Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Export

@article{citeulike:5913660, abstract = {We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.}, author = {Lieberman-Aiden, Erez and van Berkum, Nynke L. and Williams, Louise and Imakaev, Maxim and Ragoczy, Tobias and Telling, Agnes and Amit, Ido and Lajoie, Bryan R. and Sabo, Peter J. and Dorschner, Michael O. and Sandstrom, Richard and Bernstein, Bradley and Bender, M. A. and Groudine, Mark and Gnirke, Andreas and Stamatoyannopoulos, John and Mirny, Leonid A. and Lander, Eric S. and Dekker, Job}, citeulike-article-id = {5913660}, citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1181369}, citeulike-linkout-1 = {http://www.sciencemag.org/content/326/5950/289.abstract}, citeulike-linkout-2 = {http://www.sciencemag.org/content/326/5950/289.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19815776}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19815776}, comment = {FRACTAL GLOBULE! DNA is self-organising, globules form and become beads on a string, then these globules condense and then again to make globules of globules of globules etc. Yet DNA can still be unpacked, used and re-packed. Does this mean that the least used DNA is packed first, most deeply? Where would ubiquitiously expressed genes reside, at what level of globule packing? or would they be in inter-globule space? }, day = {9}, doi = {10.1126/science.1181369}, issn = {1095-9203}, journal = {Science (New York, N.Y.)}, keywords = {genome\_architecture, nuclear\_architecture, transcription\_factory}, month = {October}, number = {5950}, pages = {289--293}, posted-at = {2009-10-15 14:10:09}, priority = {0}, title = {Comprehensive mapping of long-range interactions reveals folding principles of the human genome.}, url = {http://dx.doi.org/10.1126/science.1181369}, volume = {326}, year = {2009} }

TY - JOUR ID - citeulike:5913660 L3 - citeulike-article-id:5913660 N2 - We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes. IS - 5950 JF - Science (New York, N.Y.) SN - 1095-9203 EP - 293 TI - Comprehensive mapping of long-range interactions reveals folding principles of the human genome. VL - 326 SP - 289 KW - genome_architecture KW - nuclear_architecture KW - transcription_factory N1 - FRACTAL GLOBULE! DNA is self-organising, globules form and become beads on a string, then these globules condense and then again to make globules of globules of globules etc. Yet DNA can still be unpacked, used and re-packed. Does this mean that the least used DNA is packed first, most deeply? Where would ubiquitiously expressed genes reside, at what level of globule packing? or would they be in inter-globule space? AU - Lieberman-Aiden, Erez AU - van Berkum, Nynke AU - Williams, Louise AU - Imakaev, Maxim AU - Ragoczy, Tobias AU - Telling, Agnes AU - Amit, Ido AU - Lajoie, Bryan AU - Sabo, Peter AU - Dorschner, Michael AU - Sandstrom, Richard AU - Bernstein, Bradley AU - Bender, MA AU - Groudine, Mark AU - Gnirke, Andreas AU - Stamatoyannopoulos, John AU - Mirny, Leonid AU - Lander, Eric AU - Dekker, Job PY - 2009/10/09/ UR - http://dx.doi.org/10.1126/science.1181369 ER -