E-MTAB-1948 - 5C and Hi-C chromosome conformation capture study on metaphase chromosomes from human HeLa, HFF1 and K562 cell lines across the cell cycle

Released on 5 November 2013, last updated on 19 March 2015
Homo sapiens
Samples (23)
Protocols (7)
Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved. We applied chromosome conformation capture methods, 5C and Hi-C, across the cell cycle and revealed two alternative three-dimensional folding states of the human genome. We show that the highly compartmentalized and cell-type-specific organization described previously for non-synchronous cells is restricted to interphase. In metaphase, we identify a homogenous folding state, which is locus-independent, common to all chromosomes, and consistent among cell types, suggesting a general principle of metaphase chromosome organization. Using polymer simulations, we find that metaphase Hi-C data is inconsistent with classic hierarchical models, and is instead best described by a linearly-organized longitudinally compressed array of consecutive chromatin loops.
Experiment types
other, cell type comparison
Metaphase Chromosome Organization. Natalia Naumova, Maxim Imakaev, Geoffrey Fudenberg, Ye Zhan, Bryan R. Lajoie, Leonid A. Mirny, Job Dekker.
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-MTAB-1948.idf.txt
Sample and data relationshipE-MTAB-1948.sdrf.txt
Processed data (12)Click to browse processed data