title: Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality.
abstract: Expression of Pitx2 on the left side of the embryo patterns left-right (LR) organs including the dorsal mesentery (DM), whose asymmetric cell behavior directs gut looping. Despite the importance of organ laterality, chromatin-level regulation of Pitx2 remains undefined. Here, we show that genes immediately neighboring Pitx2 in chicken and mouse, including a long noncoding RNA (Pitx2 locus-asymmetric regulated RNA or Playrr), are expressed on the right side and repressed by Pitx2. CRISPR/Cas9 genome editing of Playrr, 3D fluorescent in situ hybridization (FISH), and variations of chromatin conformation capture (3C) demonstrate that mutual antagonism between Pitx2 and Playrr is coordinated by asymmetric chromatin interactions dependent on Pitx2 and CTCF. We demonstrate that transcriptional and morphological asymmetries driving gut looping are mirrored by chromatin architectural asymmetries at the Pitx2 locus. We propose a model whereby Pitx2 auto-regulation directs chromatin topology to coordinate LR transcription of this locus essential for LR organogenesis.
authors.affiliation: Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Ian C
authors.initials: IC
authors.lastname: Welsh
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Hojoong
authors.initials: H
authors.lastname: Kwak
authors.affiliation: Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Frances L
authors.initials: FL
authors.lastname: Chen
authors.affiliation: Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Werner
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Eastern Maine Medical Center Cancer Care, 33 Whiting Hill Road, Brewer, ME 04412, USA.
authors.forename: Lindsay S
authors.initials: LS
authors.lastname: Shopland
authors.affiliation: Department of Biomedical Sciences, The Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Charles G
authors.initials: CG
authors.lastname: Danko
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors.forename: John T
authors.initials: JT
authors.lastname: Lis
authors.affiliation: Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Min
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Heart Institute, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: James F
authors.initials: JF
authors.lastname: Martin
authors.affiliation: Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA. Electronic address: nk378@cornell.edu.
authors.forename: Natasza A
authors.initials: NA
authors.lastname: Kurpios
mesh_terms: D000818:Animals; D001483:Base Sequence; D000076246:CCCTC-Binding Factor; D002642:Chick Embryo; D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D056426:Genetic Loci; D018398:Homeodomain Proteins / Q000235:genetics*; D007413:Intestinal Mucosa / Q000378:metabolism*; D007422:Intestines / Q000196:embryology; D051379:Mice; D008969:Molecular Sequence Data; D009024:Morphogenesis; D062085:RNA, Long Noncoding / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics*; D000097577:Homeobox Protein PITX2
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin; D018398:Homeodomain Proteins; D062085:RNA, Long Noncoding; D012097:Repressor Proteins; D014157:Transcription Factors; D000097577:Homeobox Protein PITX2; C000619698:Ctcf protein, mouse