title: Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers.
abstract: Generic spinal motor neuron identity is established by cooperative binding of programming transcription factors (TFs), Isl1 and Lhx3, to motor-neuron-specific enhancers. How expression of effector genes is maintained following downregulation of programming TFs in maturing neurons remains unknown. High-resolution exonuclease (ChIP-exo) mapping revealed that the majority of enhancers established by programming TFs are rapidly deactivated following Lhx3 downregulation in stem-cell-derived hypaxial motor neurons. Isl1 is released from nascent motor neuron enhancers and recruited to new enhancers bound by clusters of Onecut1 in maturing neurons. Synthetic enhancer reporter assays revealed that Isl1 operates as an integrator factor, translating the density of Lhx3 or Onecut1 binding sites into transient enhancer activity. Importantly, independent Isl1/Lhx3- and Isl1/Onecut1-bound enhancers contribute to sustained expression of motor neuron effector genes, demonstrating that outwardly stable expression of terminal effector genes in postmitotic neurons is controlled by a dynamic relay of stage-specific enhancers.
authors.affiliation: Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY 10032, USA.
authors.forename: Ho Sung
authors.initials: HS
authors.lastname: Rhee
authors.affiliation: Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY 10032, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Closser
authors.affiliation: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Yuchun
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY 10032, USA.
authors.forename: Elizaveta V
authors.initials: EV
authors.lastname: Bashkirova
authors.affiliation: Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY 10032, USA.
authors.forename: G Christopher
authors.initials: GC
authors.lastname: Tan
authors.affiliation: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: David K
authors.initials: DK
authors.lastname: Gifford
authors.affiliation: Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY 10032, USA. Electronic address: hw350@cumc.columbia.edu.
authors.forename: Hynek
authors.initials: H
authors.lastname: Wichterle
mesh_terms: D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D015536:Down-Regulation; D004742:Enhancer Elements, Genetic; D018507:Gene Expression Regulation, Developmental; D051559:Hepatocyte Nuclear Factor 6 / Q000378:metabolism*; D060850:LIM-Homeodomain Proteins / Q000378:metabolism*; D051379:Mice; D009046:Motor Neurons / Q000378:metabolism*; D000066450:Mouse Embryonic Stem Cells; D009419:Nerve Tissue Proteins / Q000378:metabolism; D055495:Neurogenesis / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D051559:Hepatocyte Nuclear Factor 6; D060850:LIM-Homeodomain Proteins; D009419:Nerve Tissue Proteins; D014157:Transcription Factors; C094898:Lhx3 protein; C102938:Neurog2 protein, mouse; C496606:Onecut1 protein, mouse; C063843:insulin gene enhancer binding protein Isl-1
keywords: ATAC-seq; CRISPR genome engineering; ChIP-exo; Neurogenin 2; enhancer organization; genome-wide mapping; mouse embryonic stem cells; neuronal maturation; postmitotic motor neurons; terminal effector genes