title: Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element.
abstract: Gene regulation relies on dynamic changes in three-dimensional chromatin conformation, which are shaped by composite regulatory and architectural elements. However, mechanisms that govern such conformational switches within chromosomal domains remain unknown. We identify a novel mechanism by which cis-elements promote long-range interactions, inducing conformational changes critical for diversification of the TCRβ antigen receptor locus (Tcrb). Association between distal Vβ gene segments and the highly expressed DβJβ clusters, termed the recombination center (RC), is independent of enhancer function and recruitment of V(D)J recombinase. Instead, we find that tissue-specific folding of Tcrb relies on two distinct architectural elements located upstream of the RC. The first, a CTCF-containing element, directly tethers distal portions of the Vβ array to the RC. The second element is a chromatin barrier that protects the tether from hyperactive RC chromatin. When the second element is removed, active RC chromatin spreads upstream, forcing the tether to serve as a new barrier. Acquisition of barrier function by the CTCF element disrupts contacts between distal Vβ gene segments and significantly alters Tcrb repertoires. Our findings reveal a separation of function for RC-flanking regions, in which anchors for long-range recombination must be cordoned off from hyperactive RC landscapes by chromatin barriers.
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110.
authors.forename: Kinjal
authors.initials: K
authors.lastname: Majumder
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110.
authors.forename: Olivia I
authors.initials: OI
authors.lastname: Koues
authors.affiliation: Department of Immunology, Duke University Medical Center, Durham, NC 27710.
authors.forename: Elizabeth A W
authors.initials: EA
authors.lastname: Chan
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110.
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Kyle
authors.affiliation: Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
authors.forename: Julie E
authors.initials: JE
authors.lastname: Horowitz
authors.affiliation: Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
authors.forename: Katherine
authors.initials: K
authors.lastname: Yang-Iott
authors.affiliation: Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
authors.forename: Craig H
authors.initials: CH
authors.lastname: Bassing
authors.affiliation: Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Ichiro
authors.initials: I
authors.lastname: Taniuchi
authors.affiliation: Department of Immunology, Duke University Medical Center, Durham, NC 27710.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Krangel
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 eoltz@wustl.edu.
authors.forename: Eugene M
authors.initials: EM
authors.lastname: Oltz
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D019070:Cell Lineage / Q000235:genetics; D002478:Cells, Cultured; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005786:Gene Expression Regulation; D006657:Histones / Q000378:metabolism; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D008745:Methylation; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D054448:Precursor Cells, B-Lymphoid / Q000166:cytology / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics* / Q000378:metabolism; D012097:Repressor Proteins / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D060168:Thymocytes / Q000166:cytology / Q000378:metabolism*; D060152:V(D)J Recombination / Q000235:genetics; D045567:VDJ Recombinases / Q000378:metabolism
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin; C000619698:Ctcf protein, mouse; D006657:Histones; D016693:Receptors, Antigen, T-Cell, alpha-beta; D012097:Repressor Proteins; D045567:VDJ Recombinases