Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing
Abstract The nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2018-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-018-19494-9 |
| _version_ | 1818345516630540288 |
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| author | Mari Mito Mitsutaka Kadota Kaori Tanaka Yasuhide Furuta Kuniya Abe Shintaro Iwasaki Shinichi Nakagawa |
| author_facet | Mari Mito Mitsutaka Kadota Kaori Tanaka Yasuhide Furuta Kuniya Abe Shintaro Iwasaki Shinichi Nakagawa |
| author_sort | Mari Mito |
| collection | DOAJ |
| description | Abstract The nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq). FLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner. Subsequent chromatin immunoprecipitation using antibodies against H3K4me3—a chromatin modification mainly associated with active promoters—allowed us to survey the histone modifications in Camk2a-positive neurons. Indeed, tChIP-Seq identified hundreds of H3K4me3 modifications in promoter regions located upstream of genes associated with neuronal functions and genes with unknown functions in cortical neurons. tChIP-Seq provides a versatile approach to investigating the epigenetic modifications of particular cell types in vivo. |
| first_indexed | 2024-12-13T17:03:37Z |
| format | Article |
| id | doaj.art-b817dfc4416a44bf93684049f0cb2b37 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-13T17:03:37Z |
| publishDate | 2018-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-b817dfc4416a44bf93684049f0cb2b372022-12-21T23:37:45ZengNature PortfolioScientific Reports2045-23222018-01-018111410.1038/s41598-018-19494-9Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation SequencingMari Mito0Mitsutaka Kadota1Kaori Tanaka2Yasuhide Furuta3Kuniya Abe4Shintaro Iwasaki5Shinichi Nakagawa6RNA Biology Laboratory, RIKEN, 2-1 HirosawaPhyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-Minamimachi, Chuou-kuPhyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-Minamimachi, Chuou-kuAnimal Resource Development Unit and RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-kuTechnology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Center, 3-1-1 Koyadai, TsukubaRNA Systems Biochemistry Laboratory, RIKEN, 2-1 HirosawaRNA Biology Laboratory, RIKEN, 2-1 HirosawaAbstract The nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq). FLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner. Subsequent chromatin immunoprecipitation using antibodies against H3K4me3—a chromatin modification mainly associated with active promoters—allowed us to survey the histone modifications in Camk2a-positive neurons. Indeed, tChIP-Seq identified hundreds of H3K4me3 modifications in promoter regions located upstream of genes associated with neuronal functions and genes with unknown functions in cortical neurons. tChIP-Seq provides a versatile approach to investigating the epigenetic modifications of particular cell types in vivo.https://doi.org/10.1038/s41598-018-19494-9 |
| spellingShingle | Mari Mito Mitsutaka Kadota Kaori Tanaka Yasuhide Furuta Kuniya Abe Shintaro Iwasaki Shinichi Nakagawa Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing Scientific Reports |
| title | Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing |
| title_full | Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing |
| title_fullStr | Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing |
| title_full_unstemmed | Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing |
| title_short | Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing |
| title_sort | cell type specific survey of epigenetic modifications by tandem chromatin immunoprecipitation sequencing |
| url | https://doi.org/10.1038/s41598-018-19494-9 |
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