Study of FOXL2 Regulation on Ovarian Function in Chlamys farreri Through Comparative ChIP-Seq and Transcriptome Analysis Using RNA Interference

<i>FOXL2</i> (forkhead box protein L2) is a transcription factor, its function and regulatory mechanism have been mainly studied in mammals; related research on marine invertebrates is still insufficient. It was found that oogenesis was affected, and even a small number of cells resembling spermatogonial morphology appeared in <i>C. farreri</i> ovaries after the <i>FOXL2</i> was knocked down through RNA interference (RNAi) technology in our laboratory previously. Based on previous research, this paper conducted transcriptome sequencing and differential expression analysis on the ovarian tissues between the experimental group (post-RNAi) and the control group (pre-RNAi) of <i>C. farreri</i>, and used recombinant <i>C. farreri FOXL2</i> protein for antibody production in Chromatin Immunoprecipitation Sequencing (ChIP seq) experiments to comprehensively analyze the pathways and key genes regulated by <i>FOXL2</i> during oogenesis. The results showed that in the RNAi experimental group, 389 genes were upregulated, and 1615 genes were downregulated. Among the differentially expressed genes (DEGs), the differential genes related to gender or gonadal development are relatively concentrated in physiological processes such as steroid hormone synthesis, spermatogenesis, gonadal development, and ovarian function maintenance, as well as the FoxO and estrogen signaling pathways. Combining transcriptome and ChIP-seq data, it was found that there were some genes related to sex gonadal development among genes which were directly regulated by FOXL2, such as <i>Wnt4</i>, <i>SIRT1</i>, <i>HSD17B8</i>, <i>GABABR1</i>, <i>KRAS</i>, <i>NOTCH1</i>, <i>HSD11B1</i>, <i>cPLA2</i>, <i>ADCY9</i>, <i>IP3R1</i>, <i>PLCB4</i>, and <i>Wnt1</i>. This study lays the foundation for a deeper understanding of the FOXL2's specific regulatory mechanism during oogenesis in scallops as a transcription factor.