- About this Journal
- Abstracting and Indexing
- Aims and Scope
- 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
- Submit a Manuscript
- Subscription Information
- Table of Contents
Volume 2013 (2013), Article ID 913273, 8 pages
Locus-Specific Biochemical Epigenetics/Chromatin Biochemistry by Insertional Chromatin Immunoprecipitation
Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
Received 7 November 2012; Accepted 27 November 2012
Academic Editors: J. Bonnet, M. Frank-Kamenetskii, and J.-J. Lin
Copyright © 2013 Toshitsugu Fujita and Hodaka Fujii. 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.
- R. D. Kornberg and Y. Lorch, “Chromatin rules,” Nature Structural and Molecular Biology, vol. 14, no. 11, pp. 986–988, 2007.
- X. Y. Zhang and W. Hörz, “Analysis of highly purified satellite DNA containing chromatin from the mouse,” Nucleic Acids Research, vol. 10, no. 5, pp. 1481–1494, 1982.
- J. L. Workman and J. P. Langmore, “Nucleoprotein hybridization: a method for isolating specific genes as high molecular weight chromatin,” Biochemistry, vol. 24, no. 25, pp. 7486–7497, 1985.
- L. C. Boffa, E. M. Carpaneto, and V. G. Allfrey, “Isolation of active genes containing CAG repeats by DNA strand invasion by a peptide nucleic acid,” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 6, pp. 1901–1905, 1995.
- A. Jasinskas and B. A. Hamkalo, “Purification and initial characterization of primate satellite chromatin,” Chromosome Research, vol. 7, no. 5, pp. 341–354, 1999.
- J. Griesenbeck, H. Boeger, J. S. Strattan, and R. D. Kornberg, “Affinity purification of specific chromatin segments from chromosomal loci in yeast,” Molecular and Cellular Biology, vol. 23, no. 24, pp. 9275–9282, 2003.
- R. Ghirlando and G. Felsenfeld, “Hydrodynamic studies on defined heterochromatin fragments support a 30-nm fiber having six nucleosomes per turn,” Journal of Molecular Biology, vol. 376, no. 5, pp. 1417–1425, 2008.
- J. Déjardin and R. E. Kingston, “Purification of proteins associated with specific genomic loci,” Cell, vol. 136, no. 1, pp. 175–186, 2009.
- C. M. Gorman, L. F. Moffat, and B. H. Howard, “Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells,” Molecular and Cellular Biology, vol. 2, no. 9, pp. 1044–1051, 1982.
- S. Aparicio, A. Morrison, A. Gould et al., “Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 5, pp. 1684–1688, 1995.
- G. A. Maston, S. G. Landt, M. Snyder, and M. R. Green, “Characterization of enhancer function from genome-wide analyses,” Annual Review of Genomics and Human Genetics, vol. 13, pp. 29–57, 2012.
- C. G. Spilianakis, M. D. Lalioti, T. Town, G. R. Lee, and R. A. Flavell, “Interchromosomal associations between alternatively expressed loci,” Nature, vol. 435, no. 7042, pp. 637–645, 2005.
- S. A. Sajan and R. D. Hawkins, “Method for identifying higher-order chromatin structure,” Annual Review of Genomics and Human Genetics, vol. 13, pp. 59–82, 2012.
- D. W. Heermann, “Physical nuclear organization: loops and entropy,” Current Opinion in Cell Biology, vol. 23, no. 3, pp. 332–337, 2011.
- B. Dey, S. Thukral, S. Krishman et al., “DNA-protein interactions: methods for detection and analysis,” Molecular and Cellular Biochemistry, vol. 365, no. 1-2, pp. 279–299, 2012.
- M. J. Solomon, P. L. Larsen, and A. Varshavsky, “Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene,” Cell, vol. 53, no. 6, pp. 937–947, 1988.
- P. Collas, “The current state of chromatin immunoprecipitation,” Molecular Biotechnology, vol. 45, no. 1, pp. 87–100, 2010.
- A. G. Fisher and M. Merkenschlager, “Gene silencing, cell fate and nuclear organisation,” Current Opinion in Genetics and Development, vol. 12, no. 2, pp. 193–197, 2002.
- P. Fraser and W. Bickmore, “Nuclear organization of the genome and the potential for gene regulation,” Nature, vol. 447, no. 7143, pp. 413–417, 2007.
- J. Dekker, K. Rippe, M. Dekker, and N. Kleckner, “Capturing chromosome conformation,” Science, vol. 295, no. 5558, pp. 1306–1311, 2002.
- S. Lomvardas, G. Barnea, D. J. Pisapia, M. Mendelsohn, J. Kirkland, and R. Axel, “Interchromosomal interactions and olfactory receptor choice,” Cell, vol. 126, no. 2, pp. 403–413, 2006.
- M. Simonis, P. Klous, E. Splinter et al., “Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C),” Nature Genetics, vol. 38, no. 11, pp. 1348–1354, 2006.
- 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.
- E. de Wit and W. de Laat, “A decade of 3C technologies: insights into nuclear organization,” Genes and Development, vol. 26, no. 1, pp. 11–24, 2012.
- J. Dosite and W. A. Bickmore, “Chromosome organization in the nucleus—charting new territory across the Hi-Cs,” Current Opinion in Genetics and Development, vol. 22, no. 2, pp. 125–131, 2012.
- A. Hoshino and H. Fujii, “Insertional chromatin immunoprecipitation: a method for isolating specific genomic regions,” Journal of Bioscience and Bioengineering, vol. 108, no. 5, pp. 446–449, 2009.
- A. S. Belmont, “Visualizing chromosome dynamics with GFP,” Trends in Cell Biology, vol. 11, no. 6, pp. 250–257, 2001.
- C. O. Pabo, E. Peisach, and R. A. Grant, “Design and selection of novel Cys2His2 zinc finger proteins,” Annual Review of Biochemistry, vol. 70, pp. 313–340, 2001.
- A. J. Bogdanove and D. F. Voytas, “TAL effectors: customizable proteins for DNA targeting,” Science, vol. 333, no. 6051, pp. 1843–1846, 2011.
- T. Fujita and H. Fujii, “Direct idenification of insulator components by insertional chromatin immunoprecipitation,” PLoS One, vol. 6, no. 10, article e26109, 2011.
- E. P. Lei and V. G. Corces, “RNA interference machinery influences the nuclear organization of a chromatin insulator,” Nature Genetics, vol. 38, no. 8, pp. 936–941, 2006.
- H. Yao, K. Brick, Y. Evrard, T. Xiao, R. D. Camerini-Otero, and G. Felsenfeld, “Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA,” Genes and Development, vol. 24, no. 22, pp. 2543–2555, 2010.
- J. H. Chung, M. Whiteley, and G. Felsenfeld, “A element of the chicken β-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila,” Cell, vol. 74, no. 3, pp. 505–514, 1993.
- A. Murrell, S. Heeson, and W. Reik, “Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops,” Nature Genetics, vol. 36, no. 8, pp. 889–893, 2004.
- E. McCullagh, A. Seshan, H. El-Samad, and H. D. Madhani, “Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway,” Nature Cell Biology, vol. 12, no. 10, pp. 954–962, 2010.
- T. Fujita and H. Fujii, “Efficient isolation of specific genomic regions by insertional chromatin immunoprecipitation (iChIP) with a second-generation tagged LexA DNA-binding domain,” Advances in Bioscience and Biotechnology, vol. 3, no. 5, pp. 626–629, 2012.
- S. E. Ong, B. Blagoev, I. Kratchmarova et al., “Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics,” Molecular & Cellular Proteomics, vol. 1, no. 5, pp. 376–386, 2002.
- P. L. Ross, Y. N. Huang, J. N. Marchese et al., “Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents,” Molecular and Cellular Proteomics, vol. 3, no. 12, pp. 1154–1169, 2004.
- S. D. Byrum, A. Raman, S. D. Taverna, and A. Tackett, “ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus,” Cell Reports, vol. 2, no. 1, pp. 198–205, 2012.
- A. J. Ruthenburg, H. Li, D. J. Patel, and C. D. Allis, “Multivalent engagement of chromatin modifications by linked binding modules,” Nature Reviews Molecular Cell Biology, vol. 8, no. 12, pp. 983–994, 2007.
- M. Tan, H. Luo, S. D. Lee et al., “Identification of 67 histone markes and histone lysine crotonylation as a new type of histone modification,” Cell, vol. 146, no. 6, pp. 1016–1028, 2011.
- M. Agelopoulos, D. J. McKay, and R. S. Mann, “Developmental regulation of chromain conformation by Hox proteins in Drosophila,” Cell Reports, vol. 1, no. 4, pp. 350–359, 2012.