ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

Ou, Horng D.; Phan, Sébastien; Deerinck, Thomas J.; Thor, Andrea; Ellisman, Mark H.; O’Shea, Clodagh C.

doi:10.1126/science.aag0025

Cited by 772 publications

(803 citation statements)

References 93 publications

Supporting

Mentioning

706

Contrasting

Unclassified

Order By: Relevance

“…This indicates that there are other mechanisms by which chromatin fibers become condensed during mitosis. Our simulations also show that to achieve agreement with Hi-C data, chromatin should also be condensed (computationally analogous to poor solvent conditions) forming densely packed chromatin loops within mitotic chromosomes analogous to the dense packing of chromatin observed in mitotic chromosomes by electron microscopy (46, 78, 79). The molecular basis for this condensation is not known but may involve mitosis-specific chromatin modifications (80, 81) or active motor proteins such as KIF4A (82, 83).…”

Section: Discussionsupporting

confidence: 64%

A pathway for mitotic chromosome formation

Gibcus

Samejima

Goloborodko

et al. 2018

Science

676

106

871

View full text Add to dashboard Cite

Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C of synchronous DT40 cell cultures with polymer simulations. We show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner and arrays of consecutive 60 kb loops are formed. During prometaphase ~80 kb inner loops are nested within ~400 kb outer loops. The loop array acquires a helical arrangement with consecutive loops emanating from a central spiral-staircase condensin scaffold. The size of helical turns progressively increases during prometaphase to ~12 Mb. Acute depletion of condensin I or II shows that nested loops form by differential action of the two condensins while condensin II is required for helical winding.

show abstract

Section: Discussionsupporting

confidence: 64%

A pathway for mitotic chromosome formation

Gibcus

Samejima

Goloborodko

et al. 2018

Science

676

106

871

View full text Add to dashboard Cite

show abstract

“…During the interphase of the cell cycle, when DNA is transcribed into RNA, chromatin exhibits a dynamic, three-dimensional organization (Cremer and Cremer, 2001;Pombo and Branco, 2007;Nagano et al, 2017;Nozaki et al, 2017). Although chromatin organization has often been described in terms of structures with discrete length scales, recent work has suggested that it is characterized by a continuum of packing densities (Ricci et al, 2015;Ou et al, 2017). This raises the question how such packing is achieved.…”

Section: Introductionmentioning

confidence: 96%

Transcription organizes euchromatin similar to an active microemulsion

Hilbert

Sato

Kimurâ

et al. 2017

Preprint

View full text Add to dashboard Cite

Graphical abstract HighlightsThe copyright holder for this preprint (which was . http://dx.doi.org/10.1101/234112 doi: bioRxiv preprint first posted online Dec. 15, 2017; Page 2 of 46 SummaryThe three-dimensional organization of the genome is essential for development and health. Although the organization of euchromatin (transcriptionally permissive chromatin) dynamically adjusts to changes in transcription, the underlying mechanisms remain elusive. Here, we studied how transcription organizes euchromatin, using experiments in zebrafish embryonic cells and theory. We show that transcription establishes an interspersed pattern of chromatin domains and RNA-enriched microenvironments. Specifically, accumulation of RNA in the vicinity of transcription sites creates microenvironments that locally remodel chromatin by displacing not transcribed chromatin. Ongoing transcriptional activity stabilizes the interspersed pattern of chromatin domains and RNA-enriched microenvironments by establishing contacts between chromatin and RNA. We explain our observations with an active microemulsion model based on two macromolecular mechanisms: RNA/RNA-binding protein complexes generally segregate from chromatin, while transcribed chromatin is retained among RNA/RNA-binding protein accumulations. We propose that microenvironments might be central to genome architecture and serve as gene regulatory hubs.

show abstract

“…Several major approaches (3C, ChromEMT, and super-resolution microscopy) are indicative of a disordered array of loopy fibers that emanate from an axial core (Dostie and Bickmore 2012;Dekker et al 2013;Ou et al 2017). The hierarchical models of structural intermediates building from 11 to 30 nm and larger fibers are not borne out in these recent 3D and live-cell studies (Ou et al 2017). DNA looping was first observed in squash preparations of salamander eggs under the light microscope by the embryologist Oskar Hertwig in the early 1900s (Hertwig 1906).…”

mentioning

confidence: 99%

RotoStep: A Chromosome Dynamics Simulator Reveals Mechanisms of Loop Extrusion

Lawrimore

Friedman

Doshi

et al. 2017

Cold Spring Harb Symp Quant Biol

View full text Add to dashboard Cite

ChromoShake is a three-dimensional simulator designed to explore the range of configurational states a chromosome can adopt based on thermodynamic fluctuations of the polymer chain. Here, we refine ChromoShake to generate dynamic simulations of a DNA-based motor protein such as condensin walking along the chromatin substrate. We model walking as a rotation of DNAbinding heat-repeat proteins around one another. The simulation is applied to several configurations of DNA to reveal the consequences of mechanical stepping on taut chromatin under tension versus loop extrusion on single-tethered, floppy chromatin substrates. These simulations provide testable hypotheses for condensin and other DNA-based motors functioning along interphase chromosomes. Our model reveals a novel mechanism for condensin enrichment in the pericentromeric region of mitotic chromosomes. Increased condensin dwell time at centromeres results in a high density of pericentric loops that in turn provide substrate for additional condensin.There has been a revolution in understanding the higher-order structure and organization of chromosome in the past decade. Several major approaches (3C, ChromEMT, and super-resolution microscopy) are indicative of a disordered array of loopy fibers that emanate from an axial core (Dostie and Bickmore 2012;Dekker et al. 2013;Ou et al. 2017). The hierarchical models of structural intermediates building from 11 to 30 nm and larger fibers are not borne out in these recent 3D and live-cell studies (Ou et al. 2017). DNA looping was first observed in squash preparations of salamander eggs under the light microscope by the embryologist Oskar Hertwig in the early 1900s (Hertwig 1906). Paulson and Laemmli (1977) observed DNA loops when examining chromosome spreads in isolated mammalian cells. In metaphase, the loops emanate from a protein-rich chromosome scaffold. The chromosome scaffold is enriched in topology-adjusting proteins, such as topoisomerase II and the SMC (structural maintenance of chromosomes) proteins, known as condensin (Earnshaw et al. 1985;Hirano 2006).Loops are a natural consequence of the entropic fluctuations and excluded volume interactions of tethered polymer chains in a confined space, such as the nucleus (Vasquez et al. 2016). If we consider the genome as a ball of yarn, the formation of loops can be appreciated as chains that randomly collide and wiggle around one another. Energy-requiring processes are also involved in loop formation. The earliest suggestion of loop extrusion came from the trombone model of DNA replication (Sinha et al. 1980;Alberts et al. 1983) and direct visualization of DNA looping at the replication fork (Park et al. 1998). More recently, SMC proteins (e.g., cohesin and condensin), which bind and hydrolyze ATP, have been cited as having loop extrusion potential (Alipour and Marko 2012). Condensin has garnered attention based on recent studies showing it to be a DNA translocase (Terekawa et al. 2017).Condensin is composed of five subunits, two coiledcoils SMC2 and 4, a kleisin ...

show abstract

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

Cited by 772 publications

References 93 publications

A pathway for mitotic chromosome formation

A pathway for mitotic chromosome formation

Transcription organizes euchromatin similar to an active microemulsion

RotoStep: A Chromosome Dynamics Simulator Reveals Mechanisms of Loop Extrusion

Contact Info

Product

Resources

About