Abstract
Genomic DNA is dynamically associated with protein factors and folded to form chromatin fibers. The 3-dimensional (3D) configuration of the chromatin will enable the distal genetic elements to come into close proximity, allowing transcriptional regulation. Noncoding RNA can mediate the 3D structure of chromatin. Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a valuable and powerful technique in molecular biology which allows the study of unbiased, genome-wide de novo chromatin interactions with paired-end tags. Here, we describe the standard version of ChIA-PET and a Multiplex ChIA-PET version.
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References
Bartkuhn M, Renkawitz R (2008) Long range chromatin interactions involved in gene regulation. Biochim Biophys Acta 1783:2161–2166
Ma W, Ay F, Lee C et al (2015) Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat Methods 12:71–78
Lai F, Orom UA, Cesaroni M et al (2013) Activating RNAs associate with mediator to enhance chromatin architecture and transcription. Nature 494:497–501
Xiang JF, Yin QF, Chen T et al (2014) Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res 24:513–531
Fullwood MJ, Liu MH, Pan YF et al (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58–64
Zhang J, Poh HM, Peh SQ et al (2012) ChIA-PET analysis of transcriptional chromatin interactions. Methods 58:289–299
Li G, Fullwood MJ, Xu H et al (2010) ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 11:R22
Zhang Y, Wong CH, Birnbaum RY et al (2013) Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 504:306–310
Chen D, Fu LY, Zhang Z et al (2014) Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res 42:3028–3043
Acknowledgments
This work was supported by the National Research Foundation (NRF) Fellowship Grant to Melissa Jane Fullwood. The NRF grant number is R-713-000-143-281. In addition, this work is supported by NRF Funding and Ministry of Education funding to the Cancer Science Institute under the Research Centre of Excellence framework, as well as Yale-NUS and NTU start-up funds. This research is supported by the RNA Biology Center at the Cancer Science Institute of Singapore, NUS, as part of the funding under the Singapore Ministry of Education’s Tier 3 grants.
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Choy, J., Fullwood, M.J. (2017). Deciphering Noncoding RNA and Chromatin Interactions: Multiplex Chromatin Interaction Analysis by Paired-End Tag Sequencing (mChIA-PET). In: Ørom, U. (eds) Enhancer RNAs. Methods in Molecular Biology, vol 1468. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-4035-6_7
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DOI: https://doi.org/10.1007/978-1-4939-4035-6_7
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Online ISBN: 978-1-4939-4035-6
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