4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis

Methods - Tập 170 - Trang 17-32 - 2020
Peter H.L. Krijger1, Geert Geeven1, Valerio Bianchi1, Catharina R.E. Hilvering1, Wouter de Laat1
1Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands

Tài liệu tham khảo

Dekker, 2002, Capturing chromosome conformation, Science, 295, 1306, 10.1126/science.1067799 Denker, 2016, The second decade of 3C technologies: detailed insights into nuclear organization, Genes Dev., 30, 1357, 10.1101/gad.281964.116 Vermunt, 2019, The interdependence of gene-regulatory elements and the 3D genome, J. Cell Biol., 218, 12, 10.1083/jcb.201809040 Dixon, 2016, Chromatin domains: the unit of chromosome organization, Mol. Cell, 62, 668, 10.1016/j.molcel.2016.05.018 Dixon, 2012, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, 485, 376, 10.1038/nature11082 Sexton, 2012, Three-dimensional folding and functional organization principles of the Drosophila genome, Cell, 148, 458, 10.1016/j.cell.2012.01.010 Nora, 2012, Spatial partitioning of the regulatory landscape of the X-inactivation centre, Nature, 485, 381, 10.1038/nature11049 Rowley, 2018, Organizational principles of 3D genome architecture, Nat. Rev. Genet., 19, 789, 10.1038/s41576-018-0060-8 Haarhuis, 2017, e cohesin release factor WAPL restricts chromatin loop extension, Cell, 169, 693, 10.1016/j.cell.2017.04.013 Simonis, 2006, Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C), Nat. Genet., 38, 1348, 10.1038/ng1896 Lieberman-Aiden, 2009, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, 326, 289, 10.1126/science.1181369 Rao, 2014, A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, 159, 1665, 10.1016/j.cell.2014.11.021 Wijchers, 2016, Cause and consequence of tethering a SubTAD to different nuclear compartments, Mol. Cell, 61, 461, 10.1016/j.molcel.2016.01.001 Nuebler, 2018, Chromatin organization by an interplay of loop extrusion and compartmental segregation, Proc. Natl. Acad. Sci. USA, 115, E6697, 10.1073/pnas.1717730115 Dekker, 2017, The 4D nucleome project, Nature, 549, 219, 10.1038/nature23884 Schwartzman, 2016, UMI-4C for quantitative and targeted chromosomal contact profiling, Nat. Meth., 13, 685, 10.1038/nmeth.3922 Hughes, 2014, Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment, Nat. Genet., 46, 205, 10.1038/ng.2871 van de Werken, 2012, Robust 4C-seq data analysis to screen for regulatory DNA interactions, Nat. Meth., 9, 969, 10.1038/nmeth.2173 de Wit, 2015, CTCF binding polarity determines chromatin looping, Mol. Cell, 60, 676, 10.1016/j.molcel.2015.09.023 Lupianez, 2015, Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions, Cell, 161, 1012, 10.1016/j.cell.2015.04.004 Groschel, 2014, A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia, Cell, 157, 369, 10.1016/j.cell.2014.02.019 de Wit, 2013, The pluripotent genome in three dimensions is shaped around pluripotency factors, Nature, 501, 227, 10.1038/nature12420 Geeven, 2018, peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data, Nucl. Acids Res., 46, e91, 10.1093/nar/gky443 Krijger, 2013, Identical cells with different 3D genomes; cause and consequences?, Curr. Opin. Genet. Dev., 23, 191, 10.1016/j.gde.2012.12.010 Finn, 2019, Extensive heterogeneity and intrinsic variation in spatial genome organization, Cell, 176, 1502, 10.1016/j.cell.2019.01.020 Splinter, 2012, Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation, Methods, 58, 221, 10.1016/j.ymeth.2012.04.009 van de Werken, 2012, 4C technology: protocols and data analysis, Meth. Enzymol., 513, 89, 10.1016/B978-0-12-391938-0.00004-5 Rozen, 2000, Primer3 on the WWW for general users and for biologist programmers, Meth. Mol. Biol., 132, 365 Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Brouwer, 2017, Unbiased interrogation of 3D genome topology using chromosome conformation capture coupled to high-throughput sequencing (4C-Seq), Meth. Mol. Biol., 1507, 199, 10.1007/978-1-4939-6518-2_15 Walter, 2019, Benchmarking of 4C-seq pipelines based on real and simulated data, Bioinformatics, 10.1093/bioinformatics/btz426 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Meth., 9, 357, 10.1038/nmeth.1923 Simonis, 2009, High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology, Nat. Meth., 6, 837, 10.1038/nmeth.1391 Kent, 2002, The human genome browser at UCSC, Genome Res., 12, 996, 10.1101/gr.229102 Robinson, 2011, Integrative genomics viewer, Nat. Biotechnol., 29, 24, 10.1038/nbt.1754 Andrey, 2013, A switch between topological domains underlies HoxD genes collinearity in mouse limbs, Science, 340, 1234167, 10.1126/science.1234167 Allahyar, 2018, Enhancer hubs and loop collisions identified from single-allele topologies, Nat. Genet., 50, 1151, 10.1038/s41588-018-0161-5 Redolfi, 2019, DamC reveals principles of chromatin folding in vivo without crosslinking and ligation, Nat. Struct. Mol. Biol., 26, 471, 10.1038/s41594-019-0231-0