Integration Analysis of ATAC-seq and RNA-seq Provides Insight into Fatty Acid Biosynthesis in Schizochytrium limacinum under Nitrogen Limitation Stress
Schizochytrium limacinum is an important microalga for the commercial production of natural DHA. Previous research has shown that nitrogen-limited treatment can effectively increase the content of fatty acids and DHA, but there is currently no research on chromatin accessibility during the process of transcript regulation. This study aimed to explore the mechanism of fatty acid biosynthesis in S. limacinum under nitrogen-limited treatment by analyzing promoter accessibility and gene expression profiles. The results showed that differentially accessible chromatin regions (DARs)-associated genes were enriched in fatty acid metabolism, degradation, biosynthesis of unsaturated fatty acids, lipid transport and metabolism, signal transduction mechanisms, MYB transcription factors, and energy production and conversion. Some of the identified genes include SlSCP2, SlSLD, SlSNQ2, SlALDH, SlMYB98, and SlMKK. By identifying and annotating DARs-associated motifs, the study obtained 54 target transcription factor classes, including BPC, RAMOSA1, SPI1, MYC, and MYB families. Transcriptomics results revealed that several differentially expressed genes (DEGs), including SlFAD2, SlALDH, SlHSD17B8, SlglpQ, SlACADS, SlSMT1, SlCAS1, SlNSDHL, SlSLC27A4, SlLPCAT2, and SlDGKI, are directly related to the biosynthesis of fatty acids, while SlRPS6KA, SlSTE11, SlCALM, SlCAMK1, SlMYB3R1, and SlMYB3R5 are transcription factors that may be involved in the regulation of fatty acid biosynthesis. In the integration analysis of DARs and ATAC-seq, 13 genes were identified, which were shared by both DEGs and DARs-associated genes, including SlCAKM, SlIFT74, SlRP2, SlSHOC2, SlTN, SlSGK2, SlHMP, SlOGT, SlclpB, and SlDNAAF3. Among them, SlCAKM may act as a negative regulator of fatty acid and DHA synthesis, while SlSGK2 may act as a positive regulator, which requires further study in the future. These findings provide a deeper understanding of the mechanism of fatty acid and DHA biosynthesis and molecular regulation in S. limacinum, and offer theoretical basis and technical support for the construction of high content fatty acid and DHA strains.