Systematic Analysis of Long Noncoding RNA and mRNA in Granulosa Cells during the Hen Ovulatory Cycle

SIMPLE SUMMARY: Chicken is one of the most economically important farm poultry, and providing many food products, such as meat and eggs for human consumption. However, follicle transcriptome studies in chickens with timepoints relating to changes in luteinizing hormone level remain unknown. In this study, the largest preovulatory follicle of chicken underwent the early, middle, and terminal stages of ovulatory cycle. Our work provides a comprehensive analysis of lncRNAs and mRNAs in chicken granulosa cells during the ovulatory cycle. A total of 12,479 mRNAs and 7528 lncRNAs were identified among the three stages. Thousands of lncRNAs were annotated, and the most differentially abundant genes were detected in the luteinizing hormone surge stage. Functional features of the lncRNAs and mRNAs at each stage were revealed, which was also associated with the changes in serum luteinizing hormone level. Especially, genes related to oxidative stress, steroids regulation, and inflammatory process were enriched in the luteinizing hormone surge stage, The comprehensive data generated in this study provides the foundation for future investigations to improve the reproductive performance of chickens and explore the mechanisms responsible for female ovarian diseases. ABSTRACT: Long non-coding RNAs (lncRNAs) and mRNAs are temporally expressed during chicken follicle development. However, follicle transcriptome studies in chickens with timepoints relating to changes in luteinizing hormone (LH) levels are rare. In this study, gene expression in Rohman layers was investigated at three distinct stages of the ovulatory cycle: zeitgeber time 0 (ZT0, 9:00 a.m.), zeitgeber time 12 (ZT12, 9:00 p.m.), and zeitgeber time 20 (ZT20, 5:00 a.m.) representing the early, middle, and LH surge stages, respectively, of the ovulatory cycle. Gene expression profiles were explored during follicle development at ZT0, ZT12, and ZT20 using Ribo-Zero RNA sequencing. The three stages were separated into two major stages, including the pre-LH surge and the LH surge stages. A total of 12,479 mRNAs and 7528 lncRNAs were identified among the three stages, and 4531, 523 differentially expressed genes (DEGs) and 2367, 211 differentially expressed lncRNAs (DELs) were identified in the ZT20 vs. ZT12, and ZT12 vs. ZT0, comparisons. Functional enrichment analysis revealed that genes involved in cell proliferation and metabolism processes (lipid-related) were mainly enriched in the ZT0 and ZT12 stages, respectively, and genes related to oxidative stress, steroids regulation, and inflammatory process were enriched in the ZT20 stage. These findings provide the basis for further investigation of the specific genetic and molecular functions of follicle development in chickens.