title: Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.
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.
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306;
authors.forename: Emily M
authors.initials: EM
authors.lastname: Darrow
authors.affiliation: The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138; Broad Institute of MIT and Harvard, Cambridge, MA 02139;
authors.forename: Miriam H
authors.initials: MH
authors.lastname: Huntley
authors.affiliation: The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030;
authors.forename: Olga
authors.initials: O
authors.lastname: Dudchenko
authors.affiliation: The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; Broad Institute of MIT and Harvard, Cambridge, MA 02139;
authors.forename: Elena K
authors.initials: EK
authors.lastname: Stamenova
authors.affiliation: The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;
authors.forename: Neva C
authors.initials: NC
authors.lastname: Durand
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306;
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Sun
authors.affiliation: The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;
authors.forename: Su-Chen
authors.initials: SC
authors.lastname: Huang
authors.affiliation: 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;
authors.forename: Adrian L
authors.initials: AL
authors.lastname: Sanborn
authors.affiliation: The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;
authors.forename: Ido
authors.initials: I
authors.lastname: Machol
authors.affiliation: The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;
authors.forename: Muhammad
authors.initials: M
authors.lastname: Shamim
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306;
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Seberg
authors.affiliation: 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; erez@erez.com lander@broadinstitute.org chadwick@bio.fsu.edu.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306; erez@erez.com lander@broadinstitute.org chadwick@bio.fsu.edu.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Chadwick
authors.affiliation: The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; Broad Institute of MIT and Harvard, Cambridge, MA 02139; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030; Department of Computer Science, Rice University, Houston, TX 77005; Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005 erez@erez.com lander@broadinstitute.org chadwick@bio.fsu.edu.
authors.forename: Erez Lieberman
authors.initials: EL
authors.lastname: Aiden
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D000076246:CCCTC-Binding Factor / Q000378:metabolism; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D041321:Chromosomes, Human, X / Q000235:genetics*; D005260:Female; D017353:Gene Deletion; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008253:Macaca mulatta; D051379:Mice; D018895:Microsatellite Repeats / Q000235:genetics*; D011485:Protein Binding; D049951:X Chromosome Inactivation
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin
keywords: CTCF; Hi‐C; X chromosome inactivation; genome engineering; inactive X chromosome