Table of Contents Author Guidelines Submit a Manuscript
Comparative and Functional Genomics
Volume 2012 (2012), Article ID 979168, 8 pages
http://dx.doi.org/10.1155/2012/979168
Review Article

Tackling Skeletal Muscle Cells Epigenome in the Next-Generation Sequencing Era

Department of Biomolecular Sciences and Biotechnology, University of Milano, Via Celoria 26, 20133 Milan, Italy

Received 3 February 2012; Accepted 3 April 2012

Academic Editor: Lucia Latella

Copyright © 2012 Raffaella Fittipaldi and Giuseppina Caretti. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. J. Barrero, S. Boué, and J. C. Izpisúa Belmonte, “Epigenetic mechanisms that regulate cell identity,” Cell Stem Cell, vol. 7, no. 5, pp. 565–570, 2010. View at Publisher · View at Google Scholar · View at Scopus
  2. C. Prezioso and V. Orlando, “Polycomb proteins in mammalian cell differentiation and plasticity,” FEBS Letters, vol. 585, no. 13, pp. 2067–2077, 2011. View at Publisher · View at Google Scholar · View at Scopus
  3. V. Sartorelli and A. H. Juan, “Sculpting chromatin beyond the double helix: epigenetic control of skeletal myogenesis,” Current Topics in Developmental Biology, vol. 96, pp. 57–83, 2011. View at Publisher · View at Google Scholar · View at Scopus
  4. M. Maroto, R. Reshef, A. E. Münsterberg, S. Koester, M. Goulding, and A. B. Lassar, “Ectopic Pax-3 activates MyoD and Myf-5 expression in embryonic mesoderm and neural tissue,” Cell, vol. 89, no. 1, pp. 139–148, 1997. View at Google Scholar · View at Scopus
  5. S. Tajbakhsh and G. Cossu, “Establishing myogenic identity during somitogenesis,” Current Opinion in Genetics and Development, vol. 7, no. 5, pp. 634–641, 1997. View at Publisher · View at Google Scholar · View at Scopus
  6. D. Palacios and P. L. Puri, “The epigenetic network regulating muscle development and regeneration,” Journal of Cellular Physiology, vol. 207, no. 1, pp. 1–11, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. V. Guasconi and P. L. Puri, “Chromatin: the interface between extrinsic cues and the epigenetic regulation of muscle regeneration,” Trends in Cell Biology, vol. 19, no. 6, pp. 286–294, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. E. Perdiguero, P. Sousa-Victor, E. Ballestar, and P. Muñoz-Cánoves, “Epigenetic regulation of myogenesis,” Epigenetics, vol. 4, no. 8, pp. 541–550, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. I. W. McKinnell, J. Ishibashi, F. Le Grand et al., “Pax7 activates myogenic genes by recruitment of a histone methyltransferase complex,” Nature Cell Biology, vol. 10, no. 1, pp. 77–84, 2008. View at Publisher · View at Google Scholar · View at Scopus
  10. S. Rampalli, L. Li, E. Mak et al., “p38 MAPK signaling regulates recruitment of Ash2L-containing methyltransferase complexes to specific genes during differentiation,” Nature Structural and Molecular Biology, vol. 14, no. 12, pp. 1150–1156, 2007. View at Publisher · View at Google Scholar · View at Scopus
  11. Z. Wang, C. Zang, K. Cui et al., “Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes,” Cell, vol. 138, no. 5, pp. 1019–1031, 2009. View at Publisher · View at Google Scholar · View at Scopus
  12. M. Fulco, R. L. Schiltz, S. Iezzi et al., “Sir2 regulates skeletal muscle differentiation as a potential sensor of the redox state,” Molecular Cell, vol. 12, no. 1, pp. 51–62, 2003. View at Publisher · View at Google Scholar · View at Scopus
  13. R. Margueron and D. Reinberg, “The Polycomb complex PRC2 and its mark in life,” Nature, vol. 469, no. 7330, pp. 343–349, 2011. View at Publisher · View at Google Scholar · View at Scopus
  14. R. Eskeland, M. Leeb, G. R. Grimes et al., “Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination,” Molecular Cell, vol. 38, no. 3, pp. 452–464, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. G. Caretti, M. Di Padova, B. Micales, G. E. Lyons, and V. Sartorelli, “The polycomb Ezh2 methyltransferase regulates muscle gene expression and skeletal muscle differentiation,” Genes and Development, vol. 18, pp. 2627–2638, 2005. View at Google Scholar
  16. C. L. Fisher and A. G. Fisher, “Chromatin states in pluripotent, differentiated, and reprogrammed cells,” Current Opinion in Genetics and Development, vol. 21, no. 2, pp. 140–146, 2011. View at Publisher · View at Google Scholar · View at Scopus
  17. L. A. Boyer, K. Plath, J. Zeitlinger et al., “Polycomb complexes repress developmental regulators in murine embryonic stem cells,” Nature, vol. 441, no. 7091, pp. 349–353, 2006. View at Publisher · View at Google Scholar · View at Scopus
  18. T. S. Mikkelsen, M. Ku, D. B. Jaffe et al., “Genome-wide maps of chromatin state in pluripotent and lineage-committed cells,” Nature, vol. 448, no. 7153, pp. 553–560, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. B. E. Bernstein, T. S. Mikkelsen, X. Xie et al., “A bivalent chromatin structure marks key developmental genes in embryonic stem cells,” Cell, vol. 125, no. 2, pp. 315–326, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. D. Palacios, C. Mozzetta, S. Consalvi et al., “TNF/p38α/polycomb signaling to Pax7 locus in satellite cells links inflammation to the epigenetic control of muscle regeneration,” Cell Stem Cell, vol. 7, no. 4, pp. 455–469, 2010. View at Publisher · View at Google Scholar · View at Scopus
  21. A. Blais, M. Tsikitis, D. Acosta-Alvear, R. Sharan, Y. Kluger, and B. D. Dynlacht, “An initial blueprint for myogenic differentiation,” Genes and Development, vol. 19, no. 5, pp. 553–569, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. A. H. Juan, A. Derfoul, X. Feng et al., “Polycomb EZH2 controls self-renewal and safeguards the transcriptional identity of skeletal muscle stem cells,” Genes and Development, vol. 25, no. 8, pp. 789–794, 2011. View at Publisher · View at Google Scholar · View at Scopus
  23. Y. Ge and J. Chen, “MicroRNAs in skeletal myogenesis,” Cell Cycle, vol. 10, no. 3, pp. 441–448, 2011. View at Publisher · View at Google Scholar · View at Scopus
  24. M. Cesana, D. Cacchiarelli, I. Legnini et al., “A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA,” Cell, vol. 147, no. 2, pp. 358–369, 2011. View at Publisher · View at Google Scholar
  25. A. H. Juan, R. M. Kumar, J. G. Marx, R. A. Young, and V. Sartorelli, “Mir-214-Dependent Regulation of the Polycomb Protein Ezh2 in Skeletal Muscle and Embryonic Stem Cells,” Molecular Cell, vol. 36, no. 1, pp. 61–74, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. C. F. Wong and R. L. Tellam, “MicroRNA-26a targets the histone methyltransferase enhancer of zeste homolog 2 during myogenesis,” Journal of Biological Chemistry, vol. 283, no. 15, pp. 9836–9843, 2008. View at Publisher · View at Google Scholar · View at Scopus
  27. J. F. Chen, E. M. Mandel, J. M. Thomson et al., “The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation,” Nature Genetics, vol. 38, no. 2, pp. 228–233, 2006. View at Publisher · View at Google Scholar · View at Scopus
  28. H. K. Kim, Y. S. Lee, U. Sivaprasad, A. Malhotra, and A. Dutta, “Muscle-specific microRNA miR-206 promotes muscle differentiation,” Journal of Cell Biology, vol. 174, no. 5, pp. 677–687, 2006. View at Publisher · View at Google Scholar · View at Scopus
  29. E. van Rooij, D. Quiat, B. A. Johnson et al., “A family of microRNAs encoded by myosin genes governs myosin expression and muscle performance,” Developmental Cell, vol. 17, no. 5, pp. 662–673, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. S. van Leeuwen and H. Mikkers, “Long non-coding RNAs: guardians of development,” Differentiation, vol. 80, no. 4-5, pp. 175–183, 2010. View at Publisher · View at Google Scholar · View at Scopus
  31. G. Caretti, R. L. Schiltz, F. J. Dilworth et al., “The RNA Helicases p68/p72 and the Noncoding RNA SRA Are Coregulators of MyoD and Skeletal Muscle Differentiation,” Developmental Cell, vol. 11, no. 4, pp. 547–560, 2006. View at Publisher · View at Google Scholar · View at Scopus
  32. Z. Zhao, G. Tavoosidana, M. Sjölinder et al., “Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions,” Nature Genetics, vol. 38, no. 11, pp. 1341–1347, 2006. View at Publisher · View at Google Scholar · View at Scopus
  33. E. Lieberman-Aiden, N. L. Van Berkum, L. Williams et al., “Comprehensive mapping of long-range interactions reveals folding principles of the human genome,” Science, vol. 326, no. 5950, pp. 289–293, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. M. J. Fullwood, M. H. Liu, Y. F. Pan et al., “An oestrogen-receptor-α-bound human chromatin interactome,” Nature, vol. 462, no. 7269, pp. 58–64, 2009. View at Publisher · View at Google Scholar · View at Scopus
  35. G. Li, X. Ruan, R. K. Auerbach et al., “Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation,” Cell, vol. 148, no. 1-2, pp. 84–98, 2012. View at Publisher · View at Google Scholar
  36. D. E. Schones, K. Cui, S. Cuddapah et al., “Dynamic regulation of nucleosome positioning in the human genome,” Cell, vol. 132, no. 5, pp. 887–898, 2008. View at Publisher · View at Google Scholar · View at Scopus
  37. A. P. Boyle, S. Davis, H. P. Shulha et al., “High-resolution mapping and characterization of open chromatin across the genome,” Cell, vol. 132, no. 2, pp. 311–322, 2008. View at Publisher · View at Google Scholar · View at Scopus
  38. P. G. Giresi and J. D. Lieb, “Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements),” Methods, vol. 48, no. 3, pp. 233–239, 2009. View at Publisher · View at Google Scholar · View at Scopus
  39. A. Barski, S. Cuddapah, K. Cui et al., “High-resolution profiling of histone methylations in the human genome,” Cell, vol. 129, no. 4, pp. 823–837, 2007. View at Publisher · View at Google Scholar · View at Scopus
  40. S. J. Cokus, S. Feng, X. Zhang et al., “Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning,” Nature, vol. 452, no. 7184, pp. 215–219, 2008. View at Publisher · View at Google Scholar · View at Scopus
  41. C. Bock, E. M. Tomazou, A. B. Brinkman et al., “Quantitative comparison of genome-wide DNA methylation mapping technologies,” Nature Biotechnology, vol. 28, no. 10, pp. 1106–1114, 2010. View at Publisher · View at Google Scholar · View at Scopus
  42. A. B. Brinkman, F. Simmer, K. Ma, A. Kaan, J. Zhu, and H. G. Stunnenberg, “Whole-genome DNA methylation profiling using MethylCap-seq,” Methods, vol. 52, no. 3, pp. 232–236, 2010. View at Publisher · View at Google Scholar · View at Scopus
  43. R. D. Hawkins, G. C. Hon, and B. Ren, “Next-generation genomics: an integrative approach,” Nature Reviews Genetics, vol. 11, no. 7, pp. 476–486, 2010. View at Publisher · View at Google Scholar · View at Scopus
  44. Y. Cao, Z. Yao, D. Sarkar et al., “Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming,” Developmental Cell, vol. 18, no. 4, pp. 662–674, 2010. View at Publisher · View at Google Scholar · View at Scopus
  45. H. Weintraub, R. Davis, S. Tapscott et al., “The myoD gene family: nodal point during specification of the muscle cell lineage,” Science, vol. 251, no. 4995, pp. 761–766, 1991. View at Google Scholar · View at Scopus
  46. H. Weintraub, S. J. Tapscott, R. L. Davis et al., “Activation of muscle-specific genes in pigment, nerve, fat, liver, and fibroblast cell lines by forced expression of MyoD,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 14, pp. 5434–5438, 1989. View at Google Scholar · View at Scopus
  47. P. Asp, R. Blum, V. Vethantham et al., “Genome-wide remodeling of the epigenetic landscape during myogenic differentiation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 22, pp. E149–E158, 2011. View at Publisher · View at Google Scholar · View at Scopus
  48. X. Chen, H. Xu, P. Yuan et al., “Integration of external signaling pathways with the core transcriptional network in embryonic stem cells,” Cell, vol. 133, no. 6, pp. 1106–1117, 2008. View at Publisher · View at Google Scholar · View at Scopus
  49. K. Mousavi, H. Zare, A. H. Wang, and V. Sartorelli, “Polycomb protein Ezh1 promotes RNA polymerase II elongation,” Molecular Cell, vol. 45, no. 2, pp. 255–262, 2012. View at Publisher · View at Google Scholar
  50. R. Margueron, G. Li, K. Sarma et al., “Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms,” Molecular Cell, vol. 32, no. 4, pp. 503–518, 2008. View at Publisher · View at Google Scholar · View at Scopus
  51. X. Shen, Y. Liu, Y. J. Hsu et al., “EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency,” Molecular Cell, vol. 32, no. 4, pp. 491–502, 2008. View at Publisher · View at Google Scholar · View at Scopus
  52. B. C. Lim, S. Lee, J.-Y. Shin et al., “Genetic diagnosis of duchenne and becker: comprehensive mutational search in a single platform,” Journal of Medical Genetics, vol. 48, no. 11, pp. 731–736, 2011. View at Publisher · View at Google Scholar
  53. L. N. Geng, Z. Yao, L. Snider et al., “dux4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy,” Developmental Cell, vol. 22, pp. 38–51, 2012. View at Google Scholar
  54. H. Gu, C. Bock, T. S. Mikkelsen et al., “Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution,” Nature Methods, vol. 7, no. 2, pp. 133–136, 2010. View at Publisher · View at Google Scholar · View at Scopus
  55. N. D. Heintzman, R. K. Stuart, G. Hon et al., “Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome,” Nature Genetics, vol. 39, no. 3, pp. 311–318, 2007. View at Publisher · View at Google Scholar · View at Scopus
  56. S. Cuddapah, R. Jothi, D. E. Schones, T. Y. Roh, K. Cui, and K. Zhao, “Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains,” Genome Research, vol. 19, no. 1, pp. 24–32, 2009. View at Publisher · View at Google Scholar · View at Scopus
  57. C. Chu, K. Qu, F. Zhong, S. Artandi, and H. Chang, “Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions,” Molecular Cell, vol. 44, no. 4, pp. 667–678, 2011. View at Publisher · View at Google Scholar
  58. P. Shankaranarayanan, M. A. Mendoza-Parra, W. van Gool, L. M. Trindade, and H. Gronemeyer, “Single-tube linear DNA amplification for genome-wide studies using a few thousand cells,” Nature Protocols, vol. 7, pp. 328–338, 2012. View at Google Scholar
  59. E. E. Schadt, S. Turner, and A. Kasarskis, “A window into third-generation sequencing,” Human Molecular Genetics, vol. 19, no. 2, pp. R227–240, 2010. View at Google Scholar · View at Scopus
  60. C. Trapnell, B. A. Williams, G. Pertea et al., “Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation,” Nature Biotechnology, vol. 28, no. 5, pp. 511–515, 2010. View at Publisher · View at Google Scholar · View at Scopus
  61. M. D. Robinson and A. Oshlack, “A scaling normalization method for differential expression analysis of RNA-seq data,” Genome Biology, vol. 11, no. 3, article r25, 2010. View at Publisher · View at Google Scholar · View at Scopus