References
- Katib A. Mechanisms linking obesity to male infertility. Cent European J Urol. 2015;68(1):79–85. PubMed PMID: 25914843; PubMed Central PMCID: PMCPMC4408383
- Nguyen DM, El-Serag HB. The epidemiology of obesity. Gastroenterol Clin North Am. 2010 Mar;39(1):1–7. PubMed PMID: 20202574; PubMed Central PMCID: PMCPMC2833287
- Liu Y, Ding Z. Obesity, a serious etiologic factor for male subfertility in modern society. Reproduction. 2017;154(4):R123. English
- Craig JR, Jenkins TG, Carrell DT, et al. Obesity, male infertility, and the sperm epigenome. Fertil Steril. 2017 Apr 01;107(4):848–859. .
- Eisenberg ML, Kim S, Chen Z, et al. The relationship between male BMI and waist circumference on semen quality: data from the LIFE study. Hum Reprod. 2014 Feb;29(2):193–200. PubMed PMID: 24306102; PubMed Central PMCID: PMCPMC3896223.
- Bjorndal B, Burri L, Staalesen V, et al. Different adipose depots: their role in the development of metabolic syndrome and mitochondrial response to hypolipidemic agents. J Obes. 2011;2011:490650. . PubMed PMID: 21403826; PubMed Central PMCID: PMCPMC3042633
- Sethi JK, Vidal-Puig AJ. Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007;48(6):1253–1262. PubMed PMID: 17374880
- Chu Y, Huddleston GG, Clancy AN, et al. Epididymal fat is necessary for spermatogenesis, but not testosterone production or copulatory behavior. Endocrinology. 2010;151(12):5669–5679. . PubMed PMID: 20881242
- Boivin J, Bunting L, Collins JA, et al. International estimates of infertility prevalence and treatment-seeking: potential need and demand for infertility medical care. Hum Reprod. 2007 Jun;22(6):1506–1512. PubMed PMID: 17376819.
- Cooper TG, Noonan E, von Eckardstein S, et al. World Health Organization reference values for human semen characteristics. Hum Reprod Update. 2010 May-Jun;16(3):231–245. PubMed PMID: 19934213.
- Buck Louis GM, Sundaram R, Schisterman EF, et al. Semen quality and time to pregnancy: the longitudinal investigation of fertility and the environment study. Fertil Steril. 2014 Feb;101(2):453–462. PubMed PMID: 24239161; PubMed Central PMCID: PMCPMC3946620.
- Ramaraju GA, Teppala S, Prathigudupu K, et al. Association between obesity and sperm quality. Andrologia. 2018 Apr;50(3):e12888. PubMed PMID: 28929508.
- Ma J, Zhou Y, Wu L, et al. Association between BMI and semen quality: an observational study of 3966 sperm donors. Hum Reprod. 2018;34(1):155–162.
- Terashima M, Barbour S, Ren J, et al. Effect of high fat diet on paternal sperm histone distribution and male offspring liver gene expression. Epigenetics. 2015;10(9):861–871. . PubMed PMID: 26252449; eng
- Duale N, Steffensen I-L, Andersen J, et al. Impaired sperm chromatin integrity in obese mice. Andrology. 2014;2(2):234–243.
- Kaati G, Bygren LO, Edvinsson S. Cardiovascular and diabetes mortality determined by nutrition during parents’ and grandparents’ slow growth period. Eur J Hum Genet. 2002 Nov;10(11):682–688. PubMed PMID: 12404098
- Pembrey ME, Bygren LO, Kaati G, et al. Sex-specific, male-line transgenerational responses in humans. Eur J Hum Genet. 2006 Feb;14(2):159–166. PubMed PMID: 16391557.
- Chen Y-P, Xiao X-M, Li J, et al. Paternal body mass index (BMI) is associated with offspring intrauterine growth in a gender dependent manner. PLoS One. 2012;7(5):e36329.
- Bakos HW, Henshaw RC, Mitchell M, et al. Paternal body mass index is associated with decreased blastocyst development and reduced live birth rates following assisted reproductive technology. Fertil Steril. 2011;95(5):1700–1704.
- Ornellas F, Carapeto PV, Mandarim-de-Lacerda CA, et al. Obese fathers lead to an altered metabolism and obesity in their children in adulthood: review of experimental and human studies. J Pediatr (Rio J). 2017 Nov 01;93(6):551–559. .
- Zhang Y, Zhang X, Shi J, et al. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nat Cell Biol. 2018;20(5):535–540. . PubMed PMID: 29695786; eng
- Radford EJ, Ito M, Shi H, et al. In utero effects. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism. Science. 2014 Aug 15;345(6198):1255903. PubMed PMID: 25011554; PubMed Central PMCID: PMCPMC4404520.
- Rando OJ. Intergenerational Transfer of Epigenetic Information in Sperm. Cold Spring Harb Perspect Med. 2016 May 02;6(5):a022988. PubMed PMID: 26801897.
- Sharma U, Rando OJ. Metabolic Inputs into the Epigenome. Cell Metab. 2017 Mar;25(3):544–558. PubMed PMID: 28273477; eng
- Carone BR, Fauquier L, Habib N, et al. Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell. 2010 Dec 23;143(7):1084–1096. PubMed PMID: 21183072; PubMed Central PMCID: PMCPMC3039484.
- Ng SF, Lin RCY, Laybutt DR, et al. Chronic high-fat diet in fathers programs beta-cell dysfunction in female rat offspring. Nature. 2010 Oct 21;467(7318):963–U103. PubMed PMID: WOS:000283254700038; English.
- Zhang Y, Shi J, Rassoulzadegan M, et al. Sperm RNA code programmes the metabolic health of offspring. Nat Rev Endocrinol. 2019;15:489–498. .
- Ortega FJ, Mercader JM, Catalán V, et al. Targeting the Circulating MicroRNA Signature of Obesity. Clin Chem. 2013;59(5):781–792.
- Donkin I, Versteyhe S, Ingerslev LR, et al. Obesity and bariatric surgery drive epigenetic variation of spermatozoa in humans. Cell Metab. 2016 Feb;23(2):369–378. PubMed PMID: 26669700; eng.
- Jodar M, Sendler E, Moskovtsev SI, et al. Absence of sperm RNA elements correlates with idiopathic male infertility. Sci Transl Med. 2015 Jul 08;7(295):295re6. PubMed PMID: 26157032; PubMed Central PMCID: PMCPMC4721635.
- Burl RB, Clough S, Sendler E, et al. Sperm RNA elements as markers of health. Syst Biol Reprod Med. 2018 Feb;64(1):25–38. PubMed PMID: 29199464.
- Godia M, Swanson G, Krawetz SA. A history of why fathers’ RNA matters. Biol Reprod. 2018 Jul 1;99(1):147–159. PubMed PMID: 29514212.
- de Castro Barbosa T, Ingerslev LR, Alm PS, et al. High-fat diet reprograms the epigenome of rat spermatozoa and transgenerationally affects metabolism of the offspring. Mol Metab. 2016 Mar;5(3):184–197. PubMed PMID: 26977389; PubMed Central PMCID: PMCPMC4770269.
- Chen Q, Yan M, Cao Z, et al. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science. 2016 Jan 22;351(6271):397–400. PubMed PMID: 26721680.
- Jenkins TG, Aston KI, Meyer TD, et al. Decreased fecundity and sperm DNA methylation patterns. Fertil Steril. 2016;105(1):51–7.e73. . PubMed PMID: 26453269; eng
- Diamond MP, Legro RS, Coutifaris C, et al. Assessment of multiple intrauterine gestations from ovarian stimulation (AMIGOS) trial: baseline characteristics. Fertil Steril. 2015 Apr;103(4):962–973.e4. PubMed PMID: 25707331; PubMed Central PMCID: PMCPMC4529113. eng.
- Estill MS, Hauser R, Krawetz SA. RNA element discovery from germ cell to blastocyst. Nucleic Acids Res. 2018. DOI:10.1093/nar/gky1223
- Team RC. R: A language and environment for statistical computing. 2013.
- Castillo J, Jodar M, Oliva R. The contribution of human sperm proteins to the development and epigenome of the preimplantation embryo. Hum Reprod Update. 2018 Sep 1;24(5):535–555. PubMed PMID: 29800303.
- Wakabayashi K-I, Okamura M, Tsutsumi S, et al. The peroxisome proliferator-activated receptor gamma/retinoid X receptor alpha heterodimer targets the histone modification enzyme PR-Set7/Setd8 gene and regulates adipogenesis through a positive feedback loop. Mol Cell Biol. 2009;29(13):3544–3555. . PubMed PMID: 19414603
- Zhang W, Ferguson J, Ng SM, et al. Effector CD4+ T cell expression signatures and immune-mediated disease associated genes. PLoS One. 2012;7(6):e38510–e38510. . PubMed PMID: 22715389
- Smith SM, Moran AP, Duggan SP, et al. Tribbles 3: A novel regulator of TLR2-mediated signaling in response to helicobacter pylori lipopolysaccharide. J Immunol. 2011;186(4):2462–2471.
- Indraccolo S, Pfeffer U, Minuzzo S, et al. Identification of genes selectively regulated by IFNs in endothelial cells. J Immunol. 2007;178(2):1122–1135.
- Lee Y, Awasthi A, Yosef N, et al. Induction and molecular signature of pathogenic TH17 cells. Nat Immunol. 2012;13(10):991–999. . PubMed PMID: 22961052
- Burton GR, Guan Y, Nagarajan R, et al. Microarray analysis of gene expression during early adipocyte differentiation. Gene. 2002 Jun 26;293(1):21–31. .
- Xie X, Lu J, Kulbokas EJ, et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals [Article]. Nature. 2005 Feb 27;434:338. https://www.nature.com/articles/nature03441#supplementary-information
- Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545–15550. PubMed PMID: 16199517; PubMed Central PMCID: PMCPMC1239896.
- Beltran M, Aparicio-Prat E, Mazzolini R, et al. Splicing of a non-coding antisense transcript controls LEF1 gene expression. Nucleic Acids Res. 2015;43(12):5785–5797. . PubMed PMID: 25990740
- De Jaime-Soguero A, Abreu de Oliveira WA, Lluis F. The pleiotropic effects of the canonical wnt pathway in early development and pluripotency. Genes (Basel). 2018;9(2):93.
- Rosmarin AG, Resendes KK, Yang Z, et al. GA-binding protein transcription factor: a review of GABP as an integrator of intracellular signaling and protein–protein interactions. Blood Cells Mol Dis. 2004 Jan 01;32(1):143–154. .
- Falkenberg KJ, Johnstone RW. Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders [Review Article]. Nat Rev Drug Discov. 2014 Aug 18;13:673. https://www.nature.com/articles/nrd4360#supplementary-information
- Gillette TG, Hill JA. Readers, writers, and erasers: chromatin as the whiteboard of heart disease. Circ Res. 2015;116(7):1245–1253. PubMed PMID: 25814685
- Medvedeva YA, Lennartsson A, Ehsani R, et al. EpiFactors: a comprehensive database of human epigenetic factors and complexes. Database (Oxford). 2015;2015:bav067. PubMed PMID: 26153137; PubMed Central PMCID: PMCPMC4494013
- Biswas S, Rao CM. Epigenetic tools (The writers, the readers and the erasers) and their implications in cancer therapy. Eur J Pharmacol. 2018 Oct 15;837: 8–24. .
- Schapira M. Structural chemistry of human RNA methyltransferases. ACS Chem Biol. 2016 Mar 18;11(3):575–582. .
- Xu Y, Zhang S, Lin S, et al. WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. Nucleic Acids Res. 2017;45(D1):D264–D270. . PubMed PMID: 27789692
- Bao Y, Shen X. SnapShot: chromatin remodeling complexes. Cell. 2007 May 4;129(3):632. PubMed PMID: 17482554.
- Sims JK, Wade PA. SnapShot: chromatin remodeling: CHD. Cell. 2011 Feb 18;144(4):626–626 e1. PubMed PMID: 21335242.
- Kutateladze TG. SnapShot: histone readers. Cell. 2011 Sep 2;146(5):842–842 e1. PubMed PMID: 21884941; PubMed Central PMCID: PMCPMC3645985.
- Kouzarides T. SnapShot: histone-modifying enzymes. Cell. 2007 Nov 16;131(4):822. PubMed PMID: 18022374.
- Biggar KK, Wang Z, Li SS. SnapShot: lysine methylation beyond histones. Mol Cell. 2017 Dec 7;68(5):1016–1016 e1. PubMed PMID: 29220647.
- Stelzer G, Rosen N, Plaschkes I, et al. The genecards suite: from gene data mining to disease genome sequence analyses. Curr Protoc Bioinformatics. 2016 Jun20;54:1 30 1–1 30 33. PubMed PMID: 27322403.
- Rouillard AD, Gundersen GW, Fernandez NF, et al. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016;2016. PubMed PMID: 27374120; PubMed Central PMCID: PMCPMC4930834. DOI:10.1093/database/baw100.
- Mognol GP, Carneiro FRG, Robbs BK, et al. Cell cycle and apoptosis regulation by NFAT transcription factors: new roles for an old player. Cell Death Dis. 2016;7(4):e2199–e2199. . PubMed PMID: 27100893
- Trussell JC, Coward RM, Santoro N, et al. Defining hypogonadism in male partners of couples with unexplained infertility. Fertil Steril. 2018;110(4):e296.
- Cardoso AM, Alves MG, Mathur PP, et al. Obesogens and male fertility. Obes Rev. 2017 Jan;18(1):109–125. PubMed PMID: 27776203.
- Lee H, Song J, Jung JH, et al. Primary cilia in energy balance signaling and metabolic disorder. BMB Rep. 2015;48(12):647–654. . PubMed PMID: 26538252
- Berbari NF, Lewis JS, Bishop GA, et al. Bardet-Biedl syndrome proteins are required for the localization of G protein-coupled receptors to primary cilia. Proc Natl Acad Sci U S A. 2008;105(11):4242–4246. . PubMed PMID: 18334641
- Dalbay MT, Thorpe SD, Connelly JT, et al. Adipogenic Differentiation of hMSCs is mediated by recruitment of IGF-1r onto the primary cilium associated with cilia elongation. Stem Cells. 2015 Jun;33(6):1952–1961. PubMed PMID: 25693948; PubMed Central PMCID: PMCPMC4737234.
- Nishimoto S, Fukuda D, Higashikuni Y, et al. Obesity-induced DNA released from adipocytes stimulates chronic adipose tissue inflammation and insulin resistance. Sci Adv. 2016 Mar;2(3):e1501332. PubMed PMID: 27051864; PubMed Central PMCID: PMCPMC4820373.
- Konner AC, Bruning JC. Toll-like receptors: linking inflammation to metabolism. Trends Endocrinol Metab. 2011 Jan;22(1):16–23. PubMed PMID: 20888253
- Jialal I, Kaur H, Devaraj S. Toll-like receptor status in obesity and metabolic syndrome: a translational perspective. J Clin Endocrinol Metab. 2014;99(1):39–48.
- Giraud G, Terrone S, Bourgeois CF. Functions of DEAD box RNA helicases DDX5 and DDX17 in chromatin organization and transcriptional regulation. BMB Rep. 2018;51(12):613–622. PubMed PMID: 30293550
- Ismael H, Altmeyer S, Stahl H. Regulation of the U3-, U8-, and U13snoRNA Expression by the DEAD Box Proteins Ddx5/Ddx17 with Consequences for Cell Proliferation and Survival. Noncoding RNA. 2016;2(4):11.
- Wilson BJ, Bates GJ, Nicol SM, et al. The p68 and p72 DEAD box RNA helicases interact with HDAC1 and repress transcription in a promoter-specific manner [journal article]. BMC Mol Biol. 2004 August 06;5(1):11.
- Motiño O, Francés DE, Mayoral R, et al. Regulation of mir-183 by cyclooxygenase-2 in liver is dead box helicase p68 (ddx5) dependent. role in insulin signaling. Mol Cell Biol. 2015. MCB. 00198-15.
- Park HJ, Kim J, Saima FT, et al. Adipose-derived stem cells ameliorate colitis by suppression of inflammasome formation and regulation of M1-macrophage population through prostaglandin E2. Biochem Biophys Res Commun. 2018 Apr 15;498(4):988–995. .
- Goodrich RJ, Anton E, Krawetz SA. Isolating mRNA and small noncoding RNAs from human sperm. Methods Mol Biol. 2013;927:385–396. PubMed PMID: 22992930
- Goodrich R, Johnson G, Krawetz SA. The preparation of human spermatozoal RNA for clinical analysis [Research Support, Non-U.S. Gov’t]. Arch Androl. 2007 May-Jun;53(3):161–167. PubMed PMID: 17612875; eng
- Kent WJ, Sugnet CW, Furey TS, et al. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996–1006. Article published online before print in May 2002. PubMed PMID: 12045153; PubMed Central PMCID: PMCPMC186604.
- Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol. 1995;57(1):289–300.
- Futschik ME, Carlisle B. Noise-robust soft clustering of gene expression time-course data. J Bioinform Comput Biol. 2005 Aug;3(4):965–988. PubMed PMID: 16078370
- Werner T. Bioinformatics applications for pathway analysis of microarray data. Curr Opin Biotechnol. 2008 Feb;19(1):50–54. PubMed PMID: 18207385
- Liberzon A, Subramanian A, Pinchback R, et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011 Jun 15;27(12):1739–1740. PubMed PMID: 21546393; PubMed Central PMCID: PMCPMC3106198.
- Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov;13(11):2498–2504. PubMed PMID: 14597658; PubMed Central PMCID: PMCPMC403769.
- Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005;21(16):3448–3449.