Abstract
In this chapter, we introduce a generic and efficient method to identify multiscale topological domains (MSTD), including cis- and trans-interacting regions, from a variety of 3D genomic datasets. We first applied MSTD to detect promoter-anchored interaction domains (PADs) from promoter capture Hi-C datasets across 17 primary blood cell types. The boundaries of PADs are significantly enriched with one or the combination of multiple epigenetic factors. Moreover, PADs between functionally similar cell types are significantly conserved in terms of domain regions and expression states. Cell type-specific PADs involve in distinct cell type-specific activities and regulatory events by dynamic interactions within them. We also employed MSTD to define multiscale domains from typical symmetric Hi-C datasets and illustrated its distinct superiority to the state-of-the-art methods in terms of accuracy, flexibility and efficiency.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bickmore WA, van Steensel B (2013) Genome architecture: domain organization of interphase chromosomes. Cell 152(6):1270–1284
Sexton T, Cavalli G (2015) The role of chromosome domains in shaping the functional genome. Cell 160(6):1049–1059
Pombo A, Dillon N (2015) Three-dimensional genome architecture: players and mechanisms. Nat Rev Mol Cell Biol 16(4):245–257
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7):1665–1680
Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS (2010) Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 42(1):53–61
Bantignies F, Roure V, Comet I, Leblanc B, Schuettengruber B, Bonnet J, Tixier V, Mas A, Cavalli G (2011) Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144(2):214–226
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376–380
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485(7398):381–385
Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong C-T, Hookway TA, Guo C, Sun Y (2013) Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153(6):1281–1295
Dali R, Blanchette M (2017) A critical assessment of topologically associating domain prediction tools. Nucleic Acids Res 45(6):2994–3005
Norton HK, Emerson DJ, Huang H, Kim J, Titus KR, Gu S, Bassett DS, Phillips-Cremins JE (2018) Detecting hierarchical genome folding with network modularity. Nat Methods 15(2):119
Malik L, Patro R (2018) Rich chromatin structure prediction from Hi-C data. IEEE/ACM Trans Comput Biol Bioinform 16(5):1448–1458
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289–293. https://doi.org/10.1126/science.1181369
Filippova D, Patro R, Duggal G, Kingsford C (2014) Identification of alternative topological domains in chromatin. Algorithm Mol Biol 9(1):14
Weinreb C, Raphael BJ (2016) Identification of hierarchical chromatin domains. Bioinformatics 32(11):1601–1609
Zhan Y, Mariani L, Barozzi I, Schulz EG, Bluthgen N, Stadler M, Tiana G, Giorgetti L (2017) Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes. Genome Res 27(3):479–490
Fraser J, Rousseau M, Shenker S, Ferraiuolo MA, Hayashizaki Y, Blanchette M, Dostie J (2009) Chromatin conformation signatures of cellular differentiation. Genome Biol 10(4):R37
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ (2016) Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell 167(5):1369–1384. e1319
Zhang Y, Wong C-H, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E (2013) Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations. Nature 504(7479):306
Eisenberg E, Levanon EY (2013) Human housekeeping genes, revisited. Trends Genet 29(10):569–574
Fraser J, Ferrai C, Chiariello AM, Schueler M, Rito T, Laudanno G, Barbieri M, Moore BL, Kraemer DC, Aitken S (2015) Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Mol Syst Biol 11(12):852
Yaffe E, Tanay A (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43(11):1059
Rodriguez A, Laio A (2014) Clustering by fast search and find of density peaks. Science 344(6191):1492–1496
Sutherland H, Bickmore WA (2009) Transcription factories: gene expression in unions? Nat Rev Genet 10(7):457
Consortium GO (2015) Gene ontology consortium: going forward. Nucleic Acids Res 43(D1):D1049–D1056
Polager S, Ginsberg D (2009) p53 and E2f: partners in life and death. Nat Rev Cancer 9(10):738–748
Acknowledgments
Yusen Ye would like to thank the support of the Academy of Mathematics and Systems Science at CAS during his visit there. This work has been supported by the National Natural Science Foundation of China [No. 61873198, 61532014, 61432010, 61672407 to LG; 11661141019, 61621003, the Key Research Program of the Chinese Academy of Sciences [No. KFZD-SW-219], National Key Research and Development Program of China (2017YFC0908405) and CAS Frontier Science Research Key Project for Top Young Scientist [No. QYZDB-SSW-SYS008].
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Ye, Y., Gao, L., Zhang, S. (2020). MSTD for Detecting Topological Domains from 3D Genomic Maps. In: Kidder, B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, vol 2117. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0301-7_4
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0301-7_4
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0300-0
Online ISBN: 978-1-0716-0301-7
eBook Packages: Springer Protocols