Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation

Biotechnology for Biofuels and Bioproducts

Research

Kexin Wang¹  Kexin Feng¹  Xiangchen Gao¹  Yinghong Jin²  Li Wei²  Hongping Wu²  Tongtong Yan²  Wenfei Zhang² 

[1] Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, 571158, Haikou, China;Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, 571158, Haikou, China;Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, 571129, Haikou, China;

关键词: Marine microalgae;    Nannochloropsis;    Chromatin 3D architecture;    Histone modification;    Nitrogen deprivation;   

DOI  :  10.1186/s13068-023-02378-0

 received in 2023-05-17, accepted in 2023-07-29,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundGenomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized.ResultsAccordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the ‘fatty acid metabolism’, ‘response to stress’, ‘carbon fixation’ and ‘photosynthesis’ functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression.ConclusionsOverall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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