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...
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/178210 2023-05-15T18:43:49+02:00 Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus Xing, Lili Liu, Shilin Zhang, Libin Yang, Hongsheng Sun, Lina 2022-04-01 http://ir.qdio.ac.cn/handle/337002/178209 http://ir.qdio.ac.cn/handle/337002/178210 https://doi.org/10.1016/j.aqrep.2022.101040 英语 eng ELSEVIER AQUACULTURE REPORTS http://ir.qdio.ac.cn/handle/337002/178209 http://ir.qdio.ac.cn/handle/337002/178210 doi:10.1016/j.aqrep.2022.101040 Pigmentation Colour morph Apostichopus japonicus Chromatin accessibility ATAC-seq Fisheries 期刊论文 2022 ftchinacasciocas https://doi.org/10.1016/j.aqrep.2022.101040 2022-07-29T12:11:41Z 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. Report White Sea Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR White Sea Aquaculture Reports 23 101040 |
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Open Polar |
collection |
Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
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ftchinacasciocas |
language |
English |
topic |
Pigmentation Colour morph Apostichopus japonicus Chromatin accessibility ATAC-seq Fisheries |
spellingShingle |
Pigmentation Colour morph Apostichopus japonicus Chromatin accessibility ATAC-seq Fisheries Xing, Lili Liu, Shilin Zhang, Libin Yang, Hongsheng Sun, Lina Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus |
topic_facet |
Pigmentation Colour morph Apostichopus japonicus Chromatin accessibility ATAC-seq Fisheries |
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. |
format |
Report |
author |
Xing, Lili Liu, Shilin Zhang, Libin Yang, Hongsheng Sun, Lina |
author_facet |
Xing, Lili Liu, Shilin Zhang, Libin Yang, Hongsheng Sun, Lina |
author_sort |
Xing, Lili |
title |
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_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_sort |
landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber apostichopus japonicus |
publisher |
ELSEVIER |
publishDate |
2022 |
url |
http://ir.qdio.ac.cn/handle/337002/178209 http://ir.qdio.ac.cn/handle/337002/178210 https://doi.org/10.1016/j.aqrep.2022.101040 |
geographic |
White Sea |
geographic_facet |
White Sea |
genre |
White Sea |
genre_facet |
White Sea |
op_relation |
AQUACULTURE REPORTS http://ir.qdio.ac.cn/handle/337002/178209 http://ir.qdio.ac.cn/handle/337002/178210 doi:10.1016/j.aqrep.2022.101040 |
op_doi |
https://doi.org/10.1016/j.aqrep.2022.101040 |
container_title |
Aquaculture Reports |
container_volume |
23 |
container_start_page |
101040 |
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1766234333076520960 |