Expression characteristics and potential function of non-coding RNA in mouse cortical cells
Non-coding RNAs (ncRNAs) play essential regulatory functions in various physiological and pathological processes in the brain. To systematically characterize the ncRNA profile in cortical cells, we downloaded single-cell SMART-Seq v4 data of mouse cerebral cortex. Our results revealed that the ncRNA...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-04-01
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| Series: | Frontiers in Molecular Neuroscience |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnmol.2024.1365978/full |
| _version_ | 1827288684908511232 |
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| author | Yanrong Wei Yanrong Wei Junjie Lei Junjie Lei Yujie Peng Huizhong Chang Ting Luo Yuanchun Tang Yuanchun Tang Lifang Wang Huiying Wen Huiying Wen Giacomo Volpe Longqi Liu Longqi Liu Lei Han Lei Han |
| author_facet | Yanrong Wei Yanrong Wei Junjie Lei Junjie Lei Yujie Peng Huizhong Chang Ting Luo Yuanchun Tang Yuanchun Tang Lifang Wang Huiying Wen Huiying Wen Giacomo Volpe Longqi Liu Longqi Liu Lei Han Lei Han |
| author_sort | Yanrong Wei |
| collection | DOAJ |
| description | Non-coding RNAs (ncRNAs) play essential regulatory functions in various physiological and pathological processes in the brain. To systematically characterize the ncRNA profile in cortical cells, we downloaded single-cell SMART-Seq v4 data of mouse cerebral cortex. Our results revealed that the ncRNAs alone are sufficient to define the identity of most cortical cell types. We identified 1,600 ncRNAs that exhibited cell type specificity, even yielding to distinguish microglia from perivascular macrophages with ncRNA. Moreover, we characterized cortical layer and region specific ncRNAs, in line with the results by spatial transcriptome (ST) data. By constructing a co-expression network of ncRNAs and protein-coding genes, we predicted the function of ncRNAs. By integrating with genome-wide association studies data, we established associations between cell type-specific ncRNAs and traits related to neurological disorders. Collectively, our study identified differentially expressed ncRNAs at multiple levels and provided the valuable resource to explore the functions and dysfunctions of ncRNAs in cortical cells. |
| first_indexed | 2024-04-24T11:35:55Z |
| format | Article |
| id | doaj.art-16a8960dd76f4b51871b54f7c9dbbf81 |
| institution | Directory Open Access Journal |
| issn | 1662-5099 |
| language | English |
| last_indexed | 2024-04-24T11:35:55Z |
| publishDate | 2024-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Neuroscience |
| spelling | doaj.art-16a8960dd76f4b51871b54f7c9dbbf812024-04-10T05:20:58ZengFrontiers Media S.A.Frontiers in Molecular Neuroscience1662-50992024-04-011710.3389/fnmol.2024.13659781365978Expression characteristics and potential function of non-coding RNA in mouse cortical cellsYanrong Wei0Yanrong Wei1Junjie Lei2Junjie Lei3Yujie Peng4Huizhong Chang5Ting Luo6Yuanchun Tang7Yuanchun Tang8Lifang Wang9Huiying Wen10Huiying Wen11Giacomo Volpe12Longqi Liu13Longqi Liu14Lei Han15Lei Han16College of Life Sciences, University of Chinese Academy of Sciences, Beijing, ChinaBGI Research, Hangzhou, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing, ChinaBGI Research, Hangzhou, ChinaBGI Research, Hangzhou, ChinaBGI Research, Hangzhou, ChinaBGI Research, Hangzhou, ChinaBGI Research, Hangzhou, ChinaBGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, ChinaBGI Research, Hangzhou, ChinaBGI Research, Hangzhou, ChinaSchool of Biology and Biological Engineering, South China University of Technology, Guangzhou, ChinaHematology and Cell Therapy Unit, IRCCS–Istituto Tumori ‘Giovanni Paolo II’, Bari, ItalyCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing, ChinaBGI Research, Hangzhou, ChinaBGI Research, Hangzhou, ChinaBGI Research, Shenzhen, ChinaNon-coding RNAs (ncRNAs) play essential regulatory functions in various physiological and pathological processes in the brain. To systematically characterize the ncRNA profile in cortical cells, we downloaded single-cell SMART-Seq v4 data of mouse cerebral cortex. Our results revealed that the ncRNAs alone are sufficient to define the identity of most cortical cell types. We identified 1,600 ncRNAs that exhibited cell type specificity, even yielding to distinguish microglia from perivascular macrophages with ncRNA. Moreover, we characterized cortical layer and region specific ncRNAs, in line with the results by spatial transcriptome (ST) data. By constructing a co-expression network of ncRNAs and protein-coding genes, we predicted the function of ncRNAs. By integrating with genome-wide association studies data, we established associations between cell type-specific ncRNAs and traits related to neurological disorders. Collectively, our study identified differentially expressed ncRNAs at multiple levels and provided the valuable resource to explore the functions and dysfunctions of ncRNAs in cortical cells.https://www.frontiersin.org/articles/10.3389/fnmol.2024.1365978/fullnon-coding RNAsingle-cell SMART-Seq v4cerebral cortexcell-type specific noncoding RNAspatial transcriptomehdWGCNA |
| spellingShingle | Yanrong Wei Yanrong Wei Junjie Lei Junjie Lei Yujie Peng Huizhong Chang Ting Luo Yuanchun Tang Yuanchun Tang Lifang Wang Huiying Wen Huiying Wen Giacomo Volpe Longqi Liu Longqi Liu Lei Han Lei Han Expression characteristics and potential function of non-coding RNA in mouse cortical cells Frontiers in Molecular Neuroscience non-coding RNA single-cell SMART-Seq v4 cerebral cortex cell-type specific noncoding RNA spatial transcriptome hdWGCNA |
| title | Expression characteristics and potential function of non-coding RNA in mouse cortical cells |
| title_full | Expression characteristics and potential function of non-coding RNA in mouse cortical cells |
| title_fullStr | Expression characteristics and potential function of non-coding RNA in mouse cortical cells |
| title_full_unstemmed | Expression characteristics and potential function of non-coding RNA in mouse cortical cells |
| title_short | Expression characteristics and potential function of non-coding RNA in mouse cortical cells |
| title_sort | expression characteristics and potential function of non coding rna in mouse cortical cells |
| topic | non-coding RNA single-cell SMART-Seq v4 cerebral cortex cell-type specific noncoding RNA spatial transcriptome hdWGCNA |
| url | https://www.frontiersin.org/articles/10.3389/fnmol.2024.1365978/full |
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