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scChIX-seq infers dynamic relationships between histone modifications in single cells. Nat Biotechnol 2023:10.1038/s41587-022-01560-3. [PMID: 36593403 DOI: 10.1038/s41587-022-01560-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/12/2022] [Indexed: 01/03/2023]
Abstract
Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.
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2
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Hiraga K, Inoue YU, Asami J, Hotta M, Morimoto Y, Tatsumoto S, Hoshino M, Go Y, Inoue T. Redundant type II cadherins define neuroepithelial cell states for cytoarchitectonic robustness. Commun Biol 2020; 3:574. [PMID: 33060832 PMCID: PMC7567090 DOI: 10.1038/s42003-020-01297-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 09/15/2020] [Indexed: 02/07/2023] Open
Abstract
Individual cell shape and integrity must precisely be orchestrated during morphogenesis. Here, we determine function of type II cadherins, Cdh6, Cdh8, and Cdh11, whose expression combinatorially demarcates the mouse neural plate/tube. While CRISPR/Cas9-based single type II cadherin mutants show no obvious phenotype, Cdh6/8 double knockout (DKO) mice develop intermingled forebrain/midbrain compartments as these two cadherins' expression opposes at the nascent boundary. Cdh6/8/11 triple, Cdh6/8 or Cdh8/11 DKO mice further cause exencephaly just within the cranial region where mutated cadherins' expression merges. In the Cdh8/11 DKO midbrain, we observe less-constricted apical actin meshwork, ventrally-directed spreading, and occasional hyperproliferation among dorsal neuroepithelial cells as origins for exencephaly. These results provide rigid evidence that, by conferring distinct adhesive codes to each cell, redundant type II cadherins serve essential and shared roles in compartmentalization and neurulation, both of which proceed under the robust control of the number, positioning, constriction, and fluidity of neuroepithelial cells.
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Affiliation(s)
- Kou Hiraga
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Junko Asami
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Mayuko Hotta
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
- Graduate School of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Koganei, Tokyo, 184-8588, Japan
| | - Yuki Morimoto
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Shoji Tatsumoto
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Saigo-naka 38, Myoudaiji, Okazaki, Aichi, 444-8585, Japan
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Yasuhiro Go
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Saigo-naka 38, Myoudaiji, Okazaki, Aichi, 444-8585, Japan
- Department of System Neuroscience, National Institute for Physiological Sciences, Saigo-naka 38, Myoudaiji, Okazaki, Aichi, 444-8585, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Saigo-naka 38, Myoudaiji, Okazaki, Aichi, 444-8585, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan.
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Li J, Li SH, Wu J, Weisel RD, Yao A, Stanford WL, Liu SM, Li RK. Young Bone Marrow Sca-1 Cells Rejuvenate the Aged Heart by Promoting Epithelial-to-Mesenchymal Transition. Am J Cancer Res 2018; 8:1766-1781. [PMID: 29556355 PMCID: PMC5858499 DOI: 10.7150/thno.22788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/13/2018] [Indexed: 01/13/2023] Open
Abstract
Background: To improve the regenerative capacity of aged individuals, we reconstituted bone marrow (BM) of aged mice with young Sca-1 cells, which repopulated cardiac progenitors and prevented cardiac dysfunction after a myocardial infarction (MI). However, the mechanisms involved were incompletely elucidated. This study aimed to investigate whether young, highly regenerative BM Sca-1 cells exert their cardio-protective effects on the aged heart through reactivation of the epithelial-to-mesenchymal transition (EMT) process. Methods:In vitro, BM Sca-1 cells were co-cultured with epicardial-derived cells (EPDCs) under hypoxia condition; mRNA and protein levels of EMT genes were measured along with cellular proliferation and migration. In vivo, BM Sca-1+ or Sca-1- cells from young mice (2-3 months) were transplanted into lethally-irradiated old mice (20-22 months) to generate chimeras. In addition, Sca-1 knockout (KO) mice were reconstituted with wild type (WT) BM Sca-1+ cells. The effects of BM Sca-1 cell on EMT reactivation and improvement of cardiac function after MI were evaluated. Results:In vitro, BM Sca-1+ cells increased EPDC proliferation, migration, and EMT relative to Sca-1- cells and these effects were inhibited by a TGF-β blocker. In vivo, more young BM Sca-1+ than Sca-1- cells homed to the epicardium and induced greater host EPDC proliferation, migration, and EMT after MI. Furthermore, reconstitution of Sca-1 KO mice with WT Sca-1+ cells was associated with the reactivation of EMT and improved cardiac function after MI. Conclusions: Young BM Sca-1+ cells improved cardiac regeneration through promoting EPDC proliferation, migration and reactivation of EMT via the TGF-β signaling pathway.
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Affiliation(s)
- Jiao Li
- Department of Cardiology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Toronto General Research Institute, Division of Cardiovascular Surgery, University Health Network, Toronto, Canada,Division of Cardiac Surgery, Department of Surgery, University of Toronto; Toronto, Canada
| | - Shu-Hong Li
- Toronto General Research Institute, Division of Cardiovascular Surgery, University Health Network, Toronto, Canada
| | - Jun Wu
- Toronto General Research Institute, Division of Cardiovascular Surgery, University Health Network, Toronto, Canada
| | - Richard D. Weisel
- Toronto General Research Institute, Division of Cardiovascular Surgery, University Health Network, Toronto, Canada,Division of Cardiac Surgery, Department of Surgery, University of Toronto; Toronto, Canada
| | - Alina Yao
- Toronto General Research Institute, Division of Cardiovascular Surgery, University Health Network, Toronto, Canada
| | - William L. Stanford
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Department of Cellular and Molecular Medicine, University of Ottawa
| | - Shi-Ming Liu
- Department of Cardiology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,✉ Corresponding author: Shi-Ming Liu, MD, Department of Cardiology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China. Tel: 86-020-34153522; Fax: 86-20-3415-3709; and Ren-Ke Li, MD, PhD, Toronto Medical Discovery Tower, Room 3-702, 101 College Street, Toronto, Ontario, Canada M5G 1L7. Tel: 1-416-581-7492; Fax: 1-416-581-7493;
| | - Ren-Ke Li
- Toronto General Research Institute, Division of Cardiovascular Surgery, University Health Network, Toronto, Canada,Division of Cardiac Surgery, Department of Surgery, University of Toronto; Toronto, Canada,✉ Corresponding author: Shi-Ming Liu, MD, Department of Cardiology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China. Tel: 86-020-34153522; Fax: 86-20-3415-3709; and Ren-Ke Li, MD, PhD, Toronto Medical Discovery Tower, Room 3-702, 101 College Street, Toronto, Ontario, Canada M5G 1L7. Tel: 1-416-581-7492; Fax: 1-416-581-7493;
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4
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Brain enhancer activities at the gene-poor 5p14.1 autism-associated locus. Sci Rep 2016; 6:31227. [PMID: 27503586 PMCID: PMC4977510 DOI: 10.1038/srep31227] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/14/2016] [Indexed: 12/19/2022] Open
Abstract
Due to the vast clinical and genetic heterogeneity, identification of causal genetic determinants for autism spectrum disorder (ASD) has proven to be complex. Whereas several dozen ‘rare’ genetic variants for ASD susceptibility have been identified, studies are still underpowered to analyse ‘common’ variants for their subtle effects. A recent application of genome-wide association studies (GWAS) to ASD indicated significant associations with the single nucleotide polymorphisms (SNPs) on chromosome 5p14.1, located in a non-coding region between cadherin10 (CDH10) and cadherin9 (CDH9). Here we apply an in vivo bacterial artificial chromosome (BAC) based enhancer-trapping strategy in mice to scan the gene desert for spatiotemporal cis-regulatory activities. Our results show that the ASD-associated interval harbors the cortical area, striatum, and cerebellum specific enhancers for a long non-coding RNA, moesin pseudogene1 antisense (MSNP1AS) during the brain developing stages. Mouse moesin protein levels are not affected by exogenously expressed human antisense RNAs in our transgenic brains, demonstrating the difficulty in modeling rather smaller effects of common variants. Our first in vivo evidence for the spatiotemporal transcription of MSNP1AS however provides a further support to connect this intergenic variant with the ASD susceptibility.
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Egusa SF, Inoue YU, Asami J, Terakawa YW, Hoshino M, Inoue T. Classic cadherin expressions balance postnatal neuronal positioning and dendrite dynamics to elaborate the specific cytoarchitecture of the mouse cortical area. Neurosci Res 2016; 105:49-64. [DOI: 10.1016/j.neures.2015.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/20/2015] [Accepted: 09/24/2015] [Indexed: 11/25/2022]
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6
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Seto Y, Nakatani T, Masuyama N, Taya S, Kumai M, Minaki Y, Hamaguchi A, Inoue YU, Inoue T, Miyashita S, Fujiyama T, Yamada M, Chapman H, Campbell K, Magnuson MA, Wright CV, Kawaguchi Y, Ikenaka K, Takebayashi H, Ishiwata S, Ono Y, Hoshino M. Temporal identity transition from Purkinje cell progenitors to GABAergic interneuron progenitors in the cerebellum. Nat Commun 2015; 5:3337. [PMID: 24535035 DOI: 10.1038/ncomms4337] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 01/29/2014] [Indexed: 11/09/2022] Open
Abstract
In the cerebellum, all GABAergic neurons are generated from the Ptf1a-expressing ventricular zone (Ptf1a domain). However, the machinery to produce different types of GABAergic neurons remains elusive. Here we show temporal regulation of distinct GABAergic neuron progenitors in the cerebellum. Within the Ptf1a domain at early stages, we find two subpopulations; dorsally and ventrally located progenitors that express Olig2 and Gsx1, respectively. Lineage tracing reveals the former are exclusively Purkinje cell progenitors (PCPs) and the latter Pax2-positive interneuron progenitors (PIPs). As development proceeds, PCPs gradually become PIPs starting from ventral to dorsal. In gain- and loss-of-function mutants for Gsx1 and Olig1/2, we observe abnormal transitioning from PCPs to PIPs at inappropriate developmental stages. Our findings suggest that the temporal identity transition of cerebellar GABAergic neuron progenitors from PCPs to PIPs is negatively regulated by Olig2 and positively by Gsx1, and contributes to understanding temporal control of neuronal progenitor identities.
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Affiliation(s)
- Yusuke Seto
- 1] Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan [2] Department of Physics, Major in Integrative Bioscience and Biomedical Engineering, Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Tomoya Nakatani
- KAN Research Institute Inc., 3F, Kobe MI R&D Center, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Norihisa Masuyama
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Shinichiro Taya
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Minoru Kumai
- KAN Research Institute Inc., 3F, Kobe MI R&D Center, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Yasuko Minaki
- 1] KAN Research Institute Inc., 3F, Kobe MI R&D Center, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan [2]
| | - Akiko Hamaguchi
- KAN Research Institute Inc., 3F, Kobe MI R&D Center, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Satoshi Miyashita
- 1] Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan [2] Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Tomoyuki Fujiyama
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Mayumi Yamada
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Heather Chapman
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229-3026, USA
| | - Kenneth Campbell
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229-3026, USA
| | - Mark A Magnuson
- Department of Molecular Physiology and Biophysics and Center for Stem Cell Biology, Vanderbilt University School of Medicine, 2213 Garland Avenue, 9465 MRB IV, Nashville, Tennessee 37232-0494, USA
| | - Christopher V Wright
- Vanderbilt University Program in Developmental Biology, Department of Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Avenue, 9465 MRB IV, Nashville, Tennessee 37232-0494, USA
| | - Yoshiya Kawaguchi
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kazuhiro Ikenaka
- 1] Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan [2] Department of Physiological Sciences, School of Life Sciences, Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawa 240-0193, Japan
| | - Hirohide Takebayashi
- 1] Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan [2] Department of Physiological Sciences, School of Life Sciences, Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawa 240-0193, Japan [3] Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan
| | - Shin'ichi Ishiwata
- 1] Department of Physics, Major in Integrative Bioscience and Biomedical Engineering, Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan [2] Waseda Bioscience Research Institute in Singapore, Waseda University, 11 Biopolis Way, #05-01/02, Helios, Singapore 138667, Republic of Singapore
| | - Yuichi Ono
- KAN Research Institute Inc., 3F, Kobe MI R&D Center, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
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7
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Hass MR, Liow HH, Chen X, Sharma A, Inoue YU, Inoue T, Reeb A, Martens A, Fulbright M, Raju S, Stevens M, Boyle S, Park JS, Weirauch MT, Brent MR, Kopan R. SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers. Mol Cell 2015; 59:685-97. [PMID: 26257285 DOI: 10.1016/j.molcel.2015.07.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/11/2015] [Accepted: 07/02/2015] [Indexed: 12/20/2022]
Abstract
We developed Split DamID (SpDamID), a protein complementation version of DamID, to mark genomic DNA bound in vivo by interacting or juxtapositioned transcription factors. Inactive halves of DAM (DNA adenine methyltransferase) were fused to protein pairs to be queried. Either direct interaction between proteins or proximity enabled DAM reconstitution and methylation of adenine in GATC. Inducible SpDamID was used to analyze Notch-mediated transcriptional activation. We demonstrate that Notch complexes label RBP sites broadly across the genome and show that a subset of these complexes that recruit MAML and p300 undergo changes in chromatin accessibility in response to Notch signaling. SpDamID differentiates between monomeric and dimeric binding, thereby allowing for identification of half-site motifs used by Notch dimers. Motif enrichment of Notch enhancers coupled with SpDamID reveals co-targeting of regulatory sequences by Notch and Runx1. SpDamID represents a sensitive and powerful tool that enables dynamic analysis of combinatorial protein-DNA transactions at a genome-wide level.
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Affiliation(s)
- Matthew R Hass
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Hien-Haw Liow
- Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, MO 63108, USA
| | - Xiaoting Chen
- School of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH 45221, USA; Center for Autoimmune Genomics and Etiology (CAGE) and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ankur Sharma
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Ashley Reeb
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Andrew Martens
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Mary Fulbright
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Saravanan Raju
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Michael Stevens
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Scott Boyle
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Joo-Seop Park
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Pediatric Urology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Autoimmune Genomics and Etiology (CAGE) and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael R Brent
- Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, MO 63108, USA
| | - Raphael Kopan
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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8
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Additive dominant effect of a SOX10 mutation underlies a complex phenotype of PCWH. Neurobiol Dis 2015; 80:1-14. [PMID: 25959061 DOI: 10.1016/j.nbd.2015.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 04/26/2015] [Accepted: 04/29/2015] [Indexed: 01/26/2023] Open
Abstract
Distinct classes of SOX10 mutations result in peripheral demyelinating neuropathy, central dysmyelinating leukodystrophy, Waardenburg syndrome, and Hirschsprung disease, collectively known as PCWH. Meanwhile, SOX10 haploinsufficiency caused by allelic loss-of-function mutations leads to a milder non-neurological disorder, Waardenburg-Hirschsprung disease. The cellular pathogenesis of more complex PCWH phenotypes in vivo has not been thoroughly understood. To determine the pathogenesis of PCWH, we have established a transgenic mouse model. A known PCWH-causing SOX10 mutation, c.1400del12, was introduced into mouse Sox10-expressing cells by means of bacterial artificial chromosome (BAC) transgenesis. By crossing the multiple transgenic lines, we examined the effects produced by various copy numbers of the mutant transgene. Within the nervous systems, transgenic mice revealed a delay in the incorporation of Schwann cells in the sciatic nerve and the terminal differentiation of oligodendrocytes in the spinal cord. Transgenic mice also showed defects in melanocytes presenting as neurosensory deafness and abnormal skin pigmentation, and a loss of the enteric nervous system. Phenotypes in each lineage were more severe in mice carrying higher copy numbers, suggesting a gene dosage effect for mutant SOX10. By uncoupling the effects of gain-of-function and haploinsufficiency in vivo, we have demonstrated that the effect of a PCWH-causing SOX10 mutation is solely pathogenic in each SOX10-expressing cellular lineage in a dosage-dependent manner. In both the peripheral and central nervous systems, the primary consequence of SOX10 mutations is hypomyelination. The complex neurological phenotypes in PCWH patients likely result from a combination of haploinsufficiency and additive dominant effect.
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9
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Matsunaga E, Okanoya K. Cadherins: potential regulators in the faculty of language. Curr Opin Neurobiol 2014; 28:28-33. [PMID: 24988490 DOI: 10.1016/j.conb.2014.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/20/2014] [Accepted: 06/04/2014] [Indexed: 12/22/2022]
Abstract
The cadherin superfamily is a large (now more than 100 proteins) protein family originally identified as cell adhesion molecules. Each cadherin shows distinct expression patterns in the nervous system, and their expressions are both spatially and temporally regulated and diverse among different species. Mounting evidence has suggested that cadherins play multiple roles in neural development and functions. Recently, using songbirds and mice, the potential role of cadherins in vocal behavior has been demonstrated. Here, we will briefly introduce general function of cadherins, and analyze the potential involvement of cadherins in vocal behaviors and their evolution.
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Affiliation(s)
- Eiji Matsunaga
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, Japan.
| | - Kazuo Okanoya
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan; ERATO Okanoya Emotional Information Project, JST-ERATO, Japan; Emotional Information Joint Research Laboratory, RIKEN Brain Science Institute, Japan.
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10
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Zhao L, Ng ET, Koopman P. ApiggyBactransposon- and gateway-enhanced system for efficient BAC transgenesis. Dev Dyn 2014; 243:1086-94. [DOI: 10.1002/dvdy.24153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 05/20/2014] [Accepted: 06/05/2014] [Indexed: 11/07/2022] Open
Affiliation(s)
- Liang Zhao
- Institute for Molecular Bioscience; The University of Queensland; Brisbane QLD 4072 Australia
| | - Ee Ting Ng
- Institute for Molecular Bioscience; The University of Queensland; Brisbane QLD 4072 Australia
| | - Peter Koopman
- Institute for Molecular Bioscience; The University of Queensland; Brisbane QLD 4072 Australia
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11
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Taneyhill LA, Schiffmacher AT. Cadherin dynamics during neural crest cell ontogeny. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 116:291-315. [PMID: 23481200 DOI: 10.1016/b978-0-12-394311-8.00013-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Cell membrane-associated junctional complexes mediate cell-cell adhesion, intercellular interactions, and other fundamental processes required for proper embryo morphogenesis. Cadherins are calcium-dependent transmembrane proteins at the core of adherens junctions and are expressed in distinct spatiotemporal patterns throughout the development of an important vertebrate cell type, the neural crest. Multipotent neural crest cells arise from the ectoderm as epithelial cells under the influence of inductive cues, undergo an epithelial-to-mesenchymal transition, migrate throughout the embryonic body, and then differentiate into multiple derivatives at predetermined destinations. Neural crest cells change their expressed cadherin repertoires as they undergo each new morphogenetic transition, providing insight into distinct functions of expressed cadherins that are essential for proper completion of each specific stage. Cadherins modulate neural crest cell morphology, segregation, migration, and tissue formation. This chapter reviews the knowledge base of cadherin regulation, expression, and function during the ontogeny of the neural crest.
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Affiliation(s)
- Lisa A Taneyhill
- Department of Animal and Avian Sciences, University of Maryland, 1405 Animal Sciences Center, College Park, Maryland, USA
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12
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XU LIN, WANG ZHU, LI XIAOFEI, HE XIA, GUAN LINLIN, TUO JIULING, WANG YANG, LUO YANFEN, ZHONG HUILING, QIU SHAOPENG, CAO KAIYUAN. Screening and identification of significant genes related to tumor metastasis and PSMA in prostate cancer using microarray analysis. Oncol Rep 2013; 30:1920-8. [DOI: 10.3892/or.2013.2656] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 07/18/2013] [Indexed: 11/06/2022] Open
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Paulson AF, Prasad MS, Thuringer AH, Manzerra P. Regulation of cadherin expression in nervous system development. Cell Adh Migr 2013; 8:19-28. [PMID: 24526207 DOI: 10.4161/cam.27839] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
This review addresses our current understanding of the regulatory mechanisms for classical cadherin expression during development of the vertebrate nervous system. The complexity of the spatial and temporal expression patterns is linked to morphogenic and functional roles in the developing nervous system. While the regulatory networks controlling cadherin expression are not well understood, it is likely that the multiple signaling pathways active in the development of particular domains also regulate the specific cadherins expressed at that time and location. With the growing understanding of the broader roles of cadherins in cell-cell adhesion and non-adhesion processes, it is important to understand both the upstream regulation of cadherin expression and the downstream effects of specific cadherins within their cellular context.
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Affiliation(s)
- Alicia F Paulson
- Division of Basic Biomedical Sciences; Sanford School of Medicine of The University of South Dakota; Vermillion, SD USA
| | - Maneeshi S Prasad
- Department of Molecular Biosciences; Northwestern University; Evanston, IL USA
| | | | - Pasquale Manzerra
- Division of Basic Biomedical Sciences; Sanford School of Medicine of The University of South Dakota; Vermillion, SD USA
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A Peculiarly Cerebroid Convex Zygo-Dodecahedron is an Axiomatically Balanced “House of Blues”: The Circle of Fifths to the Circle of Willis to Cadherin Cadenzas. Symmetry (Basel) 2012. [DOI: 10.3390/sym4040644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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15
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Terakawa YW, Inoue YU, Asami J, Hoshino M, Inoue T. A sharp cadherin-6 gene expression boundary in the developing mouse cortical plate demarcates the future functional areal border. ACTA ACUST UNITED AC 2012; 23:2293-308. [PMID: 22875867 DOI: 10.1093/cercor/bhs221] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mammalian cerebral cortex can be tangentially subdivided into tens of functional areas with distinct cyto-architectures and neural circuitries; however, it remains elusive how these areal borders are genetically elaborated during development. Here we establish original bacterial artificial chromosome transgenic mouse lines that specifically recapitulate cadherin-6 (Cdh6) mRNA expression profiles in the layer IV of the somatosensory cortex and by detailing their cortical development, we show that a sharp Cdh6 gene expression boundary is formed at a mediolateral coordinate along the cortical layer IV as early as the postnatal day 5 (P5). By further applying mouse genetics that allows rigid cell fate tracing with CreERT2 expression, it is demonstrated that the Cdh6 gene expression boundary set at around P4 eventually demarcates the areal border between the somatosensory barrel and limb field at P20. In the P6 cortical cell pellet culture system, neurons with Cdh6 expression preferentially form aggregates in a manner dependent on Ca(2+) and electroporation-based Cdh6 overexpression limited to the postnatal stages perturbs area-specific cell organization in the barrel field. These results suggest that Cdh6 expression in the nascent cortical plate may serve solidification of the protomap for cortical functional areas.
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Affiliation(s)
- Youhei W Terakawa
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
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16
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Prasad MS, Paulson AF. A combination of enhancer/silencer modules regulates spatially restricted expression of cadherin-7 in neural epithelium. Dev Dyn 2011; 240:1756-68. [PMID: 21674686 DOI: 10.1002/dvdy.22675] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The spatially restricted expression of cadherin-7 to the intermediate domain of the neural epithelium and in migrating neural crest cells during early neural development is potentially regulated by multiple signaling inputs. To identify the regulatory modules involved in regulation of cadherin-7, evolutionary conserved non-coding sequences in the cadherin-7 locus were analyzed. This led to the identification of an evolutionary conserved region of 606 bp (ECR1) that together with the cadherin-7 promoter recapitulates endogenous cadherin-7 expression in intermediate neural tube, spinal motor neurons, interneurons, and dorsal root ganglia. Deletion analysis of ECR1 revealed a 19-bp block that is essential for ECR1 enhancer activity, while two separate blocks of 10 and 12 bp were found to be essential for ECR1 silencer activity in the dorsal and ventral neural epithelium, respectively. Together, these data provide an insight into tissue-specific regulatory regions that might be involved in regulation of cadherin-7 gene expression.
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Affiliation(s)
- Maneeshi S Prasad
- Department of Biology, University of South Dakota, Vermillion, South Dakota, USA.
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Smith CL, Baek ST, Sung CY, Tallquist MD. Epicardial-derived cell epithelial-to-mesenchymal transition and fate specification require PDGF receptor signaling. Circ Res 2011; 108:e15-26. [PMID: 21512159 DOI: 10.1161/circresaha.110.235531] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
RATIONALE In early heart development, platelet-derived growth factor (PDGF) receptor expression in the heart ventricles is restricted to the epicardium. Previously, we showed that PDGFRβ is required for coronary vascular smooth muscle cell (cVSMC) development, but a role for PDGFRα has not been identified. Therefore, we investigated the combined and independent roles of these receptors in epicardial development. OBJECTIVE To understand the contribution of PDGF receptors in epicardial development and epicardial-derived cell fate determination. METHODS AND RESULTS By generating mice with epicardial-specific deletion of the PDGF receptors, we found that epicardial epithelial-to-mesenchymal transition (EMT) was defective. Sox9, an SRY-related transcription factor, was reduced in PDGF receptor-deficient epicardial cells, and overexpression of Sox9 restored epicardial migration, actin reorganization, and EMT gene expression profiles. The failure of epicardial EMT resulted in hearts that lacked epicardial-derived cardiac fibroblasts and cVSMC. Loss of PDGFRα resulted in a specific disruption of cardiac fibroblast development, whereas cVSMC development was unperturbed. CONCLUSIONS Signaling through both PDGF receptors is necessary for epicardial EMT and formation of epicardial-mesenchymal derivatives. PDGF receptors also have independent functions in the development of specific epicardial-derived cell fates.
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Affiliation(s)
- Christopher L Smith
- Department of Molecular Biology, MC9148, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
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18
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Asami J, Inoue YU, Terakawa YW, Egusa SF, Inoue T. Bacterial artificial chromosomes as analytical basis for gene transcriptional machineries. Transgenic Res 2010; 20:913-24. [PMID: 21132362 PMCID: PMC3139094 DOI: 10.1007/s11248-010-9469-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 11/23/2010] [Indexed: 11/08/2022]
Abstract
Bacterial Artificial Chromosomes (BACs) had been minimal components of various genome-sequencing projects, constituting perfect analytical basis for functional genomics. Here we describe an enhancer screening strategy in which BAC clones that cover any genomic segments of interest are modified to harbor a reporter cassette by transposon tagging, then processed to carry selected combinations of gene regulatory modules by homologous recombination mediated systematic deletions. Such engineered BAC-reporter constructs in bacterial cells are ready for efficient transgenesis in mice to evaluate activities of gene regulatory modules intact or absent in the constructs. By utilizing the strategy, we could speedily identify a critical genomic fragment for spatio-temporally regulated expression of a mouse cadherin gene whose structure is extraordinarily huge and intricate. This BAC-based methodology would hence provide a novel screening platform for gene transcriptional machineries that dynamically fluctuate during development, pathogenesis and/or evolution.
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Affiliation(s)
- Junko Asami
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
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19
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Shibata S, Yasuda A, Renault-Mihara F, Suyama S, Katoh H, Inoue T, Inoue YU, Nagoshi N, Sato M, Nakamura M, Akazawa C, Okano H. Sox10-Venus mice: a new tool for real-time labeling of neural crest lineage cells and oligodendrocytes. Mol Brain 2010; 3:31. [PMID: 21034515 PMCID: PMC2989948 DOI: 10.1186/1756-6606-3-31] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Accepted: 10/31/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While several mouse strains have recently been developed for tracing neural crest or oligodendrocyte lineages, each strain has inherent limitations. The connection between human SOX10 mutations and neural crest cell pathogenesis led us to focus on the Sox10 gene, which is critical for neural crest development. We generated Sox10-Venus BAC transgenic mice to monitor Sox10 expression in both normal development and in pathological processes. RESULTS Tissue fluorescence distinguished neural crest progeny cells and oligodendrocytes in the Sox10-Venus mouse embryo. Immunohistochemical analysis confirmed that Venus expression was restricted to cells expressing endogenous Sox10. Time-lapse imaging of various tissues in Sox10-Venus mice demonstrated that Venus expression could be visualized at the single-cell level in vivo due to the intense, focused Venus fluorescence. In the adult Sox10-Venus mouse, several types of mature and immature oligodendrocytes along with Schwann cells were clearly labeled with Venus, both before and after spinal cord injury. CONCLUSIONS In the newly-developed Sox10-Venus transgenic mouse, Venus fluorescence faithfully mirrors endogenous Sox10 expression and allows for in vivo imaging of live cells at the single-cell level. This Sox10-Venus mouse will thus be a useful tool for studying neural crest cells or oligodendrocytes, both in development and in pathological processes.
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Affiliation(s)
- Shinsuke Shibata
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
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20
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Fujiyama T, Yamada M, Terao M, Terashima T, Hioki H, Inoue YU, Inoue T, Masuyama N, Obata K, Yanagawa Y, Kawaguchi Y, Nabeshima YI, Hoshino M. Inhibitory and excitatory subtypes of cochlear nucleus neurons are defined by distinct bHLH transcription factors, Ptf1a and Atoh1. Development 2009; 136:2049-58. [PMID: 19439493 DOI: 10.1242/dev.033480] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cochlear nucleus (CN), which consists of dorsal and ventral cochlear nuclei (DCN and VCN), plays pivotal roles in processing and relaying auditory information to the brain. Although it contains various types of neurons, the origins of the distinct subtypes and their developmental molecular machinery are still elusive. Here we reveal that two basic helix-loop-helix transcription factors play crucial roles in specifying neuron subtypes in the CN. Pancreatic transcription factor 1a (Ptf1a) and atonal homolog 1 (Atoh1) were found to be expressed in discrete dorsolateral regions of the embryonic neuroepithelia of the middle hindbrain (rhombomeres 2-5). Genetic lineage tracing using mice that express Cre recombinase from the Ptf1a locus or under the control of the Atoh1 promoter revealed that inhibitory (GABAergic and glycinergic) or excitatory (glutamatergic) neurons of both DCN and VCN are derived from the Ptf1a- and Atoh1-expressing neuroepithelial regions, respectively. In the Ptf1a or Atoh1 null embryos, production of inhibitory or excitatory neurons, respectively, was severely inhibited in the CN. These findings suggest that inhibitory and excitatory subtypes of CN neurons are defined by Ptf1a and Atoh1, respectively and, furthermore, provide important insights into understanding the machinery of neuron subtype specification in the dorsal hindbrain.
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Affiliation(s)
- Tomoyuki Fujiyama
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Kodaira, Tokyo 187-8502, Japan
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Inoue YU, Asami J, Inoue T. Genetic labeling of mouse rhombomeres by Cadherin-6::EGFP-BAC transgenesis underscores the role of cadherins in hindbrain compartmentalization. Neurosci Res 2009; 63:2-9. [DOI: 10.1016/j.neures.2008.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 09/11/2008] [Accepted: 09/17/2008] [Indexed: 01/30/2023]
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Inoue YU, Asami J, Inoue T. Cadherin-6 gene regulatory patterns in the postnatal mouse brain. Mol Cell Neurosci 2008; 39:95-104. [PMID: 18617008 DOI: 10.1016/j.mcn.2008.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Revised: 05/26/2008] [Accepted: 05/28/2008] [Indexed: 11/15/2022] Open
Abstract
Cadherin-6 (Cdh6, K-cadherin) is a synaptic adhesion molecule the expression of which demarcates restricted sets of neuronal circuitries in postnatal mouse brains. While roles for the cadherins in the formation and/or modulation of synaptic junctions have been implicated, that which drives cadherin expression along functional brain circuits has remained elusive. Here we investigate the genetic control of Cdh6 expression by applying a method that permits systematic integration of a reporter cassette into bacterial artificial chromosomes with extensive coverage of the huge Cdh6 gene locus, whereby the reporter activities are efficiently evaluated in stable transgenic mouse lines. Such screenings revealed that divisible genomic segments differentially control each brain region or nucleus specific expression of Cdh6 at the right phases for circuit formation. These separable regulatory modules for cadherin expressions tended to be grouped by working connectivities, suggesting their developmental and/or evolutional value in elaborating brain circuitry.
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Affiliation(s)
- Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo 187-8502, Japan
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