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Lindtner S, Catta-Preta R, Tian H, Su-Feher L, Price JD, Dickel DE, Greiner V, Silberberg SN, McKinsey GL, McManus MT, Pennacchio LA, Visel A, Nord AS, Rubenstein JLR. Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons. Cell Rep 2020; 28:2048-2063.e8. [PMID: 31433982 PMCID: PMC6750766 DOI: 10.1016/j.celrep.2019.07.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/29/2019] [Accepted: 07/08/2019] [Indexed: 11/24/2022] Open
Abstract
DLX transcription factors (TFs) are master regulators of the developing vertebrate brain, driving forebrain GABAergic neuronal differentiation. Ablation of Dlx1&2 alters expression of genes that are critical for forebrain GABAergic development. We integrated epigenomic and transcriptomic analyses, complemented with in situ hybridization (ISH), and in vivo and in vitro studies of regulatory element (RE) function. This revealed the DLX-organized gene regulatory network at genomic, cellular, and spatial levels in mouse embryonic basal ganglia. DLX TFs perform dual activating and repressing functions; the consequences of their binding were determined by the sequence and genomic context of target loci. Our results reveal and, in part, explain the paradox of widespread DLX binding contrasted with a limited subset of target loci that are sensitive at the epigenomic and transcriptomic level to Dlx1&2 ablation. The regulatory properties identified here for DLX TFs suggest general mechanisms by which TFs orchestrate dynamic expression programs underlying neurodevelopment. Lindtner et al. reveal the regulatory wiring organized by DLX transcription factors in forebrain GABAergic neuronal specification, by integrating functional genomic, epigenomic, and genetic data on a transgenic mouse model. This network determines key sequence-encoded regulatory elements and implicates a combination of histone modifications and biophysical interactions.
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Affiliation(s)
- Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rinaldo Catta-Preta
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - Hua Tian
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Linda Su-Feher
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - James D Price
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Development and Stem Cell Biology Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vanille Greiner
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shanni N Silberberg
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gabriel L McKinsey
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA.
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Development and Stem Cell Biology Program, University of California, San Francisco, San Francisco, CA 94158, USA.
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Hu JS, Vogt D, Lindtner S, Sandberg M, Silberberg SN, Rubenstein JLR. Coup-TF1 and Coup-TF2 control subtype and laminar identity of MGE-derived neocortical interneurons. Development 2017; 144:2837-2851. [PMID: 28694260 DOI: 10.1242/dev.150664] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/29/2017] [Indexed: 12/23/2022]
Abstract
Distinct cortical interneuron (CIN) subtypes have unique circuit functions; dysfunction in specific subtypes is implicated in neuropsychiatric disorders. Somatostatin- and parvalbumin-expressing (SST+ and PV+) interneurons are the two major subtypes generated by medial ganglionic eminence (MGE) progenitors. Spatial and temporal mechanisms governing their cell-fate specification and differential integration into cortical layers are largely unknown. We provide evidence that Coup-TF1 and Coup-TF2 (Nr2f1 and Nr2f2) transcription factor expression in an arc-shaped progenitor domain within the MGE promotes time-dependent survival of this neuroepithelium and the time-dependent specification of layer V SST+ CINs. Coup-TF1 and Coup-TF2 autonomously repress PV+ fate in MGE progenitors, in part through directly driving Sox6 expression. These results have identified, in mouse, a transcriptional pathway that controls SST-PV fate.
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Affiliation(s)
- Jia Sheng Hu
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daniel Vogt
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Susan Lindtner
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Magnus Sandberg
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Shanni N Silberberg
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - John L R Rubenstein
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
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Vogt D, Hunt RF, Mandal S, Sandberg M, Silberberg SN, Nagasawa T, Yang Z, Baraban SC, Rubenstein JLR. Lhx6 directly regulates Arx and CXCR7 to determine cortical interneuron fate and laminar position. Neuron 2014; 82:350-64. [PMID: 24742460 DOI: 10.1016/j.neuron.2014.02.030] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2014] [Indexed: 12/13/2022]
Abstract
Cortical GABAergic interneurons have essential roles for information processing and their dysfunction is implicated in neuropsychiatric disorders. Transcriptional codes are elucidating mechanisms of interneuron specification in the MGE (a subcortical progenitor zone), which regulate their migration, integration, and function within cortical circuitry. Lhx6, a LIM-homeodomain transcription factor, is essential for specification of MGE-derived somatostatin and parvalbumin interneurons. Here, we demonstrate that some Lhx6⁻/⁻ MGE cells acquire a CGE-like fate. Using an in vivo MGE complementation/transplantation assay, we show that Lhx6-regulated genes Arx and CXCR7 rescue divergent aspects of Lhx6⁻/⁻ cell-fate and laminar mutant phenotypes and provide insight into a neonatal role for CXCR7 in MGE-derived interneuron lamination. Finally, Lhx6 directly binds in vivo to an Arx enhancer and to an intronic CXCR7 enhancer that remains active in mature interneurons. These data define the molecular identity of Lhx6 mutants and introduce technologies to test mechanisms in GABAergic interneuron differentiation.
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Affiliation(s)
- Daniel Vogt
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Robert F Hunt
- Epilepsy Research Laboratory, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shyamali Mandal
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cancer Biology and Pharmacology University of Illinois, Peoria, IL 61656, USA
| | - Magnus Sandberg
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Shanni N Silberberg
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Takashi Nagasawa
- Department of Immunology and Hematology, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Zhengang Yang
- Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Scott C Baraban
- Epilepsy Research Laboratory, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L R Rubenstein
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA.
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Pattabiraman K, Golonzhka O, Lindtner S, Nord AS, Taher L, Hoch R, Silberberg SN, Zhang D, Chen B, Zeng H, Pennacchio LA, Puelles L, Visel A, Rubenstein JLR. Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex. Neuron 2014; 82:989-1003. [PMID: 24814534 DOI: 10.1016/j.neuron.2014.04.014] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2014] [Indexed: 11/30/2022]
Abstract
Elucidating the genetic control of cerebral cortical (pallial) development is essential for understanding function, evolution, and disorders of the brain. Transcription factors (TFs) that embryonically regulate pallial regionalization are expressed in gradients, raising the question of how discrete domains are generated. We provide evidence that small enhancer elements active in protodomains integrate broad transcriptional information. CreER(T2) and GFP expression from 14 different enhancer elements in stable transgenic mice allowed us to define a comprehensive regional fate map of the pallium. We explored transcriptional mechanisms that control the activity of the enhancers using informatics, in vivo occupancy by TFs that regulate cortical patterning (CoupTFI, Pax6, and Pbx1), and analysis of enhancer activity in Pax6 mutants. Overall, the results provide insights into how broadly expressed patterning TFs regulate the activity of small enhancer elements that drive gene expression in pallial protodomains that fate map to distinct cortical regions.
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Affiliation(s)
- Kartik Pattabiraman
- Department of Psychiatry, Program in Neuroscience, Rock Hall, University of California at San Francisco, San Francisco, CA 94158-2324, USA
| | - Olga Golonzhka
- Department of Psychiatry, Program in Neuroscience, Rock Hall, University of California at San Francisco, San Francisco, CA 94158-2324, USA; Acetylon Pharmaceuticals, Boston, MA 02210, USA
| | - Susan Lindtner
- Department of Psychiatry, Program in Neuroscience, Rock Hall, University of California at San Francisco, San Francisco, CA 94158-2324, USA
| | - Alex S Nord
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Leila Taher
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Institute for Biostatistics and Informatics in Medicine and Ageing Research, Department of Medicine, University of Rostock, 18057 Rostock, Germany
| | - Renee Hoch
- Department of Psychiatry, Program in Neuroscience, Rock Hall, University of California at San Francisco, San Francisco, CA 94158-2324, USA
| | - Shanni N Silberberg
- Department of Psychiatry, Program in Neuroscience, Rock Hall, University of California at San Francisco, San Francisco, CA 94158-2324, USA
| | - Dongji Zhang
- Department of Psychiatry, Program in Neuroscience, Rock Hall, University of California at San Francisco, San Francisco, CA 94158-2324, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - HongKui Zeng
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Len A Pennacchio
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Luis Puelles
- Department of Morphological Sciences, Faculty of Medicine, University of Murcia, E-30100 Murcia, Spain
| | - Axel Visel
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - John L R Rubenstein
- Department of Psychiatry, Program in Neuroscience, Rock Hall, University of California at San Francisco, San Francisco, CA 94158-2324, USA.
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Chen YJJ, Vogt D, Wang Y, Visel A, Silberberg SN, Nicholas CR, Danjo T, Pollack JL, Pennacchio LA, Anderson S, Sasai Y, Baraban SC, Kriegstein AR, Alvarez-Buylla A, Rubenstein JLR. Use of "MGE enhancers" for labeling and selection of embryonic stem cell-derived medial ganglionic eminence (MGE) progenitors and neurons. PLoS One 2013; 8:e61956. [PMID: 23658702 PMCID: PMC3641041 DOI: 10.1371/journal.pone.0061956] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 03/15/2013] [Indexed: 12/21/2022] Open
Abstract
The medial ganglionic eminence (MGE) is an embryonic forebrain structure that generates the majority of cortical interneurons. MGE transplantation into specific regions of the postnatal central nervous system modifies circuit function and improves deficits in mouse models of epilepsy, Parkinson's disease, pain, and phencyclidine-induced cognitive deficits. Herein, we describe approaches to generate MGE-like progenitor cells from mouse embryonic stem (ES) cells. Using a modified embryoid body method, we provided gene expression evidence that mouse ES-derived Lhx6(+) cells closely resemble immature interneurons generated from authentic MGE-derived Lhx6(+) cells. We hypothesized that enhancers that are active in the mouse MGE would be useful tools in detecting when ES cells differentiate into MGE cells. Here we demonstrate the utility of enhancer elements [422 (DlxI12b), Lhx6, 692, 1056, and 1538] as tools to mark MGE-like cells in ES cell differentiation experiments. We found that enhancers DlxI12b, 692, and 1538 are active in Lhx6-GFP(+) cells, while enhancer 1056 is active in Olig2(+) cells. These data demonstrate unique techniques to follow and purify MGE-like derivatives from ES cells, including GABAergic cortical interneurons and oligodendrocytes, for use in stem cell-based therapeutic assays and treatments.
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Affiliation(s)
- Ying-Jiun J. Chen
- Department of Psychiatry and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, California, United States of America
| | - Daniel Vogt
- Department of Psychiatry and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, California, United States of America
| | - Yanling Wang
- Department of Psychiatry and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, California, United States of America
| | - Axel Visel
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, and Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Shanni N. Silberberg
- Department of Psychiatry and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, California, United States of America
| | - Cory R. Nicholas
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, California, United States of America
| | - Teruko Danjo
- Neurogenesis and Organogenesis Group, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Joshua L. Pollack
- Lung Biology Center, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Len A. Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, and Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Stewart Anderson
- 3Children's Hospital of Philadelphia, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yoshiki Sasai
- Neurogenesis and Organogenesis Group, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Scott C. Baraban
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Arnold R. Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, California, United States of America
| | - Arturo Alvarez-Buylla
- Department of Neurosurgery and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, California, United States of America
| | - John L. R. Rubenstein
- Department of Psychiatry and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, California, United States of America
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Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JLR. A high-resolution enhancer atlas of the developing telencephalon. Cell 2013; 152:895-908. [PMID: 23375746 DOI: 10.1016/j.cell.2012.12.041] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 10/31/2012] [Accepted: 12/20/2012] [Indexed: 11/25/2022]
Abstract
The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. Though many of the genes required for its development have been identified, the distant-acting regulatory sequences orchestrating their in vivo expression are mostly unknown. Here, we describe a digital atlas of in vivo enhancers active in subregions of the developing telencephalon. We identified more than 4,600 candidate embryonic forebrain enhancers and studied the in vivo activity of 329 of these sequences in transgenic mouse embryos. We generated serial sets of histological brain sections for 145 reproducible forebrain enhancers, resulting in a publicly accessible web-based data collection comprising more than 32,000 sections. We also used epigenomic analysis of human and mouse cortex tissue to directly compare the genome-wide enhancer architecture in these species. These data provide a primary resource for investigating gene regulatory mechanisms of telencephalon development and enable studies of the role of distant-acting enhancers in neurodevelopmental disorders.
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Affiliation(s)
- Axel Visel
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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