Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture
Emily M. Darrowa,1, Miriam H. Huntleyb,c,d,e,1, Olga Dudchenkob,c,f, Elena K. Stamenovab,c,e, Neva C. Durandb,c, Zhuo Suna, Su-Chen Huangb,c, Adrian L. Sanbornb,f,g, Ido Macholb,c, Muhammad Shamimb,c, Andrew P. Seberga, Eric S. Landere,h,i,2, Brian P. Chadwicka,2, and Erez Lieberman Aidenb,c,e,f,j,k,2
Author Affiliations
aDepartment of Biological Science, Florida State University, Tallahassee, FL 32306;
bThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;
cDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;
dJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138;
eBroad Institute of MIT and Harvard, Cambridge, MA 02139;
fCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030;
gDepartment of Computer Science, Stanford University, Stanford, CA 94305;
hDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139;
iDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115;
jDepartment of Computer Science, Rice University, Houston, TX 77005;
kDepartment of Computational and Applied Mathematics, Rice University, Houston, TX 77005
Contributed by Eric S. Lander, June 24, 2016 (sent for review May 8, 2016; reviewed by Frank Alber, Marisa S. Bartolomei, Uta Francke, and Sundeep Kalantry)
Significance
In human females, one of the two X chromosomes is inactive (Xi) and adopts an unusual 3D conformation. The Xi chromosome contains superloops, large chromatin loops that are often anchored at the macrosatellite repeat DXZ4, and is partitioned into two large intervals, called superdomains, whose boundary lies at DXZ4. Here, we use spatial proximity mapping, microscopy, and genome editing to study the Xi. We find that superloops and superdomains are conserved across humans, macaque, and mouse. By mapping proximity between three or more loci, we show that superloops tend to occur simultaneously. Deletion of DXZ4 from the human Xi disrupts superloops, eliminates superdomains, and alters chromatin modifications. Finally, we show that a model in which CCCTC-binding factor (CTCF) and cohesin extrude chromatin can explain the formation of superloops and superdomains.
Next Section
Abstract
During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the “Barr body.” Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called “superdomains,” such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called “superloops.” DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4. We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.
X chromosome inactivation inactive X chromosome Hi‐C CTCF genome engineering
