Combined analysis of chromatin accessibility and gene expression profiles provide insight into Fucoxanthin biosynthesis in Isochrysis galbana under green light

• Published in: Frontiers in microbiology Vol. 14; p. 1101681
• Main Authors: Chen, Duo, Li, Huan, Chen, Jing, Han, Yuying, Zheng, Xuehai, Xiao, Yixin, Chen, Xupeng, Chen, Tao, Chen, Jiannan, Chen, Youqiang, Xue, Ting
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 10.02.2023
• Subjects: ATAC-seq; fucoxanthin; Isochrysis galbana; Microbiology; RNA-seq; transcription factor; transcription factor; Isochrysis galbana; RNA-seq; fucoxanthin; ATAC-seq
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2023.1101681

, as a potential accumulator of fucoxanthin, has become a valuable material to develop functional foods for humans. Our previous research revealed that green light effectively promotes the accumulation of fucoxanthin in , but there is little research on chromatin accessibility in the process of transcriptional regulation. This study was conducted to reveal the mechanism of fucoxanthin biosynthesis in under green light by analyzing promoter accessibility and gene expression profiles. Differentially accessible chromatin regions (DARs)-associated genes were enriched in carotenoid biosynthesis and photosynthesis-antenna protein formation, including , , , , , , and . The motifs for the MYB family were also identified as candidates controlling metabolic regulation responses to green light culture of , including , , , , , , and . The results of differential expression analysis and WGCNA showed that several genes or transcription factors (TFs) related to carotenoid metabolism and photosynthesis exhibited a higher expression level and were significantly upregulated in A-G5d compared with A-0d and A-W5d, including , , , , and . This suggests that upregulation of these genes by green light may be the key factor leading to fucoxanthin accumulation by regulating the photosynthesis-antenna protein pathway. An integrated analysis of ATAC-seq and RNA-seq showed that 3 ( , , ) of 34 DARs-associated genes displayed obvious changes in their chromatin regions in ATAC-seq data, suggesting that these genes specific for green light may play a key role in fucoxanthin biosynthesis in through a complex regulatory network of multiple metabolic pathways interacting with each other. These findings will facilitate in-depth understanding the molecular regulation mechanisms of fucoxanthin in and its role in response to green light regulation, providing technical support for the construction of high fucoxanthin content strains.