- About this Journal
- Abstracting and Indexing
- Aims and Scope
- Annual Issues
- Article Processing Charges
- Articles in Press
- Author Guidelines
- Bibliographic Information
- Citations to this Journal
- Contact Information
- Editorial Board
- Editorial Workflow
- Free eTOC Alerts
- Publication Ethics
- Reviewers Acknowledgment
- Submit a Manuscript
- Subscription Information
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 914971, 7 pages
A Quantitative Analysis of the Impact on Chromatin Accessibility by Histone Modifications and Binding of Transcription Factors in DNase I Hypersensitive Sites
1School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
2Shanghai Center for Bioinformation Technology, 1278 Ke Yuan Road, Shanghai 201203, China
Received 31 July 2013; Accepted 3 September 2013
Academic Editor: Tao Huang
Copyright © 2013 Peng Cui 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.
- K. Luger, A. W. Mäder, R. K. Richmond, D. F. Sargent, and T. J. Richmond, “Crystal structure of the nucleosome core particle at 2.8 Å resolution,” Nature, vol. 389, no. 6648, pp. 251–260, 1997.
- J. D. Anderson and J. Widom, “Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites,” Journal of Molecular Biology, vol. 296, no. 4, pp. 979–987, 2000.
- C. Dingwall, G. P. Lomonossoff, and R. A. Laskey, “High sequence specificity of micrococcal nuclease,” Nucleic Acids Research, vol. 9, no. 12, pp. 2659–2674, 1981.
- D. S. Gross and W. T. Garrard, “Nuclease hypersensitive sites in chromatin,” Annual Review of Biochemistry, vol. 57, pp. 159–197, 1988.
- P. N. Cockerill, “Structure and function of active chromatin and DNase I hypersensitive sites,” FEBS Journal, vol. 278, no. 13, pp. 2182–2210, 2011.
- X.-Y. Li, S. Thomas, P. J. Sabo, M. B. Eisen, J. A. Stamatoyannopoulos, and M. D. Biggin, “The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding,” Genome Biology, vol. 12, article R34, 2011.
- Q. Lu and R. Bruce, “DNaseI hypersensitivity analysis of chromatin structure,” in Epigenetics Protocols, pp. 77–86, Humana Press, 2004.
- 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.
- I. Dunham, A. Kundaje, S. F. Aldred, et al., “An integrated encyclopedia of DNA elements in the human genome,” Nature, vol. 489, pp. 57–74, 2012.
- P. J. Park, “ChIP-seq: advantages and challenges of a maturing technology,” Nature Reviews Genetics, vol. 10, no. 10, pp. 669–680, 2009.
- E. R. Mardis, “ChIP-seq: welcome to the new frontier,” Nature Methods, vol. 4, no. 8, pp. 613–614, 2007.
- L. Song and G. E. Crawford, “DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells,” Cold Spring Harbor Protocols, 2010.
- R. E. Thurman, E. Rynes, R. Humbert, et al., “The accessible chromatin landscape of the human genome,” Nature, vol. 489, pp. 75–82, 2012.
- C. Nello and J. Shawe-Taylor, An Introduction to Support Vector Machines and Other Kernel-Based Learning Methods, Cambridge University Press, 2000.
- C. Cheng, K.-K. Yan, K. Y. Yip et al., “A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets,” Genome Biology, vol. 12, no. 2, article R15, 2011.
- D. Evgenia, K. Hornik, F. Leisch, D. Meyer, and A. Weingessel, “Misc functions of the Department of Statistics (e1071), TU Wien,” R package pp. 1–5, 2008.
- B. S. Everitt, Cambridge Dictionary of Statistics, Cambridge University Press, New York, NY, USA, 2nd edition, 2002.
- J. Bartkova, P. Moudry, Z. Hodny, J. Lukas, R. D. Meyts, and J. Bartek, “Heterochromatin marks HP1γ, HP1α and H3K9me3, and DNA damage response activation in human testis development and germ cell tumours,” International Journal of Andrology, vol. 34, no. 4, pp. e103–e113, 2011.
- D. Sproul, N. Gilbert, and W. A. Bickmore, “The role of chromatin structure in regulating the expression of clustered genes,” Nature Reviews Genetics, vol. 6, no. 10, pp. 775–781, 2005.
- K. Regha, M. A. Sloane, R. Huang et al., “Active and repressive chromatin are interspersed without spreading in an imprinted gene cluster in the mammalian genome,” Molecular Cell, vol. 27, no. 3, pp. 353–366, 2007.
- R. Margueron and D. Reinberg, “Chromatin structure and the inheritance of epigenetic information,” Nature Reviews Genetics, vol. 11, no. 4, pp. 285–296, 2010.
- S. Chantalat, A. Depaux, P. Héry et al., “Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin,” Genome Research, vol. 21, no. 9, pp. 1426–1437, 2011.
- R. Karlić, H.-R. Chung, J. Lasserre, K. Vlahoviček, and M. Vingron, “Histone modification levels are predictive for gene expression,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 7, pp. 2926–2931, 2010.
- G. Gill, “Regulation of the initiation of eukaryotic transcription,” Essays in Biochemistry, vol. 37, pp. 33–43, 2001.
- J. L. Rinn, M. Kertesz, J. K. Wang et al., “Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs,” Cell, vol. 129, no. 7, pp. 1311–1323, 2007.
- K. Yano, N. Ueki, T. Oda, N. Seki, Y. Masuho, and M.-A. Muramatsu, “Identification and characterization of human ZNF274 cDNA, which encodes a novel Kruppel-type zinc-finger protein having nucleolar targeting ability,” Genomics, vol. 65, no. 1, pp. 75–80, 2000.
- K. L. Dunn and J. R. Davie, “The many roles of the transcriptional regulator CTCF,” Biochemistry and Cell Biology, vol. 81, no. 3, pp. 161–167, 2003.
- B. M. Turner, “Histone acetylation and an epigenetic code,” BioEssays, vol. 22, no. 9, pp. 836–845, 2000.
- S. M. Fuchs, R. N. Laribee, and B. D. Strahl, “Protein modifications in transcription elongation,” Biochimica et Biophysica Acta, vol. 1789, no. 1, pp. 26–36, 2009.
- J. Marx, “Molecular biology. Protein tail modification opens way for gene activity,” Science, vol. 311, no. 5762, p. 757, 2006.
- O. Bell, V. K. Tiwari, N. H. Thomä, and D. Schübeler, “Determinants and dynamics of genome accessibility,” Nature Reviews, vol. 12, pp. 554–564, 2011.
- L. A. Cirillo, F. R. Lin, I. Cuesta, D. Friedman, M. Jarnik, and K. S. Zaret, “Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4,” Molecular Cell, vol. 9, no. 2, pp. 279–289, 2002.