Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus

doi:10.1016/j.aqrep.2022.101040

	Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus
	Xing, Lili1,2,3,4,5 ; Liu, Shilin 1,2,3,4,5; Zhang, Libin 1,2,3,4,5,6; Yang, Hongsheng1,2,3,4,5,7 ; Sun, Lina 1,2,3,4,5
	2022-04-01
发表期刊	AQUACULTURE REPORTS
ISSN	2352-5134
卷号	23 页码:12
通讯作者	Sun, Lina(sunlina@qdio.ac.cn)
摘要	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.
关键词	Pigmentation Colour morph Apostichopus japonicus Chromatin accessibility ATAC-seq
DOI	10.1016/j.aqrep.2022.101040
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2018YFD0901602] ; Natural Science Foundation of Shandong Province Youth Program[ZR2020QD100] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA24030304] ; Agricultural Seed Project of Shandong Province[2020LZGC015] ; China Postdoctoral Science Foundation[2019M662457]
WOS研究方向	Fisheries
WOS类目	Fisheries
WOS记录号	WOS:000761305200003
出版者	ELSEVIER
引用统计
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/178210
专题	海洋生态与环境科学重点实验室
通讯作者	Sun, Lina
作者单位	1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao 266071, Shandong, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao 266237, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao 266071, Peoples R China 4.Chinese Acad Sci, Inst Oceanol, CAS Engn Lab Marine Ranching, Qingdao 266071, Peoples R China 5.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 6.Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 7.Chinese Acad Sci, Innovat Seed Design, Wuhan 430071, Peoples R China
第一作者单位	中国科学院海洋研究所; 中国科学院海洋大科学研究中心
通讯作者单位	中国科学院海洋研究所; 中国科学院海洋大科学研究中心
推荐引用方式 GB/T 7714	Xing, Lili,Liu, Shilin,Zhang, Libin,et al. Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus[J]. AQUACULTURE REPORTS,2022,23:12.
APA	Xing, Lili,Liu, Shilin,Zhang, Libin,Yang, Hongsheng,&Sun, Lina.(2022).Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus.AQUACULTURE REPORTS,23,12.
MLA	Xing, Lili,et al."Landscape and dynamics of accessible chromatin during pigmentation process in green, white and purple sea cucumber Apostichopus japonicus".AQUACULTURE REPORTS 23(2022):12.

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