Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays

Abstract

During mitosis, chromosomes fold into compacted rod shaped structures. We combined imaging and Hi-C of synchronous DT40 cell cultures with polymer simulations to determine how interphase chromosomes are converted into compressed arrays of loops characteristic of mitotic chromosomes. We found that the interphase organization is disassembled within minutes of prophase entry and by late prophase chromosomes are already folded as arrays of consecutive loops. During prometaphase, this array reorganizes to form a helical arrangement of nested loops. Polymer simulations reveal that Hi-C data are inconsistent with solenoidal coiling of the entire chromatid, but instead suggest a centrally located helically twisted axis from which consecutive loops emanate as in a spiral staircase. Chromosomes subsequently shorten through progressive helical winding, with the numbers of loops per turn increasing so that the size of a helical turn grows from around 3 Mb (~40 loops) to ~12 Mb (~150 loops) in fully condensed metaphase chromosomes. Condensin is essential to disassemble the interphase chromatin conformation. Analysis of mutants revealed differing roles for condensin I and II during these processes. Either condensin can mediate formation of loop arrays. However, condensin II was required for helical winding during prometaphase, whereas condensin I modulated the size and arrangement of loops inside the helical turns. These observations identify a mitotic chromosome morphogenesis pathway in which folding of linear loop arrays produces long thin chromosomes during prophase that then shorten by progressive growth of loops and helical winding during prometaphase. One Sentence Summary:Mitotic chromosome morphogenesis occurs through condensin-mediated disassembly of the interphase conformation and formation of extended prophase loop arrays that then shorten by loop growth and condensin-dependent helical winding.

Condensin’s ATPase Machinery Drives and Dampens Mitotic Chromosome Condensation

“…A recent preprint suggests that condensin II plays a role in the formation of a helical turn within the axis of mitotic chromosomes, and that megabase-scale contacts reflect interactions between loops that are stacked in a helical fashion around this axis (Gibcus et al, 2017). Our data would be in line with this hypothesis.…”

“…6 Strikingly, neither ∆CAP-H2 cells, nor ∆CAP-H2 cells with the AS2 LV mutation yielded a band with contacts over ~5Mb distance. Such a condensin II dependent role in the formation of longer-range contacts is in correspondence with a recent preprint using mitotic chicken cells (Gibcus et al, 2017). How then can the AS2 LV mutant yield hyper-condensed chromosomes both in wild type and in ∆CAP-H2 cells, if their interaction maps look so different?…”

HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps

“…Despite the large amounts of generated Hi-C data, major challenges remain in (i) identifying known features unambiguously [14]; (ii) discovering new features; (iii) establishing relationships between Hi-C features and known (epi)genetic profiles; (iv) establishing the effects of various genetic, biochemical and physical perturbations on chromatin organization, assessing meaningful differences between cell types [15], and changes across the cell cycle and along differentiation pathways [16]. These challenges necessitate the development of methods to visually explore, compare and share not only the raw data, but also related datasets and derived analysis results.…”

Hot debate in hot springs: Report on the second international meeting on SMC proteins

“…He then moved on to talk about a panel of recent technical advances made in his laboratory (Ohta et al., ; Samejima et al., ). One of the most impressive examples was an application of Hi‐C techniques to chicken DT40 cells whose mitotic entry was perfectly synchronized using the trick of a nucleotide analogue‐sensitive allele of the master mitotic kinase CDK1 (Gibcus et al., ). Emerging data suggested the existence of a helical core at the central part of mitotic chromosomes, which might be consistent with some of the previous cytological data reported from his own and other laboratories.…”