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Transcriptional network orchestrating regional patterning of cortical progenitors.
Ypsilanti, Athéna R; Pattabiraman, Kartik; Catta-Preta, Rinaldo; Golonzhka, Olga; Lindtner, Susan; Tang, Ke; Jones, Ian R; Abnousi, Armen; Juric, Ivan; Hu, Ming; Shen, Yin; Dickel, Diane E; Visel, Axel; Pennachio, Len A; Hawrylycz, Michael; Thompson, Carol L; Zeng, Hongkui; Barozzi, Iros; Nord, Alex S; Rubenstein, John L.
Affiliation
  • Ypsilanti AR; Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158; athena.ypsilanti@ucsf.edu john.rubenstein@ucsf.edu.
  • Pattabiraman K; Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158.
  • Catta-Preta R; Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95618.
  • Golonzhka O; Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618.
  • Lindtner S; Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158.
  • Tang K; Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158.
  • Jones IR; Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
  • Abnousi A; Institute for Human Genetics, University of California, San Francisco, CA 94143.
  • Juric I; Department of Neurology, University of California, San Francisco, CA 94143.
  • Hu M; Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195.
  • Shen Y; Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195.
  • Dickel DE; Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195.
  • Visel A; Institute for Human Genetics, University of California, San Francisco, CA 94143.
  • Pennachio LA; Department of Neurology, University of California, San Francisco, CA 94143.
  • Hawrylycz M; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
  • Thompson CL; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
  • Zeng H; School of Natural Sciences, University of California, Merced, CA 95343.
  • Barozzi I; US Department of Energy Joint Genome Institute, Berkeley, CA 94720.
  • Nord AS; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
  • Rubenstein JL; US Department of Energy Joint Genome Institute, Berkeley, CA 94720.
Proc Natl Acad Sci U S A ; 118(51)2021 12 21.
Article in En | MEDLINE | ID: mdl-34921112
ABSTRACT
We uncovered a transcription factor (TF) network that regulates cortical regional patterning in radial glial stem cells. Screening the expression of hundreds of TFs in the developing mouse cortex identified 38 TFs that are expressed in gradients in the ventricular zone (VZ). We tested whether their cortical expression was altered in mutant mice with known patterning defects (Emx2, Nr2f1, and Pax6), which enabled us to define a cortical regionalization TF network (CRTFN). To identify genomic programming underlying this network, we performed TF ChIP-seq and chromatin-looping conformation to identify enhancer-gene interactions. To map enhancers involved in regional patterning of cortical progenitors, we performed assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach has identified a CRTFN and VZ enhancers involved in cortical regional patterning in the mouse.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Transcription Factors / Cerebral Cortex / Regulatory Elements, Transcriptional / Gene Regulatory Networks Type of study: Prognostic_studies Limits: Animals Language: En Journal: Proc Natl Acad Sci U S A Year: 2021 Document type: Article
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Transcription Factors / Cerebral Cortex / Regulatory Elements, Transcriptional / Gene Regulatory Networks Type of study: Prognostic_studies Limits: Animals Language: En Journal: Proc Natl Acad Sci U S A Year: 2021 Document type: Article