Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensis
Discontinuous muscle growth during molting is an important feature of Eriocheir sinensis. Molting is a physiological process completed by the cooperation of multiple organs. Signal transmission is critical for the accurate regulation of each step in molting. However, the knowledge of the signal tran...
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2022.900160/full |
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| author | Zhanpeng Sun Zhanpeng Sun Jingjing Li Li Lv Li Lv Yifei Gou Yifei Gou Bin Wang Bin Wang Tong Hao Tong Hao |
| author_facet | Zhanpeng Sun Zhanpeng Sun Jingjing Li Li Lv Li Lv Yifei Gou Yifei Gou Bin Wang Bin Wang Tong Hao Tong Hao |
| author_sort | Zhanpeng Sun |
| collection | DOAJ |
| description | Discontinuous muscle growth during molting is an important feature of Eriocheir sinensis. Molting is a physiological process completed by the cooperation of multiple organs. Signal transmission is critical for the accurate regulation of each step in molting. However, the knowledge of the signal transduction mechanism in the molting process of E. sinensis is presently very limited. In this work, the chromatin accessibility and gene expression of the muscle in E. sinensis in pre-molt (D) and post-molt (A) stages were sequenced by assay of transposase accessible chromatin sequencing (ATAC-seq) and RNA-seq, respectively. The differentially expressed genes (DEGs) in the muscle before and after molting were analyzed by combining ATAC-seq and RNA-seq, especially the G-protein coupled receptor (GPCR) genes in the process of signal transduction. The results showed that there were 616 common DEGs in ATAC-seq and RNA-seq in A vs. D stages, of which 538 were upregulated and 78 were downregulated. In the 19 DEGs included in the signaling transduction process, 13 were located in the GPCR signaling pathway and all were upregulated in A stages, which indicated that GPCRs play a leading role in muscle signal transmission during post-molt stage in molting. In these genes, the structure of the proteins encoded by 10 membrane-located genes with transmembrane activity was further analyzed. Six candidate GPCR genes were finally identified and further verified by real-time quantitative PCR (qRT-PCR). The GPCRs include metabotropic glutamate receptor 7, Mth-like 4, and Mth2 proteins. These results show the existence of GPCRs in the muscle of E. sinensis and, for the first time, found their dominant role in the signal transduction process during molting. It provides important clues for the study of muscle discontinuous growth and molting mechanism of E. sinensis. |
| first_indexed | 2024-04-14T03:42:27Z |
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| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-04-14T03:42:27Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Marine Science |
| spelling | doaj.art-90bceef9dc5c4a9fa0918fe61cb2a77a2022-12-22T02:14:26ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452022-07-01910.3389/fmars.2022.900160900160Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensisZhanpeng Sun0Zhanpeng Sun1Jingjing Li2Li Lv3Li Lv4Yifei Gou5Yifei Gou6Bin Wang7Bin Wang8Tong Hao9Tong Hao10Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, ChinaFaculty of Education, Tianjin Normal University, Tianjin, ChinaTianjin Fisheries Research Institute, Tianjin, ChinaTianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, ChinaCollege of Life Sciences, Tianjin Normal University, Tianjin, ChinaTianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, ChinaCollege of Life Sciences, Tianjin Normal University, Tianjin, ChinaTianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, ChinaCollege of Life Sciences, Tianjin Normal University, Tianjin, ChinaTianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, ChinaCollege of Life Sciences, Tianjin Normal University, Tianjin, ChinaDiscontinuous muscle growth during molting is an important feature of Eriocheir sinensis. Molting is a physiological process completed by the cooperation of multiple organs. Signal transmission is critical for the accurate regulation of each step in molting. However, the knowledge of the signal transduction mechanism in the molting process of E. sinensis is presently very limited. In this work, the chromatin accessibility and gene expression of the muscle in E. sinensis in pre-molt (D) and post-molt (A) stages were sequenced by assay of transposase accessible chromatin sequencing (ATAC-seq) and RNA-seq, respectively. The differentially expressed genes (DEGs) in the muscle before and after molting were analyzed by combining ATAC-seq and RNA-seq, especially the G-protein coupled receptor (GPCR) genes in the process of signal transduction. The results showed that there were 616 common DEGs in ATAC-seq and RNA-seq in A vs. D stages, of which 538 were upregulated and 78 were downregulated. In the 19 DEGs included in the signaling transduction process, 13 were located in the GPCR signaling pathway and all were upregulated in A stages, which indicated that GPCRs play a leading role in muscle signal transmission during post-molt stage in molting. In these genes, the structure of the proteins encoded by 10 membrane-located genes with transmembrane activity was further analyzed. Six candidate GPCR genes were finally identified and further verified by real-time quantitative PCR (qRT-PCR). The GPCRs include metabotropic glutamate receptor 7, Mth-like 4, and Mth2 proteins. These results show the existence of GPCRs in the muscle of E. sinensis and, for the first time, found their dominant role in the signal transduction process during molting. It provides important clues for the study of muscle discontinuous growth and molting mechanism of E. sinensis.https://www.frontiersin.org/articles/10.3389/fmars.2022.900160/fullATAC-seqRNA-seqEriocheir sinensisG-protein coupled receptormolting |
| spellingShingle | Zhanpeng Sun Zhanpeng Sun Jingjing Li Li Lv Li Lv Yifei Gou Yifei Gou Bin Wang Bin Wang Tong Hao Tong Hao Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensis Frontiers in Marine Science ATAC-seq RNA-seq Eriocheir sinensis G-protein coupled receptor molting |
| title | Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensis |
| title_full | Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensis |
| title_fullStr | Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensis |
| title_full_unstemmed | Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensis |
| title_short | Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensis |
| title_sort | integration of atac seq and rna seq identifies active g protein coupled receptors functioning in molting process in muscle of eriocheir sinensis |
| topic | ATAC-seq RNA-seq Eriocheir sinensis G-protein coupled receptor molting |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2022.900160/full |
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