DamC reveals principles of chromatin folding in vivo without crosslinking and ligation
Open accessAbstract
Current understanding of chromosome folding is largely reliant on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after chromatin crosslinking. To measure chromosome structure in vivo, quantitatively and without crosslinking and ligation, we implemented a modified version of DNA adenine methyltransferase identification (DamID) named DamC, which combines DNA methylation-based detection of chromosomal interactions with next-generation sequencing and biophysical modeling of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of topologically associating domains (TADs), CTCF loops and confirms 3C-based measurements of the scaling of contact probabilities. Combining DamC with transposon-mediated genomic engineering shows that new loops can be formed between ectopic and endogenous CTCF sites, which redistributes physical interactions within TADs. DamC provides the first crosslinking- and ligation-free demonstration of the existence of key structural features of chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.
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The observed contact probability trend is consistent with previous estimations and is representative of the contact probabilities experienced by promoters in mES cells.
“This is consistent with previous estimations33 confirmed using cross-linking and ligation-free methods34 and is representative of the contact probabilities experienced by promoters in mES cells (Extended Data Fig. 2b, c).”
From Nonlinear control of transcription through enhancer–promoter interactions (2022) · cites this paper as [34]
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Cites
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895 · see citing works
Self-citationHiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Servant, N., Varoquaux, N., Lajoie, B. R., Viara, E., Chen, C.-J., Vert, J.-P., Heard, E., Dekker, J., & Barillot, E. (2015) · Genome Biology · doi:10.1186/s13059-015-0831-x · Cited by 2,565 · see citing works
Formation of chromosomal domains by loop extrusion
Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003 · see citing works
Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730 · see citing works
Nora, E. P., Goloborodko, A., Valton, A.-L., Gibcus, J. H., Uebersohn, A., Abdennur, N., Dekker, J., Mirny, L. A., & Bruneau, B. G. (2017) · Cell · doi:10.1016/j.cell.2017.05.004 · Cited by 1,709 · see citing works
The long-range interaction landscape of gene promoters
Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Imakaev, M., Fudenberg, G., McCord, R. P., Naumova, N., Goloborodko, A., Lajoie, B. R., Dekker, J., & Mirny, L. A. (2012) · Nature Methods · doi:10.1038/nmeth.2148 · Cited by 1,423 · see citing works
Multiscale 3D Genome Rewiring during Mouse Neural Development
Bonev, B., Mendelson Cohen, N., Szabo, Q., Fritsch, L., Papadopoulos, G. L., Lubling, Y., Xu, X., Lv, X., Hugnot, J.-P., Tanay, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.043 · Cited by 1,338 · see citing works
Gu, H., Zou, Y.-R., & Rajewsky, K. (1993) · Cell · doi:10.1016/0092-8674(93)90644-6 · Cited by 989 · see citing works
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function
Guo, Y., Xu, Q., Canzio, D., Shou, J., Li, J., Gorkin, D. U., Jung, I., Wu, H., Zhai, Y., Tang, Y., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.038 · Cited by 958 · see citing works
Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
Quinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M. M., Shishkin, A. A., Bhat, P., Takei, Y., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.024 · Cited by 892 · see citing works
Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C
Hsieh, T.-H. S., Weiner, A., Lajoie, B., Dekker, J., Friedman, N., & Rando, O. J. (2015) · Cell · doi:10.1016/j.cell.2015.05.048 · Cited by 788 · see citing works
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
Zuin, J., Dixon, J. R., van der Reijden, M. I. J. A., Ye, Z., Kolovos, P., Brouwer, R. W. W., van de Corput, M. P. C., van de Werken, H. J. G., Knoch, T. A., van IJcken, W. F. J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317788111 · Cited by 779 · see citing works
A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards
Wiśniewski, J. R., Hein, M. Y., Cox, J., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.037309 · Cited by 690 · see citing works
CTCF Binding Polarity Determines Chromatin Looping
de Wit, E., Vos, E. S. M., Holwerda, S. J. B., Valdes-Quezada, C., Verstegen, M. J. A. M., Teunissen, H., Splinter, E., Wijchers, P. J., Krijger, P. H. L., & de Laat, W. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.09.023 · Cited by 641 · see citing works
Self-citationThe Energetics and Physiological Impact of Cohesin Extrusion
Vian, L., Pękowska, A., Rao, S. S. P., Kieffer-Kwon, K.-R., Jung, S., Baranello, L., Huang, S.-C., El Khattabi, L., Dose, M., Pruett, N., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.072 · Cited by 581 · see citing works
Self-organization of domain structures by DNA-loop-extruding enzymes
Alipour, E., & Marko, J. F. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks925 · Cited by 540 · see citing works
Giorgetti, L., Galupa, R., Nora, E. P., Piolot, T., Lam, F., Dekker, J., Tiana, G., & Heard, E. (2014) · Cell · doi:10.1016/j.cell.2014.03.025 · Cited by 460 · see citing works
CTCF-dependent enhancer-blocking by alternative chromatin loop formation
Hou, C., Zhao, H., Tanimoto, K., & Dean, A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808506106 · Cited by 205 · see citing works
Flagged first, then by citations
Research works printed but not linked: 53
- [1]Denker A de Laat W The second decade of 3C technologies: detailed insights into nuclear organization Genes Dev 2016 30 1357 1382 27340173 PMC4926860
- [2]Lieberman-Aiden E Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome Science 2009 326 289 293 19815776 PMC2858594
- [3]Rao SSP A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping Cell 2014 159 1665 1680 25497547 PMC5635824
- [4]Norton HK Detecting hierarchical genome folding with network modularity Nat Methods 2018 15 119 122 29334377 PMC6029251
- [5]Fraser J Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation Mol Syst Biol 2015 11 852 852 26700852 PMC4704492
- [7]Dixon JR Topological domains in mammalian genomes identified by analysis of chromatin interactions Nature 2012 485 376 380 22495300 PMC3356448
- [8]Sexton T Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome Cell 2012 148 458 472 22265598
- [9]Zhan Y 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 2017 27 479 490 28057745 PMC5340975
- [16]Gavrilov A Razin SV Cavalli G In vivo formaldehyde cross-linking: it is time for black box analysis Brief Funct Genomics 2015 14 163 165 25241225 PMC6090872
- [17]Gavrilov AA Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub Nucleic Acids Res 2013 41 3563 3575 23396278 PMC3616722
- [18]Williamson I Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization Genes Dev 2014 28 2778 2791 25512564 PMC4265680
- [19]Belmont AS Large-scale chromatin organization: the good, the surprising, and the still perplexing Curr Opin Cell Biol 2014 26 69 78 24529248 PMC3927141
- [20]Fudenberg G Mirny LA Higher-order chromatin structure: bridging physics and biology Curr Opin Genet Dev 2012 22 115 124 22360992 PMC3697851
- [21]Tiana G Giorgetti L Integrating experiment, theory and simulation to determine the structure and dynamics of mammalian chromosomes Curr Opin Struct Biol 2018 49 11 17 29128709
- [23]Nichols MH Corces VG A CTCF Code for 3D Genome Architecture Cell 2015 162 703 705 26276625 PMC4745123
- [24]Wang S Spatial organization of chromatin domains and compartments in single chromosomes Science 2016 353 598 602 27445307 PMC4991974
- [25]Beagrie RA Complex multi-enhancer contacts captured by genome architecture mapping Nature 2017 543 519 524 28273065 PMC5366070
- [26]Brant L Exploiting native forces to capture chromosome conformation in mammalian cell nuclei Mol Syst Biol 2016 12 891 27940490 PMC5199122
- [28]Lebrun E Fourel G Defossez P-A Gilson E A Methyltransferase Targeting Assay Reveals Silencer-Telomere Interactions in Budding Yeast Mol Cell Biol 2003 23 1498 1508 12588971 PMC151690
- [29]Cléard F Moshkin Y Karch F Maeda RK Probing long-distance regulatory interactions in the Drosophila melanogaster bithorax complex using Dam identification Nat Genet 2006 38 931 935 16823379
- [30]van Steensel B Henikoff S Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase Nat Biotechnol 2000 18 424 428 10748524
- [31]Dekker J Rippe K Dekker M Kleckner N Capturing Chromosome Conformation Science 2002 295 1306 1311 11847345
- [32]van de Werken HJG Robust 4C-seq data analysis to screen for regulatory DNA interactions Nat Methods 2012 9 969 972 22961246
- [33]Masui O Live-Cell Chromosome Dynamics and Outcome of X Chromosome Pairing Events during ES Cell Differentiation Cell 2011 145 447 458 21529716 PMC3756906
- [34]Peric-Hupkes D Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation Mol Cell 2010 38 603 613 20513434 PMC5975946
- [35]Kind J Single-Cell Dynamics of Genome-Nuclear Lamina Interactions Cell 2013 153 178 192 23523135
- [36]Cadiñanos J Bradley A Generation of an inducible and optimized piggyBac transposon system† Nucleic Acids Res 2007 35 e87 17576687 PMC1919496
- [37]Kamionka A Bogdanska-Urbaniak J Scholz O Hillen W Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor Nucleic Acids Res 2004 32 842 847 14764926 PMC373327
- [40]Rawat P Jalan M Sadhu A Kanaujia A Srivastava M Chromatin Domain Organization of the TCRb Locus and Its Perturbation by Ectopic CTCF Binding Mol Cell Biol 2017 37 e00557 16 28137913 PMC5394274
- [41]Geeven G Teunissen H de Laat W de Wit E peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data Nucleic Acids Res 10.1093/nar/gky443 PMC6125690 29800273 · DOI
- [44]Scolari VF Mercy G Koszul R Lesne A Mozziconacci J Kinetic Signature of Cooperativity in the Irreversible Collapse of a Polymer Phys Rev Lett 2018 121 057801 30118310
- [46]Dekker J Mirny L The 3D Genome as Moderator of Chromosomal Communication Cell 2016 164 1110 1121 26967279 PMC4788811
- [47]Erickson HP Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy Biol Proced Online 2009 11 32 19495910 PMC3055910
- [48]Brackley CA Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models Genome Biol 2016 17 59 27036497 PMC4815170
- [49]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 98 PMC3782096 22198700
- [50]Rosa A Everaers R Structure and Dynamics of Interphase Chromosomes PLOS Comput Biol 2008 4 e1000153 18725929 PMC2515109
- [51]La Fortezza M DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis Epigenetics Chromatin 2018 11 27 29871666 PMC5987561
- [52]Tosti L Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo Genome Res 2018 10.1101/gr.227124.117 PMC5880248 29572359 · DOI
- [53]Tiana G Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains Biophys J 2016 110 1234 1245 27028634 PMC4816701
- [54]Gu B Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements Science 2018 359 1050 1055 29371426 PMC6590518
- [55]Germier T Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement Biophys J 2017 113 1383 1394 28978433 PMC5627313
- [57]Ernst J Kellis M ChromHMM: automating chromatin-state discovery and characterization Nat Methods 2012 9 215 216 22373907 PMC3577932
- [58]Urlinger S Exploring the sequence space for tetracycline-dependent transcriptional activators: Novel mutations yield expanded range and sensitivity Proc Natl Acad Sci 2000 97 7963 7968 10859354 PMC16653
- [59]Vogel MJ Peric-Hupkes D van Steensel B Detection of in vivo protein-DNA interactions using DamID in mammalian cells Nat Protoc 2007 2 1467 1478 17545983
- [61]Sanulli S Jarid2 Methylation via the PRC2 Complex Regulates H3K27me3 Deposition during Cell Differentiation Mol Cell 2015 57 769 783 25620564 PMC4352895
- [62]Wang Y Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells PROTEOMICS 2011 11 2019 2026 21500348 PMC3120047
- [63]Cox J Mann M MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Nat Biotechnol 2008 26 1367 1372 19029910
- [64]Cox J Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ Mol Cell Proteomics 2014 13 2513 2526 24942700 PMC4159666
- [65]Tyanova S The Perseus computational platform for comprehensive analysis of (prote)omics data Nat Methods 2016 13 731 740 27348712
- [66]MacLean B Skyline: an open source document editor for creating and analyzing targeted proteomics experiments Bioinformatics 2010 26 966 968 20147306 PMC2844992
- [67]Splinter E de Wit E van de Werken HJG Klous P de Laat W Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation Methods 2012 58 221 230 22609568
- [68]Gaidatzis D Lerch A Hahne F Stadler MB QuasR: quantification and annotation of short reads in R Bioinformatics 2015 31 1130 1132 25417205 PMC4382904
- [72]Perez-Riverol Y The PRIDE database and related tools and resources in 2019: improving support for quantification data Nucleic Acids Res 2019 47 D1 D442 D450 30395289 PMC6323896
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Nonlinear control of transcription through enhancer–promoter interactions
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Nonlinear control of transcription through enhancer-promoter interactions
Zuin, J., Roth, G., Zhan, Y., Cramard, J., Redolfi, J., Piskadlo, E., Mach, P., Kryzhanovska, M., Tihanyi, G., Kohler, H., et al. (2021) · doi:10.1101/2021.04.22.440891 · Cited by 67 · see citing works
Self-citation
- Authors
- Redolfi, J., Zhan, Y., Valdes-Quezada, C., Kryzhanovska, M., Guerreiro, I., Iesmantavicius, V., Pollex, T., Grand, R. S., Mulugeta, E., Kind, J., Tiana, G., Smallwood, S. A., de Laat, W., & Giorgetti, L.
- Affiliations
- University of Basel (CH)
- Friedrich Miescher Institute (CH)
- Royal Netherlands Academy of Arts and Sciences (NL)
- European Molecular Biology Laboratory (DE)
- Erasmus MC (NL)
- University of Milan (IT)
- Corresponding author
- Giorgetti, Luca
- ORCID
- Venue
- Nature Structural & Molecular Biology
- Published
- 2019-05-27
- Volume
- 26
- Issue
- 6
- Pages
- 471-480
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC6561777
- OpenAlex
- W2947133061
- Cited by
- 86
- References
- 19
- Citations by year
- 2026: 4 · 2025: 6 · 2024: 7 · 2023: 7 · 2022: 14 · 2021: 24 · 2020: 15 · 2019: 9
- FWCI
- 5.13
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- KNAW research portal (Royal Academy of Art and Sciences (KNAW)) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- DamID, chromatin folding, chromosome conformation, topologically associating domains, DNA methylation, contact probability, mouse embryonic stem cells, loop formation, chromatin structure
- MeSH terms
- Mouse Embryonic Stem Cells, CCCTC-Binding Factor, Animals, Bacterial Proteins, Cell Line, Chromatin, Chromosomes, Nucleic Acid Conformation, Recombinant Fusion Proteins, Site-Specific DNA-Methyltransferase (Adenine-Specific), DNA Methylation, Mice
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