Comparison of Hi-C results using in-solution versus in-nucleus ligation
Tóm tắt
Chromosome conformation capture and various derivative methods such as 4C, 5C and Hi-C have emerged as standard tools to analyze the three-dimensional organization of the genome in the nucleus. These methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. During development of single-cell Hi-C, we devised an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing in-nucleus ligation with the standard in-solution ligation. We show in-nucleus ligation results in consistently lower levels of inter-chromosomal contacts. Through chromatin mixing experiments we show that a significantly large fraction of inter-chromosomal contacts are the result of spurious ligation events formed during in-solution ligation. In-nucleus ligation significantly reduces this source of experimental noise, and results in improved reproducibility between replicates. We also find that in-nucleus ligation eliminates restriction fragment length bias found with in-solution ligation. These improvements result in greater reproducibility of long-range intra-chromosomal and inter-chromosomal contacts, as well as enhanced detection of structural features such as topologically associated domain boundaries. We conclude that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. In-nucleus ligation creates higher quality Hi-C libraries while simplifying the experimental procedure. We suggest that the entire range of 3C applications are likely to show similar benefits from in-nucleus ligation.
Tài liệu tham khảo
Hakim O, Misteli T. SnapShot: chromosome conformation capture. Cell. 2012;148:1068.
Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013;14:390–403.
Selvaraj S, Dixon JR, Bansal V, Ren B. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol. 2013;31:1111–8.
Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2012;30:90–8.
Dryden NH, Broome LR, Dudbridge F, Johnson N, Orr N, Schoenfelder S, et al. Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Genome Res. 2014;24:1854–68.
De Vree PJP, de Wit E, Yilmaz M, van de Heijning M, Klous P, Verstegen MJ, et al. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nat Biotechnol. 2014;32:1019–25.
Jäger R, Migliorini G, Henrion M, Kandaswamy R, Speedy HE, Heindl A, et al. Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat Commun. 2015;6:6178.
Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, et al. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res. 2015;25:582–97.
Dekker J. The three “C” s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006;3:17–21.
Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature. 2013;502:59–64.
Comet I, Schuettengruber B, Sexton T, Cavalli G. A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber. Proc Natl Acad Sci U S A. 2011;108:2294–9.
Gavrilov AA, Gushchanskaya ES, Strelkova O, Zhironkina O, Kireev II, Iarovaia OV, et al. Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub. Nucleic Acids Res. 2013;41:3563–75.
Sofueva S, Yaffe E, Chan W-C, Georgopoulou D, Vietri Rudan M, Mira-Bontenbal H, et al. Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J. 2013;32:3119–29.
Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D Map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159:1665–80.
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–93.
HiCUP (Hi-C User Pipeline). http://www.bioinformatics.babraham.ac.uk/projects/hicup.
Zhang Y, McCord RP, Ho Y-J, Lajoie BR, Hildebrand DG, Simon AC, et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell. 2012;148:908–21.
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376–80.
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, et al. A map of the cis-regulatory sequences in the mouse genome. Nature. 2012;488:116–20.
Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A, et al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep. 2015;10:1297–309.
Yaffe E, Tanay A. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet. 2011;43:1059–65.
Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012;9:999–1003.
Aird D, Ross MG, Chen W-S, Danielsson M, Fennell T, Russ C, et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 2011;12:R18.
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012;485:381–5.
Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell. 2012;148:458–72.
Hi-C pipeline for bias correction. http://www.wisdom.weizmann.ac.il/~eitany/hicpipe.
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576–89.
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.
Datasets deposited at Gene Expression Omnibus, GSE70181. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=wtmfywywjrshbip&acc=GSE70181.