- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Recently Accepted Articles ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 785731, 7 pages
Integrative Analysis of Methylome and Transcriptome Reveals the Importance of Unmethylated CpGs in Non-CpG Island Gene Activation
Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120 Jerusalem, Israel
Received 2 April 2013; Accepted 10 June 2013
Academic Editor: Tosso Leeb
Copyright © 2013 Amichai Marx et al. 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.
- L. Lande-Diner and H. Cedar, “Silence of the genes: mechanisms of long-term repression,” Nature Reviews Genetics, vol. 6, no. 8, pp. 648–654, 2005.
- Z. Siegfried and I. Simon, “DNA methylation and gene expression,” Wiley Interdisciplinary Reviews, vol. 2, no. 3, pp. 362–371, 2010.
- S. D. Fouse, Y. Shen, M. Pellegrini et al., “Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation,” Cell Stem Cell, vol. 2, no. 2, pp. 160–169, 2008.
- S. M. Iguchi-Ariga and W. Schaffner, “CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation,” Genes & Development, vol. 3, no. 5, pp. 612–619, 1989.
- M. R. Campanero, M. I. Armstrong, and E. K. Flemington, “CpG methylation as a mechanism for the regulation of E2F activity,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 12, pp. 6481–6486, 2000.
- F. Fuks, “DNA methylation and histone modifications: teaming up to silence genes,” Current Opinion in Genetics and Development, vol. 15, no. 5, pp. 490–495, 2005.
- Y. Zhang, H.-H. Ng, H. Erdjument-Bromage, P. Tempst, A. Bird, and D. Reinberg, “Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation,” Genes & Development, vol. 13, no. 15, pp. 1924–1935, 1999.
- P. A. Wade, A. Gegonne, P. L. Jones, E. Ballestar, F. Aubry, and A. P. Wolffe, “Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation,” Nature Genetics, vol. 23, no. 1, pp. 62–66, 1999.
- X. Nan, H.-H. Ng, C. A. Johnson et al., “Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex,” Nature, vol. 393, no. 6683, pp. 386–389, 1998.
- P. L. Jones, G. J. C. Veenstra, P. A. Wade et al., “Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription,” Nature Genetics, vol. 19, no. 2, pp. 187–191, 1998.
- N. P. Blackledge, J. C. Zhou, M. Y. Tolstorukov, A. M. Farcas, P. J. Park, and R. J. Klose, “CpG islands recruit a histone H3 lysine 36 demethylase,” Molecular Cell, vol. 38, no. 2, pp. 179–190, 2010.
- J. P. Thomson, P. J. Skene, J. Selfridge et al., “CpG islands influence chromatin structure via the CpG-binding protein Cfp1,” Nature, vol. 464, no. 7291, pp. 1082–1086, 2010.
- R. Lister, M. Pelizzola, R. H. Dowen et al., “Human DNA methylomes at base resolution show widespread epigenomic differences,” Nature, vol. 462, no. 7271, pp. 315–322, 2009.
- L. Laurent, E. Wong, G. Li et al., “Dynamic changes in the human methylome during differentiation,” Genome Research, vol. 20, no. 3, pp. 320–331, 2010.
- R. Straussman, D. Nejman, D. Roberts et al., “Developmental programming of CpG island methylation profiles in the human genome,” Nature Structural and Molecular Biology, vol. 16, no. 5, pp. 564–571, 2009.
- J. Newell-Price, A. J. L. Clark, and P. King, “DNA methylation and silencing of gene expression,” Trends in Endocrinology and Metabolism, vol. 11, no. 4, pp. 142–148, 2000.
- J. Lan, S. Hua, X. He, and Y. Zhang, “DNA methyltransferases and methyl-binding proteins of mammals,” Acta Biochimica et Biophysica Sinica, vol. 42, no. 4, pp. 243–252, 2010.
- M. Weber, I. Hellmann, M. B. Stadler et al., “Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome,” Nature Genetics, vol. 39, no. 4, pp. 457–466, 2007.
- M. B. Stadler, R. Murr, L. Burger et al., “DNA-binding factors shape the mouse methylome at distal regulatory regions,” Nature, vol. 480, no. 7378, pp. 490–495, 2011.
- M. Gardiner-Garden and M. Frommer, “CpG islands in vertebrate genomes,” Journal of Molecular Biology, vol. 196, no. 2, pp. 261–282, 1987.
- R. Illingworth, A. Kerr, D. Desousa et al., “A novel CpG island set identifies tissue-specific methylation at developmental gene loci,” PLoS Biology, vol. 6, no. 1, article e22, 2008.
- J. Boyes and A. Bird, “DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein,” Cell, vol. 64, no. 6, pp. 1123–1134, 1991.
- X. Nan, F. J. Campoy, and A. Bird, “MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin,” Cell, vol. 88, no. 4, pp. 471–481, 1997.
- R. P. Ghosh, R. A. Horowitz-Scherer, T. Nikitina, L. S. Shlyakhtenko, and C. L. Woodcock, “MeCP2 binds cooperatively to its substrate and competes with histone H1 for chromatin binding sites,” Molecular and Cellular Biology, vol. 30, no. 19, pp. 4656–4670, 2010.
- C. Trapnell, A. Roberts, L. Goff et al., “Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks,” Nature Protocols, vol. 7, no. 3, pp. 562–578, 2012.