Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.
We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic "tension globule." In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030; Department of Computer Science, Stanford University, Stanford, CA 94305;
Adrian L
AL
Sanborn
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; School of Medicine, Stanford University, Stanford, CA 94305;
Suhas S P
SS
Rao
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;
Su-Chen
SC
Huang
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;
Neva C
NC
Durand
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;
Miriam H
MH
Huntley
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;
Andrew I
AI
Jewett
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;
Ivan D
ID
Bochkov
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;
Dharmaraj
D
Chinnappan
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;
Ashok
A
Cutkosky
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030;
Jian
J
Li
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;
Kristopher P
KP
Geeting
Broad Institute of MIT and Harvard, Cambridge, MA 02139;
Andreas
A
Gnirke
Broad Institute of MIT and Harvard, Cambridge, MA 02139;
Alexandre
A
Melnikov
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Mathemaesthetics, Inc., Boulder, CO 80306;
Doug
D
McKenna
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Broad Institute of MIT and Harvard, Cambridge, MA 02139;
Elena K
EK
Stamenova
Broad Institute of MIT and Harvard, Cambridge, MA 02139; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Systems Biology, Harvard Medical School, Boston, MA 02115 lander@broadinstitute.org erez@erez.com.
Eric S
ES
Lander
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030; Broad Institute of MIT and Harvard, Cambridge, MA 02139; lander@broadinstitute.org erez@erez.com.
Erez Lieberman
EL
Aiden
D016880:Anisotropy; D020029:Base Pairing; D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics*; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism; D003198:Computer Simulation; D004058:Diffusion; D017709:Fractals; D005818:Genetic Engineering; D016678:Genome / Q000235:genetics*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs / Q000235:genetics; D011108:Polymers / Q000737:chemistry; D011336:Probability; D012097:Repressor Proteins / Q000378:metabolism; D000097722:Cohesins
D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D011108:Polymers; D012097:Repressor Proteins; D000097722:Cohesins; C000619697:CTCF protein, human
CRISPR; CTCF; chromatin loops; genome architecture; molecular dynamics