Capítulo 2. Plan de viaje 2016-09 del buque Sestao Knutsen
2.3 Plan de viaje – Descarga: Idku Aqaba
2.3.10 El cálculo del UKC previo a la salida por el Sur del Canal de Suez
Primer sequences and their product length are provided in Table S1. Single probes identified for any of the 84 adipogenic related genes from the top 1000 are given in Table S2. Gene symbols of the 84 adipogenic genes with their description, followed by the average fold change and the p-value, can be found in Table S3. The 258 genome-wide detected DMRs, with a minimum beta difference of 5%, are described in Table S4. DMRs with a minimum beta difference of 5%, found in the 84 adipogenic genes after 5-aza-dC treatment, and the association with gene expression, are provided in Table S5. Supplementary information can be found, in the online version, at http://dx.doi.org/10.1002/jcb.25568. The data sets supporting the DNA methylation results of this article are available in the Gene Expression Omnibus (GEO) with accession number GSE74609.
Chapter 3A
76
References
1. Camp, H. S.; Ren, D.; Leff, T., Adipogenesis and fat-cell function in obesity and diabetes. Trends in molecular medicine 2002, 8, (9), 442-7.
2. Symonds, M. E.; Moreno-Navarrete, J.; Fernández-Real, J., Adipocyte Differentiation. In Adipose Tissue Biology, Springer New York: 2012; pp 17-38.
3. Xie, W.; Schultz, Matthew D.; Lister, R.; Hou, Z.; Rajagopal, N.; Ray, P.; Whitaker, John W.; Tian, S.; Hawkins, R. D.; Leung, D.; Yang, H.; Wang, T.; Lee, Ah Y.; Swanson, Scott A.; Zhang, J.; Zhu, Y.; Kim, A.; Nery, Joseph R.; Urich, Mark A.; Kuan, S.; Yen, C.-a.; Klugman, S.; Yu, P.; Suknuntha, K.; Propson, Nicholas E.; Chen, H.; Edsall, Lee E.; Wagner, U.; Li, Y.; Ye, Z.; Kulkarni, A.; Xuan, Z.; Chung, W.-Y.; Chi, Neil C.; Antosiewicz-Bourget, Jessica E.; Slukvin, I.; Stewart, R.; Zhang, Michael Q.; Wang, W.; Thomson, James A.; Ecker, Joseph R.; Ren, B., Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells. Cell 2013, 153, (5), 1134-1148.
4. Smith, Z. D.; Meissner, A., DNA methylation: roles in mammalian development. Nature reviews. Genetics
2013, 14, (3), 204-20.
5. Jones, P. A., Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nature reviews. Genetics 2012, 13, (7), 484-92.
6. Baubec, T.; Schübeler, D., Genomic patterns and context specific interpretation of DNA methylation. Current
Opinion in Genetics & Development 2014, 25, 85-92.
7. Lev Maor, G.; Yearim, A.; Ast, G., The alternative role of DNA methylation in splicing regulation. Trends in Genetics 2015, 31, (5), 274-280.
8. Sakamoto, H.; Kogo, Y.; Ohgane, J.; Hattori, N.; Yagi, S.; Tanaka, S.; Shiota, K., Sequential changes in genome-wide DNA methylation status during adipocyte differentiation. Biochem Biophys Res Commun
2008, 366, (2), 360-6.
9. Yokomori, N.; Tawata, M.; Onaya, T., DNA demethylation modulates mouse leptin promoter activity during
the differentiation of 3T3-L1 cells. Diabetologia 2002, 45, (1), 140-8.
10. Noer, A.; Sorensen, A. L.; Boquest, A. C.; Collas, P., Stable CpG hypomethylation of adipogenic promoters in freshly isolated, cultured, and differentiated mesenchymal stem cells from adipose tissue. Molecular biology of the cell 2006, 17, (8), 3543-56.
11. Melzner, I.; Scott, V.; Dorsch, K.; Fischer, P.; Wabitsch, M.; Bruderlein, S.; Hasel, C.; Moller, P., Leptin gene expression in human preadipocytes is switched on by maturation-induced demethylation of distinct CpGs in its proximal promoter. J Biol Chem 2002, 277, (47), 45420-7.
12. Yokomori, N.; Tawata, M.; Onaya, T., DNA demethylation during the differentiation of 3T3-L1 cells affects the expression of the mouse GLUT4 gene. Diabetes 1999, 48, (4), 685-90.
13. Fujiki, K.; Kano, F.; Shiota, K.; Murata, M., Expression of the peroxisome proliferator activated receptor gamma gene is repressed by DNA methylation in visceral adipose tissue of mouse models of diabetes. BMC biology 2009, 7, 38.
14. Wang, X.; Zhu, H.; Snieder, H.; Su, S.; Munn, D.; Harshfield, G.; Maria, B. L.; Dong, Y.; Treiber, F.; Gutin, B.; Shi, H., Obesity related methylation changes in DNA of peripheral blood leukocytes. BMC medicine 2010, 8, 87.
15. Drummond, E. M.; Gibney, E. R., Epigenetic regulation in obesity. Current opinion in clinical nutrition and metabolic care 2013, 16, (4), 392-7.
16. Takada, H.; Saito, Y.; Mituyama, T.; Wei, Z.; Yoshihara, E.; Jacinto, S.; Downes, M.; Evans, R. M.; Kida, Y. S., Methylome, transcriptome, and PPAR(gamma) cistrome analyses reveal two epigenetic transitions in fat cells. Epigenetics : official journal of the DNA Methylation Society 2014, 9, (9), 1195-206.
17. Choi, M. R.; In, Y. H.; Park, J.; Park, T.; Jung, K. H.; Chai, J. C.; Chung, M. K.; Lee, Y. S.; Chai, Y. G., Genome- scale DNA methylation pattern profiling of human bone marrow mesenchymal stem cells in long-term culture. Experimental & molecular medicine 2012, 44, (8), 503-12.
18. Morris, T. J.; Butcher, L. M.; Feber, A.; Teschendorff, A. E.; Chakravarthy, A. R.; Wojdacz, T. K.; Beck, S., ChAMP: 450k Chip Analysis Methylation Pipeline. Bioinformatics 2014, 30, (3), 428-30.
19. Maksimovic, J.; Gordon, L.; Oshlack, A., SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome biology 2012, 13, (6), R44.
20. Hansen, K., IlluminaHumanMethylation450kanno.ilmn12.hg19: Annotation for Illumina's 450k methylation
arrays. R package version 0.2.1. . 2015.
21. Benjamini, Y.; Hochberg, Y., Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society. Series B (Methodological) 1995, 57, (1), 289-300. 22. Peters, T. J.; Buckley, M. J.; Statham, A. L.; Pidsley, R.; Samaras, K.; V Lord, R.; Clark, S. J.; Molloy, P. L., De
novo identification of differentially methylated regions in the human genome. Epigenetics & chromatin 2015, 8, 6.
23. Gesta, S.; Bezy, O.; Mori, M. A.; Macotela, Y.; Lee, K. Y.; Kahn, C. R., Mesodermal developmental gene Tbx15 impairs adipocyte differentiation and mitochondrial respiration. Proceedings of the National Academy of Sciences of the United States of America 2011, 108, (7), 2771-6.
DNA methylation and gene expression in differentiating adipocytes
24. Gesta, S.; Bluher, M.; Yamamoto, Y.; Norris, A. W.; Berndt, J.; Kralisch, S.; Boucher, J.; Lewis, C.; Kahn, C. R., Evidence for a role of developmental genes in the origin of obesity and body fat distribution. Proceedings of the National Academy of Sciences of the United States of America 2006, 103, (17), 6676-81.
25. Benz, K.; Breit, S.; Lukoschek, M.; Mau, H.; Richter, W., Molecular analysis of expansion, differentiation, and growth factor treatment of human chondrocytes identifies differentiation markers and growth-related genes. Biochemical and Biophysical Research Communications 2002, 293, (1), 284-292.
26. Hung, S.-C.; Chang, C.-F.; Ma, H.-L.; Chen, T.-H.; Low-Tone Ho, L., Gene expression profiles of early adipogenesis in human mesenchymal stem cells. Gene 2004, 340, (1), 141-150.
27. Wagner, W.; Wein, F.; Seckinger, A.; Frankhauser, M.; Wirkner, U.; Krause, U.; Blake, J.; Schwager, C.; Eckstein, V.; Ansorge, W.; Ho, A. D., Comparative characteristics of mesenchymal stem cells from human bone marrow, adipose tissue, and umbilical cord blood. Experimental Hematology 2005, 33, (11), 1402-1416. 28. Gesta, S.; Tseng, Y.-H.; Kahn, C. R., Developmental Origin of Fat: Tracking Obesity to Its Source. Cell 2007,
131, (2), 242-256.
29. Leder, S.; Czajkowska, H.; Maenz, B.; De Graaf, K.; Barthel, A.; Joost, H.-G.; Becker, W., Alternative splicing variants of dual specificity tyrosine phosphorylated and regulated kinase 1B exhibit distinct patterns of expression and functional properties. Biochemical Journal 2003, 372, (Pt 3), 881-888.
30. Liao, H. T.; Chen, C. T., Osteogenic potential: Comparison between bone marrow and adipose-derived
mesenchymal stem cells. World journal of stem cells 2014, 6, (3), 288-95.
31. Miyata, K.; Miyata, T.; Nakabayashi, K.; Okamura, K.; Naito, M.; Kawai, T.; Takada, S.; Kato, K.; Miyamoto, S.; Hata, K.; Asahara, H., DNA methylation analysis of human myoblasts during in vitro myogenic
differentiation: de novo methylation of promoters of muscle-related genes and its involvement in transcriptional down-regulation. Hum Mol Genet 2015, 24, (2), 410-23.
32. Schlesinger, F.; Smith, A. D.; Gingeras, T. R.; Hannon, G. J.; Hodges, E., De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements. Genome research 2013, 23, (10), 1601- 14.
33. Schellenberg, A.; Stiehl, T.; Horn, P.; Joussen, S.; Pallua, N.; Ho, A. D.; Wagner, W., Population dynamics of mesenchymal stromal cells during culture expansion. Cytotherapy 2012, 14, (4), 401-11.
34. Globisch, D.; Munzel, M.; Muller, M.; Michalakis, S.; Wagner, M.; Koch, S.; Bruckl, T.; Biel, M.; Carell, T., Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PloS one
2010, 5, (12), e15367.
35. Nestor, C. E.; Ottaviano, R.; Reinhardt, D.; Cruickshanks, H. A.; Mjoseng, H. K.; McPherson, R. C.; Lentini, A.; Thomson, J. P.; Dunican, D. S.; Pennings, S.; Anderton, S. M.; Benson, M.; Meehan, R. R., Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems. Genome biology
2015, 16, 11.
36. Sun, R.; Wu, Y.; Wang, Y.; Zang, K.; Wei, H.; Wang, F.; Yu, M., DNA methylation regulates bromodomain-
containing protein 2 expression during adipocyte differentiation. Mol Cell Biochem 2015, 402, (1-2), 23-31. 37. Herlofsen, S. R.; Bryne, J. C.; Hoiby, T.; Wang, L.; Issner, R.; Zhang, X.; Coyne, M. J.; Boyle, P.; Gu, H.; Meza-
Zepeda, L. A.; Collas, P.; Mikkelsen, T. S.; Brinchmann, J. E., Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells. BMC genomics 2013, 14, 105.
38. Siersbaek, R.; Nielsen, R.; John, S.; Sung, M. H.; Baek, S.; Loft, A.; Hager, G. L.; Mandrup, S., Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis. The EMBO journal 2011, 30, (8), 1459-72.
39. Mikkelsen, T. S.; Xu, Z.; Zhang, X.; Wang, L.; Gimble, J. M.; Lander, E. S.; Rosen, E. D., Comparative epigenomic analysis of murine and human adipogenesis. Cell 2010, 143, (1), 156-69.
40. Steger, D. J.; Grant, G. R.; Schupp, M.; Tomaru, T.; Lefterova, M. I.; Schug, J.; Manduchi, E.; Stoeckert, C. J., Jr.; Lazar, M. A., Propagation of adipogenic signals through an epigenomic transition state. Genes & development 2010, 24, (10), 1035-44.
41. Lefterova, M. I.; Steger, D. J.; Zhuo, D.; Qatanani, M.; Mullican, S. E.; Tuteja, G.; Manduchi, E.; Grant, G. R.; Lazar, M. A., Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. Mol Cell Biol 2010, 30, (9), 2078-89.
42. Steegenga, W. T.; Boekschoten, M. V.; Lute, C.; Hooiveld, G. J.; de Groot, P. J.; Morris, T. J.; Teschendorff, A. E.; Butcher, L. M.; Beck, S.; Müller, M., Genome-wide age-related changes in DNA methylation and gene expression in human PBMCs. Age 2014, 36, (3), 9648.