RNA-Seq of chicken embryo liver reveals transcriptional pathways influenced by egg formaldehyde treatment

Authors: OZDEMIR, MUSTAFA - Erciyes University; SAJID, GHULAM ASGHAR - Erciyes University; BEYZI, SELMA - Erciyes University; KIZILASLAN, MEHMET - University Of Wisconsin; ARZIK, YUNUS - Aksaray University; YALCIN, SERVET - Ege University; White, Stephen; CINAR, MEHMET ULAS - Erciyes University

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/16/2025
Publication Date: 4/22/2025
Citation: Ozdemir, M., Sajid, G., Beyzi, S.B., Kizilaslan, M., Arzik, Y., Yalcin, S., White, S.N., Cinar, M. 2025. RNA-Seq of Chicken Embryo Liver Reveals Transcriptional Pathways Influenced by Egg Formaldehyde Treatment. Genes. 16(5): 471. https://doi.org/10.3390/genes16050471.
DOI: https://doi.org/10.3390/genes16050471

Interpretive Summary: Hatchery fumigation is recognized as a crucial step for microbe control, and formaldehyde is one of the most widely used disinfectants to ensure successful hatchability and healthy production. While many of the benefits are thought to be derived from disinfectant properties, it is possible that additional host gene activation could contribute to these outcomes. To begin to assess such possibilities, the current study aimed to capture gene activation data from chick embryos following egg formaldehyde treatment. Bioinformatics analysis revealed 908 differentially expressed genes (DEGs), among which 814 were known genes and 94 were novel genes. Key DEGs and transcription factors were involved in immuno-inflammatory responses, oxidative stress, epigenetic modification and cellular adaptation related activities. Once these genes and pathways are more fully understood, they could empower breeding programs to enhance egg and poultry production systems. Specifically, these findings could 1) empower genetic selection to improve FA treatment response and effectiveness across the population, and 2) they could point to other interventions that would activate similar genes or pathways to achieve hatchability and production benefits.

Technical Abstract: Hatchery fumigation is recognized as a crucial step to control the microbial bloom in the environment, and formaldehyde is one of the most widely used disinfectants to ensure successful hatchability and healthy production. While many of the benefits are thought to be derived from disinfectant properties, it is possible that additional host gene and genetic pathway modulation could contribute to these outcomes. The current study aimed to capture the in ovo transcriptional response of liver tissue to formaldehyde treatment. Chick embryos were subjected to formaldehyde fumigation treatment for 25 minutes at 24-25°C and 75% relative humidity, keeping a control group as untreated. On the 18th day of incubation at 37.8°C and 58-63% humidity, eggs were broken, and liver tissue were obtained for RNA isolation, cDNA library preparation and RNA sequencing. Bioinformatics analysis revealed 908 significant differentially expressed genes (DEGs), among which 814 were known genes and 94 were novel genes. Key DEGs and transcription factors were involved in immuno-inflammatory responses, oxidative stress, epigenetic modification and cellular adaptation related activities. Once these genes and pathways are more fully understood, they could empower breeding programs to enhance egg and poultry production systems. Specifically, these findings could 1) empower genetic selection to improve FA treatment response and effectiveness across the population, and 2) they could point to other interventions that would activate similar genes or pathways to achieve hatchability and production benefits.