Abstract
Chromosome conformation capture (3C) is a biochemical assay to reveal higher order chromosomal organizations mediated by physical contact between discrete DNA segments in vivo. Chromosomal organizations are involved in transcriptional regulation of a number of genes in various cell types. We have adapted 3C for analyzing the intrachromosomal looping organization of rod and cone photoreceptor genes in the mammalian retina. Here, we describe a detailed protocol for 3C assays on whole mouse retinas. Using the M-cone opsin gene as an example, we demonstrate how to genetically distinguish 3C signals from cones versus rods in retinal 3C assays. We also describe the challenges and key points of 3C design and performance as well as appropriate controls and result interpretations.
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References
Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306–1311
Hagege H et al (2007) Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc 2:1722–1733
Vassetzky Y et al (2009) Chromosome conformation capture (from 3C to 5C) and its ChIP-based modification. Methods Mol Biol 567:171–188
Tolhuis B, Palstra RJ, Splinter E, Grosveld F, de Laat W (2002) Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell 10:1453–1465
Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P (2002) Long-range chromatin regulatory interactions in vivo. Nat Genet 32:623–626
Palstra RJ et al (2003) The beta-globin nuclear compartment in development and erythroid differentiation. Nat Genet 35:190–194
Eivazova ER, Aune TM (2004) Dynamic alterations in the conformation of the Ifng gene region during T helper cell differentiation. Proc Natl Acad Sci USA 101:251–256
Eivazova ER, Vassetzky YS, Aune TM (2007) Selective matrix attachment regions in T helper cell subsets support loop conformation in the Ifng gene. Genes Immun 8:35–43
Liu Z, Garrard WT (2005) Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3′ boundary sequence spanning 46 kilobases. Mol Cell Biol 25:3220–3231
Liu Z, Ma Z, Terada LS, Garrard WT (2009) Divergent roles of RelA and c-Rel in establishing chromosomal loops upon activation of the Igkappa gene. J Immunol 183:3819–3830
Murrell A, Heeson S, Reik W (2004) Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat Genet 36:889–893
Spilianakis CG, Flavell RA (2004) Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol 5:1017–1027
Zhou GL et al (2006) Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Mol Cell Biol 26:5096–5105
Horike S, Cai S, Miyano M, Cheng JF, Kohwi-Shigematsu T (2005) Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat Genet 37:31–40
Akimoto M et al (2006) Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors. Proc Natl Acad Sci USA 103:3890–3895
van Beijnum JR, Rousch M, Castermans K, van der Linden E, Griffioen AW (2008) Isolation of endothelial cells from fresh tissues. Nat Protoc 3:1085–1091
Furukawa T, Morrow EM, Li T, Davis FC, Cepko CL (1999) Retinopathy and attenuated circadian entrainment in Crx-deficient mice. Nat Genet 23:466–470
Chen J, Rattner A, Nathans J (2005) The rod photoreceptor-specific nuclear receptor Nr2e3 represses transcription of multiple cone-specific genes. J Neurosci 25:118–129
Corbo JC, Cepko CL (2005) A hybrid photoreceptor expressing both rod and cone genes in a mouse model of enhanced S-cone syndrome. PLoS Genet 1:e11
Peng GH, Ahmad O, Ahmad F, Liu J, Chen S (2005) The photoreceptor-specific nuclear receptor Nr2e3 interacts with Crx and exerts opposing effects on the transcription of rod versus cone genes. Hum Mol Genet 14:747–764
Peng GH, Chen S (2011) Active opsin loci adopt intrachromosomal loops that depend on the photoreceptor transcription factor Ânetwork. Proc Natl Acad Sci USA. 108:17821–17826
Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3:1101–1108
Acknowledgment
We thank Dr. Anand Swaroop and Dr. Connie Cepko for providing Nrl −/− and Crx −/− mice, Hui Wang for technical assistance, and Anne Hennig for critical reading of the manuscript. This work was supported by NIH EY012543 (to SC), NIH EY02687 (to WU-DOVS), Lew Wasserman Merit Award (to SC), and unrestricted fund from Research to Prevent Blindness (to WU-DOVS).
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Peng, GH., Chen, S. (2012). Revealing Looping Organization of Mammalian Photoreceptor Genes Using Chromosome Conformation Capture (3C) Assays. In: Wang, SZ. (eds) Retinal Development. Methods in Molecular Biology, vol 884. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-848-1_22
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DOI: https://doi.org/10.1007/978-1-61779-848-1_22
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Publisher Name: Humana Press, Totowa, NJ
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Online ISBN: 978-1-61779-848-1
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