW, James KD, Turner DJ, et al. Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 2010;6:e1001134.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000;16:418–20.
Article
CAS
PubMed
Google Scholar
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32:D493–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The Human Genome Browser at UCSC. Genome Res. 2002;12:996–1006.
Article
CAS
PubMed
PubMed Central
Google Scholar