Abstract
Genome-wide derivatives of the chromosome conformation capture (3C) technique are now well-established approaches to study the multiscale average organization of chromosomes from bacteria to mammals. However, the experimental parameters of the protocol have to be optimized for different species, and the downstream experimental products (i.e., pair-end sequences) are influenced by these parameters. Here, we describe a complete pipeline to generate 3C-seq libraries and compute chromosomal contact maps of yeast species.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Duan Z, Andronescu M, Schutz K et al (2010) A three-dimensional model of the yeast genome. Nature 465:363–367
Dekker J, Rippe K, Dekker M et al (2002) Capturing chromosome conformation. Science 295:1306–1311
Sexton T, Yaffe E, Kenigsberg E et al (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148:458–472
Marie-Nelly H, Marbouty M, Cournac A et al (2014) Filling annotation gaps in yeast genomes using genome-wide contact maps. Bioinformatics 30(15):13
Lieberman-Aiden E, van Berkum NL, Williams L et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293
de Laat W, Dekker J (2012) 3C-Based technologies to study the shape of the genome. Methods 58:189–191
Marbouty M, Cournac A, Flot J-F et al (2014) Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. eLife 3, e03318
Oza P, Jaspersen SL, Miele A et al (2009) Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev 23:912–927
O’Sullivan JM, Tan-Wong SM, Morillon A et al (2004) Gene loops juxtapose promoters and terminators in yeast. Nat Genet 36:1014–1018
Lajoie BR, Dekker J, Kaplan N (2015) The Hitchhiker’s guide to Hi-C analysis: practical guidelines. Methods 72:65–75
Gavrilov AA, Gushchanskaya ES, Strelkova O et al (2013) Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub. Nucleic Acids Res 41(6):3563–3575
Nagano T, Lubling Y, Stevens TJ et al (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502:59–64
van de Werken HJG, Landan G, Holwerda SJB et al (2012) Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods 9:969–972
Thompson DA, Roy S, Chan M et al (2013) Evolutionary principles of modular gene regulation in yeasts. eLife 2, e00603
Yaffe E, Tanay A (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43:1059–1065
Cournac A, Marie-Nelly H, Marbouty M et al (2012) Normalization of a chromosomal contact map. BMC Genomics 13:436
Imakaev M, Fudenberg G, McCord RP et al (2012) Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9:999–1003
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
Marie-Nelly H, Marbouty M, Cournac A et al (2014) High-quality genome (re)assembly using chromosomal contact data. Nat Commun 5:5695
Witten DM, Noble WS (2012) On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements. Nucleic Acids Res 40:3849–3855
Acknowledgements
This research was supported by funding to R.K. from the European Research Council under the 7th Framework Program (FP7/2007-2013)/ERC grant agreement 260822. M.M. is the recipient of an Association pour la Recherche sur le Cancer fellowship 20100600373.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Cournac, A., Marbouty, M., Mozziconacci, J., Koszul, R. (2016). Generation and Analysis of Chromosomal Contact Maps of Yeast Species. In: Devaux, F. (eds) Yeast Functional Genomics. Methods in Molecular Biology, vol 1361. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3079-1_13
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3079-1_13
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3078-4
Online ISBN: 978-1-4939-3079-1
eBook Packages: Springer Protocols