Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus
Cis-regulatory sequences, such as enhancers, control development and physiology by regulating gene expression. The identification and functional characterization of these distal regulatory elements remains challenging, especially in non-model aquatic organisms like sea cucumbers. Apostichopus japoni...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-04-01
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| Series: | Aquaculture Reports |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352513422000369 |
| _version_ | 1828859164871360512 |
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| author | Lili Xing Shilin Liu Libin Zhang Hongsheng Yang Lina Sun |
| author_facet | Lili Xing Shilin Liu Libin Zhang Hongsheng Yang Lina Sun |
| author_sort | Lili Xing |
| collection | DOAJ |
| description | Cis-regulatory sequences, such as enhancers, control development and physiology by regulating gene expression. The identification and functional characterization of these distal regulatory elements remains challenging, especially in non-model aquatic organisms like sea cucumbers. Apostichopus japonicus, an important echinoderm species, exhibits diverse body colour. Pigmentation is an important stage of growth and development in this species, but the regulatory mechanism remains poorly understood, especially the extent to which epigenetic changes regulate pigmentation. Herein, we globally profiled chromatin accessibility using the assay for transposase-accessible chromatin sequencing technique during pigmentation in green, white and purple sea cucumbers. We have got 27, 817 peaks in total and discovered 1427 peaks showing differentially accessed DNA sites across the genome, which were categorized into four distinct clusters via unsupervised hierarchical clustering. Among three colour morphs, white sea cucumber exhibited the most extensive changes and the greatest differences from the other two colour morphs. Global increases in chromatin accessibility occur in the late pigmentation stage suggesting that active function in the late pigmentation stage drives body colour formation. The screened key cis-regulatory elements KIT, RPS6KB2 and IRF8 may contributed to the albinism, slow growth and poor disease resistance of white sea cucumber. In conclusion, our study provides a framework for understanding the accessible chromatin dynamics of body colour diversity during echinoderm pigmentation process and a new avenue to unravel the transcriptional regulatory mechanisms that facilitate the occurrence of relevant molecular events. |
| first_indexed | 2024-12-13T02:12:59Z |
| format | Article |
| id | doaj.art-23af458bb9624ff2a30bc8b257673a5a |
| institution | Directory Open Access Journal |
| issn | 2352-5134 |
| language | English |
| last_indexed | 2024-12-13T02:12:59Z |
| publishDate | 2022-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Aquaculture Reports |
| spelling | doaj.art-23af458bb9624ff2a30bc8b257673a5a2022-12-22T00:02:58ZengElsevierAquaculture Reports2352-51342022-04-0123101040Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicusLili Xing0Shilin Liu1Libin Zhang2Hongsheng Yang3Lina Sun4CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430071, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Correspondence to: CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, Shandong, China.Cis-regulatory sequences, such as enhancers, control development and physiology by regulating gene expression. The identification and functional characterization of these distal regulatory elements remains challenging, especially in non-model aquatic organisms like sea cucumbers. Apostichopus japonicus, an important echinoderm species, exhibits diverse body colour. Pigmentation is an important stage of growth and development in this species, but the regulatory mechanism remains poorly understood, especially the extent to which epigenetic changes regulate pigmentation. Herein, we globally profiled chromatin accessibility using the assay for transposase-accessible chromatin sequencing technique during pigmentation in green, white and purple sea cucumbers. We have got 27, 817 peaks in total and discovered 1427 peaks showing differentially accessed DNA sites across the genome, which were categorized into four distinct clusters via unsupervised hierarchical clustering. Among three colour morphs, white sea cucumber exhibited the most extensive changes and the greatest differences from the other two colour morphs. Global increases in chromatin accessibility occur in the late pigmentation stage suggesting that active function in the late pigmentation stage drives body colour formation. The screened key cis-regulatory elements KIT, RPS6KB2 and IRF8 may contributed to the albinism, slow growth and poor disease resistance of white sea cucumber. In conclusion, our study provides a framework for understanding the accessible chromatin dynamics of body colour diversity during echinoderm pigmentation process and a new avenue to unravel the transcriptional regulatory mechanisms that facilitate the occurrence of relevant molecular events.http://www.sciencedirect.com/science/article/pii/S2352513422000369PigmentationColour morphApostichopus japonicusChromatin accessibilityATAC-seq |
| spellingShingle | Lili Xing Shilin Liu Libin Zhang Hongsheng Yang Lina Sun Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus Aquaculture Reports Pigmentation Colour morph Apostichopus japonicus Chromatin accessibility ATAC-seq |
| title | Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus |
| title_full | Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus |
| title_fullStr | Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus |
| title_full_unstemmed | Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus |
| title_short | Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus |
| title_sort | landscape and dynamics of accessible chromatin during pigmentation process in green white and purple sea cucumber apostichopus japonicus |
| topic | Pigmentation Colour morph Apostichopus japonicus Chromatin accessibility ATAC-seq |
| url | http://www.sciencedirect.com/science/article/pii/S2352513422000369 |
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