Dynamic regulation of genetic pathways and targets during aging in Caenorhabditis elegans

Aging

Volumn 6, Issue 3, 2014, Pages 215-230

  He, Kan ^a   Zhou, Tao ^a   Shao, Jiaofang ^b   Ren, Xiaoliang ^b   Zhao, Zhongying ^b   Liu, Dahai ^a  

^a ANHUI UNIVERSITY   (China)

^b HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

Author keywords

Aging; C. elegans; Network; Pathways

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN;

AGING; ANIMAL; CAENORHABDITIS ELEGANS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GENOME; GROWTH, DEVELOPMENT AND AGING; METABOLISM; SIGNAL TRANSDUCTION; WNT SIGNALING PATHWAY;

AGING; ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; GENOME, HELMINTH; MAP KINASE SIGNALING SYSTEM; SIGNAL TRANSDUCTION; WNT SIGNALING PATHWAY;

EID: 84897972050     PISSN: 19454589     EISSN: None     Source Type: Journal    
DOI: 10.18632/aging.100648     Document Type: Article

References (47)

1. Gems D and de la Guardia Y. Alternative Perspectives on Aging in Caenorhabditis elegans: Reactive Oxygen Species or Hyperfunction? Antioxidants&redox signaling. 2013; 19:321-329.
2. Yanos ME, Bennett CF and Kaeberlein M. Genome-Wide RNAi Longevity Screens in Caenorhabditis elegans. Curr Genomics. 2012; 13:508-518.
3. McCormick MA and Kennedy BK. Genome-scale studies of aging: challenges and opportunities. Curr Genomics. 2012; 13:500-507.
4. Kenyon CJ. The genetics of ageing. Nature. 2010; 464:504-512.
5. Golden TR and Melov S. Gene expression changes associated with aging in C. elegans. WormBook. 2007:1-12.
6. Fisher AL and Lithgow GJ. The nuclear hormone receptor DAF-12 has opposing effects on Caenorhabditis elegans lifespan and regulates genes repressed in multiple long-lived worms. Aging Cell. 2006; 5:127-138.
7. Lund J, Tedesco P, Duke K, Wang J, Kim SK and Johnson TE. Transcriptional profile of aging in C. elegans. Curr Biol. 2002; 12:1566-1573.
8. Viswanathan M, Kim SK, Berdichevsky A and Guarente L. A role for SIR-2.1 regulation of ER stress response genes in determining C. elegans life span. Dev Cell. 2005; 9:605-615.
9. Suarez-Farinas M, Lowes MA, Zaba LC and Krueger JG. Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA). PLoS One. 2010; 5:e10247.
10. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES and Mesirov JP. Gene set enrichment analysis: a knowledgebased approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102:15545-15550.
11. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature methods. 2007; 4651-657.
12. Johnson DS, Mortazavi A, Myers RM and Wold B. Genomewide mapping of in vivo protein-DNA interactions. Science. 2007; 316:1497-1502.
13. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, et al. Unlocking the secrets of the genome. Nature. 2009; 459:927-930.
14. Youngman MJ, Rogers ZN and Kim DH. A decline in p38 MAPK signaling underlies immunosenescence in Caenorhabditis elegans. PLoS Genet. 2011; 7:e1002082.
15. Schlessinger J. Cell signaling by receptor tyrosine kinases. Cell. 2000; 103:211-225.
16. Aroian RV, Koga M, Mendel JE, Ohshima Y and Sternberg PW. The let-23 gene necessary for Caenorhabditis elegans vulval induction encodes a tyrosine kinase of the EGF receptor subfamily. Nature. 1990; 348:693-699.
17. Jacobs D, Beitel GJ, Clark SG, Horvitz HR and Kornfeld K. Gain-of-function mutations in the Caenorhabditis elegans lin-1 ETS gene identify a C-terminal regulatory domain phosphorylated by ERK MAP kinase. Genetics. 1998; 149:1809-1822.
18. Hsu V, Zobel CL, Lambie EJ, Schedl T and Kornfeld K. Caenorhabditis elegans lin-45 raf is essential for larval viability, fertility and the induction of vulval cell fates. Genetics. 2002; 160:481-492.
19. Moon RT, Bowerman B, Boutros M and Perrimon N. The promise and perils of Wnt signaling through beta-catenin. Science. 2002; 296:1644-1646.
20. Heldin CH, Miyazono K and ten Dijke P. TGF-beta signalling from cell membrane to nucleus through SMAD proteins. Nature. 1997; 390:465-471.
21. Tomioka M, Adachi T, Suzuki H, Kunitomo H, Schafer WR and Iino Y. The insulin/PI 3-kinase pathway regulates salt chemotaxis learning in Caenorhabditis elegans. Neuron. 2006; 51:613-625.
22. Riesen M, Feyst I, Rattanavirotkul N, Ezcurra M, Tullet JM, Papatheodorou I, Ziehm M, Au C, Gilliat AF, Hellberg J, Thornton JM and Gems D. MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans. Aging. 2014; 6:98-117.
23. Gems D and Partridge L. Genetics of longevity in model organisms: debates and paradigm shifts. Annual review of physiology. 2013; 75:621-644.
24. Blagosklonny MV. An anti-aging drug today: from senescence-promoting genes to anti-aging pill. Drug discovery today. 2007; 12:218-224.
25. Blagosklonny MV. Aging and immortality: quasi-programmed senescence and its pharmacologic inhibition. Cell cycle (Georgetown, Tex). 2006; 5:2087-2102.
26. Demidenko ZN, Shtutman M and Blagosklonny MV. Pharmacologic inhibition of MEK and PI-3K converges on the mTOR/S6 pathway to decelerate cellular senescence. Cell cycle (Georgetown, Tex). 2009; 8:1896-1900.
27. Luo S, Kleemann GA, Ashraf JM, Shaw WM and Murphy CT. TGF-beta and insulin signaling regulate reproductive aging via oocyte and germline quality maintenance. Cell. 2010; 143:299-312.
28. Derynck R and Zhang YE. Smad-dependent and Smadindependent pathways in TGF-beta family signalling. Nature. 2003; 425:577-584.
29. Yarden Y and Sliwkowski MX. Untangling the ErbB signalling network. Nature reviews Molecular cell biology. 2001; 2:127-137.
30. Sundaram MV. RTK/Ras/MAPK signaling. WormBook. 2006:1-19.
31. de la Cova C and Greenwald I. SEL-10/Fbw7-dependent negative feedback regulation of LIN-45/Braf signaling in C. elegans via a conserved phosphodegron. Genes&development. 2012; 26:2524-2535.
32. Yamanaka A, Yada M, Imaki H, Koga M, Ohshima Y and Nakayama K. Multiple Skp1-related proteins in Caenorhabditis elegans: diverse patterns of interaction with Cullins and F-box proteins. Curr Biol. 2002; 12:267-275.
33. Nayak S, Santiago FE, Jin H, Lin D, Schedl T and Kipreos ET. The Caenorhabditis elegans Skp1-related gene family: diverse functions in cell proliferation, morphogenesis, and meiosis. Curr Biol. 2002; 12:277-287.
34. Van Voorhies WA and Ward S. Genetic and environmental conditions that increase longevity in Caenorhabditis elegans decrease metabolic rate. Proc Natl Acad Sci U S A. 1999; 96:11399-11403.
35. Braeckman BP, Houthoofd K, Brys K, Lenaerts I, De Vreese A, Van Eygen S, Raes H and Vanfleteren JR. No reduction of energy metabolism in Clk mutants. Mech Ageing Dev. 2002; 123:1447-1456.
36. Braeckman BP, Houthoofd K, De Vreese A and Vanfleteren JR. Assaying metabolic activity in ageing Caenorhabditis elegans. Mech Ageing Dev. 2002; 123:105-119.
37. Chamoli M, Singh A, Malik Y and Mukhopadhyay A. A novel kinase regulates dietary restriction-mediated longevity in Caenorhabditis elegans. Aging Cell. 2014.
38. Dai DF, Karunadharma PP, Chiao YA, Basisty N, Crispin D, Hsieh EJ, Chen T, Gu H, Djukovic D, Raftery D, Beyer RP, Maccoss MJ and Rabinovitch PS. Altered proteome turnover and remodeling by short-term caloric restriction or rapamycin rejuvenate the aging heart. Aging Cell. 2014.
39. Van Nostrand EL, Sanchez-Blanco A, Wu B, Nguyen A and Kim SK. Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans. PLoS Genet. 2013; 9:e1003325.
40. Hiatt SM, Duren HM, Shyu YJ, Ellis RE, Hisamoto N, Matsumoto K, Kariya K, Kerppola TK and Hu CD. Caenorhabditis elegans FOS-1 and JUN-1 regulate plc-1 expression in the spermatheca to control ovulation. Molecular biology of the cell. 2009; 20:3888-3895.
41. Gautier L, Cope L, Bolstad BM and Irizarry RA. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004; 20:307-315.
42. Chiaretti S, Li X, Gentleman R, Vitale A, Vignetti M, Mandelli F, Ritz J and Foa R. Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood. 2004; 103:2771-2778.
43. He K, Chen Z, Ma Y and Pan Y. Identification of high-copperresponsive target pathways in Atp7b knockout mouse liver by GSEA on microarray data sets. Mamm Genome. 2011; 22:703-713.
44. Van Nostrand EL and Kim SK. Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions. Genome Res. 2013.
45. Langmead B and Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature methods. 2012; 9:357-359.
46. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W and Liu XS. Modelbased analysis of ChIP-Seq (MACS). Genome biology. 2008; 9:R137.
47. Guan D, Shao J, Deng Y, Wang P, Zhao Z, Liang Y, Wang J and Yan B. CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data. Bioinformatics. 2014; Epub ahead of print.