Determining chromatin architecture with Micro Capture-C

Joseph C. Hamley, Hangpeng Li, Nicholas Denny, Damien Downes, James O. J. Davies

Published: 2023-03-28 DOI: 10.1038/s41596-023-00817-8

chromatin architecture

Micro Capture-C

3C method

proximity ligation

resolution

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Hua, P. et al. Defining genome architecture at base-pair resolution. Nature 595, 125–129 (2021).
Cavalli, G. & Misteli, T. Functional implications of genome topology. Nat. Struct. Mol. Biol. 20, 290–299 (2013).
Lam, M. T. Y., Li, W., Rosenfeld, M. G. & Glass, C. K. Enhancer RNAs and regulated transcriptional programs. Trends Biochem. Sci. https://doi.org/10.1016/j.tibs.2014.02.007 (2014).
Arnould, C. et al. Loop extrusion as a mechanism for formation of DNA damage repair foci. Nature 590, 660–665 (2021).
Marchal, C., Sima, J. & Gilbert, D. M. Control of DNA replication timing in the 3D genome. Nat. Rev. Mol. Cell Biol. 20, 721–737 (2019).
Jain, S., Ba, Z., Zhang, Y., Dai, H. Q. & Alt, F. W. CTCF-binding elements mediate accessibility of RAG substrates during chromatin scanning. Cell 174, 102–116.e14 (2018).
Hirota, T., Gerlich, D., Koch, B., Ellenberg, J. & Peters, J. M. Distinct functions of condensin I and II in mitotic chromosome assembly. J. Cell Sci. 117, 6435–6445 (2004).
Lee, T. I. & Young, R. A. Transcriptional regulation and its misregulation in disease. Cell 152, 1237–1251 (2013).
Krumm, A. & Duan, Z. Understanding the 3D genome: emerging impacts on human disease. Semin. Cell Dev. Biol. 90, 62–77 (2019).
Cremer, T. & Cremer, M. Chromosome territories. Cold Spring Harb. Perspect. Biol. 2, a003889 (2010).
Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).
Fortin, J. P. & Hansen, K. D. Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. Genome Biol. 16, 1–23 (2015).
Falk, M. et al. Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature 570, 395–399 (2019).
S, S. & P, F. Long-range enhancer-promoter contacts in gene expression control. Nat. Rev. Genet. 20, 437–455 (2019).
Aljahani, A. et al. Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nat. Commun. 13, 2139 (2022).
Lakadamyali, M. & Cosma, M. P. Visualizing the genome in high resolution challenges our textbook understanding. Nat. Methods 17, 371–379 (2020).
Beagrie, R. A. Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543, 519–524 (2017).
Davies, J. O. J., Oudelaar, A. M., Higgs, D. R. & Hughes, J. R. How best to identify chromosomal interactions: a comparison of approaches. Nat. Methods 14, 125–134 (2017).
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306–1311 (2002).
Cairns, J. et al. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol. 17, 127 (2016).
Cullen, K. E., Kladde, M. P. & Seyfred, M. A. Interaction between transcription regulatory regions of prolactin chromatin. Science 261, 203–206 (1993).
Hagege, H. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat. Protoc. 2, 1722–1733 (2007).
Marbouty, M. et al. Condensin- and replication-mediated bacterial chromosome folding and origin condensation revealed by Hi-C and super-resolution imaging. Mol. Cell 59, 588–602 (2015).
Sexton, T. et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458–472 (2012).
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
Ma, W. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat. Methods 12, 71–78 (2014).
Ramani, V. et al. Mapping 3D genome architecture through in situ DNase Hi-C. Nat. Protoc. 11, 2104–2121 (2016).
Hsieh, T. H. S. Mapping nucleosome resolution chromosome folding in yeast by Micro-C. Cell 162, 108–119 (2015).
Hughes, J. R. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat. Genet. 46, 205–212 (2014).
Zhao, Z. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38, 1341–1347 (2006).
Davies, J. O. J. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat. Methods 13, 74–80 (2016).
Downes, D. J. High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nat. Commun. 12, 531 (2021).
Downes, D. J. et al. Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nat. Protoc. 17, 445–475 (2022).
Akgol Oksuz, B. et al. Systematic evaluation of chromosome conformation capture assays. Nat. Methods 18, 1046–1055 (2021).
Mieczkowski, J. et al. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat. Commun. 7, 11485 (2016).
Krietenstein, N. et al. Ultrastructural details of mammalian chromosome architecture. Mol. Cell 78, 554–565.e7 (2020).
Galas, D. J. & Schmitz, A. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157 (1978).
Aljahani, A. et al. Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nat. Commun. 13, 2139 (2022).
Xie, T. et al. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res. 13, 2621 (2003).
Nasser, J. et al. Genome-wide enhancer maps link risk variants to disease genes. Nature 593, 238–243 (2021).
King, A. J. et al. Reactivation of a developmentally silenced embryonic globin gene. Nat. Commun. 12, 4439 (2021).
The Severe Covid-19 GWAS Group. Genomewide Association Study of Severe Covid-19 with Respiratory Failure. N. Engl. J. Med. 383, 1522–1534 (2020).
Downes, D. J. et al. Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. Nat. Genet. 53, 1606–1615 (2021).
Schmitt, A. D. et al. A compendium of chromatin contact maps reveals spatially active regions in the human genome. Cell Rep. 17, 2042–2059 (2016).
Giorgetti, L. et al. Structural organization of the inactive X chromosome in the mouse. Nature 535, 575–579 (2016).
van Bemmel, J. G. et al. The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist. Nat. Genet. 51, 1024–1034 (2019).
Monahan, K., Horta, A. & Lomvardas, S. Lhx2/Ldb1-mediated trans interactions regulate olfactory receptor choice. Nature 565, 448 (2019).
Rao, S. S. P. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).
Li, G. Chromatin interaction analysis with paired-end tag (ChIA-PET) sequencing technology and application. BMC Genomics 15, S11 (2014).
Fang, R. et al. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 26, 1345–1348 (2016).
Mumbach, M. R. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat. Methods 13, 919–922 (2016).
Schwartzman, O. UMI-4C for quantitative and targeted chromosomal contact profiling. Nat. Methods 13, 685–691 (2016).
Andrey, G. et al. A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science 340, 1234167 (2013).
Smemo, S. et al. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature 507, 371 (2014).
Ghavi-Helm, Y. et al. Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512, 96–100 (2014).
Oudelaar, A. M. et al. Dynamics of the 4D genome during in vivo lineage specification and differentiation. Nat. Commun. 11, 2722 (2020).
Mifsud, B. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet. 47, 598–606 (2015).
Oudelaar, A. M., Downes, D., Davies, J. & Hughes, J. Low-input capture-C: a chromosome conformation capture assay to analyze chromatin architecture in small numbers of cells. Bio. Protoc. 7, e2645 (2017).
Beagrie, R. A. et al. Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C. Preprint at bioRxiv https://doi.org/10.1101/2020.07.31.230284 (2020).
Winick-Ng, W. et al. Cell-type specialization is encoded by specific chromatin topologies. Nature 599, 684–691 (2021).
Quinodoz, S. A. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell 174, 744–757.e24 (2018).
Takei, Y. et al. Integrated spatial genomics reveals global architecture of single nuclei. Nature 590, 344–350 (2021).
Tan, L., Xing, D., Chang, C. H., Li, H. & Xie, X. S. Three-dimensional genome structures of single diploid human cells. Science 361, 924–928 (2018).
Owens, D. D. G. et al. Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development. Nat. Commun. 13, 773 (2022).
Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999–1003 (2012).
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome https://doi.org/10.1186/s13059-015-0831-x (2015).
Buckle, A., Gilbert, N., Marenduzzo, D. & Brackley, C. A. capC-MAP: software for analysis of Capture-C data. Bioinformatics https://doi.org/10.1093/bioinformatics/btz480 (2019).
Thongjuea, S., Stadhouders, R., Grosveld, F. G., Soler, E. & Lenhard, B. R3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res. 41, e132 (2013).
Smith, A. & Rue-Albrecht, K. sims-lab/CapCruncher. Zenodo https://doi.org/10.5281/zenodo.5113088 (2021).
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 1006–1019 (2018).
Hentges, L. D., Sergeant, M. J., Downes, D. J., Hughes, J. R. & Taylor, S. LanceOtron: a deep learning peak caller for genome sequencing experiments. Bioinformatics 38, 4255–4263 (2022).
Oudelaar, A. M. et al. Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nat. Genet. 50, 1744–1751 (2018).
Schoenfelder, S. et al. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res. 25, 582–597 (2015).
Cheng, L. et al. Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression. Nat. Genet. 53, 869–880 (2021).

Determining chromatin architecture with Micro Capture-C

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