Here, we shall post materials related to scientific talks and discussions.

Comments and references for Noam Kaplan's talk ("Encoding and decoding 3D genome organization"):

  • One interesting result that I did not have time to show (but appears in the slides I have uploaded) is how, during cell cycle when chromosomes condense, all interaction patterns disappear and re-emerge later when chromosomes are decondensed. Given that some of these patterns (genomic compartments, TADs and point interactions) are associated with biological function, this brings up the interesting open question of how these structures are inherited so they can be re-established in the daughter cells. For more details see the paper by Naumova et al. (2013).
  • How structures are inherited relates to another interesting point that I did not have time to discuss. There seems to be an inverse relation between dynamics and cell-to-cell "reproducibility". In terms of dynamics, the largest structures (starting from chromosome territories) do not change much during the lifetime of the cell, while the smallest structures (such as point interactions) are quite fast. In terms of cell-to-cell reproducibility, chromosome territories are the least reproducible (in the sense that different cells in the population will have very relative organizations layouts of chromosome territories), while the faster smaller structures are much more consistent between cells. This has been called "reproducibility" because it relates to how accurately structure is be reproduced after cell division. For more details see the review by Gibcus et al. (2013).

Some relevant references:
  • Original 3C paper: Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002). Capturing chromosome conformation. Science (New York, N.Y.), 295(5558), 1306–11. http://doi.org/10.1126/science.1067799
  • Original Hi-C paper (also relevant for chromosomes territories, genomic compartments and fractal globule): Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., … Dekker, J. (2009). Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science, 326(5950), 289–293. http://doi.org/10.1126/science.1181369
  • Single-cell Hi-C: Nagano, T., Lubling, Y., Stevens, T. J., Schoenfelder, S., Yaffe, E., Dean, W., … Fraser, P. (2013). Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature, 502(7469), 59–64. http://doi.org/10.1038/nature12593
  • First genome-wide measurement of TAD structures (“topologically associating domains”): Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., … Ren, B. (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485(7398), 376–380. http://doi.org/10.1038/nature11082
  • High resolution Hi-C (where point interactions are observed): Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., … Aiden, E. L. (2014). A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159(7), 1665–80. http://doi.org/10.1016/j.cell.2014.11.021
  • Cell cycle Hi-C (genomic structures disappear when chromosomes are condensed): Naumova, N., Imakaev, M., Fudenberg, G., Zhan, Y., Lajoie, B. R., Mirny, L. A., & Dekker, J. (2013). Organization of the Mitotic Chromosome. Science (New York, N.Y.), 342, 948–53. http://doi.org/10.1126/science.1236083


  • Solving problems in 1D genome assembly by using Hi-C data: Kaplan, N., & Dekker, J. (2013). High-throughput genome scaffolding from in vivo DNA interaction frequency. Nature Biotechnology, 31, 1143–1147. http://doi.org/10.1038/nbt.2768
  • Effect of DNA sequence on genomic nucleosome organization: Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A. J., Tillo, D., Field, Y., … Segal, E. (2009). The DNA-encoded nucleosome organization of a eukaryotic genome. Nature, 458(7236), 362–6. http://doi.org/10.1038/nature07667


References for Alexander Grosberg's talk ("Nuclear Chromodynamics"):


Review article, 2014:


Jonathan D. Halverson, Jan Smrek, Kurt Kremer, and Alexander Y. Grosberg "From a melt of rings to chromosome territories: the role of topological constraints in genome folding," Reports on Progress in Physics, v. 77, 022601, 2014.

Active hydrodynamics of chromatin:


Robijn Bruinsma, Alexander Y. Grosberg, Yitzhak Rabin, and Alexandra Zidovska "Chromatin Hydrodynamics," Biophysical Journal, v. 106, n. 9, p. 1871-1881, 2014.

Rings in terms of annealed trees:


Alexander Y. Grosberg "Annealed lattice animal model and Flory theory for the melt of non-concatenated rings: Towards the physics of crumpling" Soft Matter, v. 10, n. 4, p. 560-565, 2014.

Jan Smrek, and Alexander Y. Grosberg "Understanding the dynamics of rings in the melt in terms of the annealed tree model," Journal of Physics: Condensed Matter, v. 27, n. 6, 064117, 2015.

See also paper by M.Rubinstein et al., which is to appear in Macromolecules soon as well as


S. Obukhov, A. Johner, J. Baschnagel, H. Meyer, and
J. P. Wittmer, Europhys. Lett. 105, 48005 (2014)



Original 3C paper:
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002). Capturing chromosome conformation. Science (New York, N.Y.), 295(5558), 1306–11.
http://doi.org/10.1126/science.1067799
Original Hi-C paper (also relevant for chromosomes territories, genomic compartments and fractal globule):
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., … Dekker, J. (2009). Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science, 326(5950), 289–293.
http://doi.org/10.1126/science.1181369
Single-cell Hi-C:
Nagano, T., Lubling, Y., Stevens, T. J., Schoenfelder, S., Yaffe, E., Dean, W., … Fraser, P. (2013). Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature, 502(7469), 59–64.
http://doi.org/10.1038/nature12593
First genome-wide measurement of TAD structures (“topologically associating domains”):
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., … Ren, B. (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485(7398), 376–380.
http://doi.org/10.1038/nature11082
High resolution Hi-C (where point interactions are observed):
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., … Aiden, E. L. (2014). A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159(7), 1665–80.
http://doi.org/10.1016/j.cell.2014.11.021
Cell cycle Hi-C (genomic structures disappear when chromosomes are condensed):
Naumova, N., Imakaev, M., Fudenberg, G., Zhan, Y., Lajoie, B. R., Mirny, L. A., & Dekker, J. (2013). Organization of the Mitotic Chromosome. Science (New York, N.Y.), 342, 948–53.
http://doi.org/10.1126/science.1236083
Biological review of Hi-C/genome structure:
Gibcus, J. H., & Dekker, J. (2013). The Hierarchy of the 3D Genome. Molecular Cell.
http://doi.org/10.1016/j.molcel.2013.02.011
Review on structural modeling of Hi-C:
Imakaev, M. V., Fudenberg, G., & Mirny, L. A. (2015). Modeling chromosomes: Beyond pretty pictures. FEBS Letters, 589(20), 3031–3036.
http://doi.org/10.1016/j.febslet.2015.09.004
Overview of Hi-C data processing and analysis (descriptive):
Lajoie, B. R., Dekker, J., & Kaplan, N. (2014). The Hitchhiker’s Guide to Hi-C Analysis: Practical guidelines. Methods, 72, 65–75
http://doi.org/10.1016/j.ymeth.2014.10.031
Solving problems in 1D genome assembly by using Hi-C data:
Kaplan, N., & Dekker, J. (2013). High-throughput genome scaffolding from in vivo DNA interaction frequency. Nature Biotechnology, 31, 1143–1147.
http://doi.org/10.1038/nbt.2768
Effect of DNA sequence on genomic nucleosome organization:
Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A. J., Tillo, D., Field, Y., … Segal, E. (2009). The DNA-encoded nucleosome organization of a eukaryotic genome. Nature, 458(7236), 362–6.
http://doi.org/10.1038/nature07667