Cross-species Regulatory Network Analysis Identifies FOXO1 as a Driver of Ovarian Follicular Recruitment
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE266767 | GEO | 2024/11/19
REPOSITORIES: GEO
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Project description:To investigate the difference between the pre-ovulatory F5 and pre-recruitment follicular stages in laying hens and identify master regulators that control the processes in these two follicular stages. RNA was isolated from a group of 3-5 pre-recruitment follicles and the most recently recruited pre-ovulatory follicle (F5). After RNA isolation, follicles underwent RNA sequencing and differential gene expression analysis occurred.
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Project description:we compared the phosphoproteomes of SY and F6 follicles in laying hens and identified several genes involved in chicken follicle selection.
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Project description:Ovarian follicle selection plays an important role in the reproduction of sexually mature hens, and this process can directly affect the growth and development of follicles until the final ovulation, thus affecting laying performance and fecundity of hens. In the laying hen ovary, one follicle from a cohort of 8-13 follicles of 6-8 mm in diameter is selected daily to enter the preovulatory hierarchy. In this study, we globally compared the proteomes of chicken ovarian follicles before and after follicle selection. A total of 5883 proteins were identified in the proteomes of chicken 6-8 mm prehierarchical follicles and 12-15 mm hierarchical follicles. 259 proteins are differentially expressed in 12-15 mm hierarchical follicle compared with prehierarchical follicle, of which 175 proteins are up-regulated and 84 proteins are down-regulated. The Gene Ontology enrichment of differentially expressed proteins revealed enriched GO terms for peptidase activity, acrosin binding for their molecular function and in the process of negative regulation of peptidase activity, and regulation of fertilization. The KEGG pathway analysis indicated that differentially expressed proteins were enriched for ribosome, lysine degradation, and endocytosis pathways. Nine differentially expressed proteins including vitellogenin-1 were validated with Parallel Reaction Monitoring (PRM) analysis, and their functions were discussed. This study provided a global proteomic view of the development of chicken ovarian follicles, which will serve as a foundation for understanding the molecular signatures and pathways of follicle selection in hens.
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Project description:TMT labeled proteome and acetylated proteome were used to reveal molecular mechanisms adapting to the physiological changes between pre- and peak-laying hens
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Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide varitey of tissues has discovered. The aim of this study are to perform transcriptome profiling (RNA-seq) of magnum to determine differently expressed genes in laying and non-laying hens and to further validate the expression of candidate genes using real-time quantitative reverse transcription polymerase chain reaction (qRT–PCR) in laying, non-laying and molting hens. Methods: Magnum mRNA profiles of 35-60 weeks-old laying and non-laying hens, three each, were generated with NextSeq 500 sequencer in single-end mode with a read length of 1x76 bp. Raw sequencing reads were cleaned and trimmmed with Prinseq tool and good reads were aligned against the chicken reference gemone (Galgal 5.0) in Array Studio. Differential gene expression analysis was performed by the DESeq2 algorithm as implemented in Array Studio. The genes with at least three-fold change (FC) and Benjamini and Hochberg q-value < 0.05 were called differentially expressed. Results: Using an optimized data analysis workflow, we mapped about 30.5 million reads from layers and 33.4 million reads from non-layers to the chicken genome. A total of 19,152 gene transcripts were annotated from Ensembl alignment which represents 50.24% of the chicken genome assembly. Differential gene expression analysis showed 540 were differentially expressed between layer and non-layer hens. 152 DEGs were significantly up-regulated and 388 were significantly down-regulated in the laying hens when compared to the non-laying hens. Conclusions: Our study reports the expression of several pre-discovered and many novel genes that may be involved in the transport of precurosor molecules for biosynthesis and secretion of the egg-white proteins in the magnum. These genes can be used as quantitative basis of selecting hens with an improved egg quality.
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Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide variety of tissues has been discovered. The aim of this study are to perform uterine transcriptome profiling (RNA-seq) to determine differently expressed genes in laying and non-laying hens and to further validate the expression of candidate genes using real-time quantitative reverse transcription polymerase chain reaction (qRT–PCR) in laying, non-laying and molting hens. Methods: Uterine mRNA profiles of 35-60 weeks-old laying and non-laying hens, three each, were generated with NextSeq 500 sequencer in single-end mode with a read length of 1x76 bp. Raw sequencing reads were cleaned and trimmmed with Prinseq tool and good reads were aligned against the chicken reference gemone (Galgal 5.0) in Array Studio. Differential gene expression analysis was performed by the DESeq2 algorithm as implemented in Array Studio. The genes with at least two-fold change (FC) and Benjamini and Hochberg q-value < 0.05 were called differentially expressed. Results: Using an optimized data analysis workflow, we mapped about 32 million reads from layers and 28 million reads from non-layers to the chicken genome. A total of 19,152 gene transcripts were annotated from Ensembl alignment which represents 50.24% of the chicken genome assembly. Differential gene expression analysis showed 616 were differentially expressed between layer and non-layer hens. 229 DEGs were significantly up-regulated and 286 were significantly down-regulated in the laying hens when compared to the non-laying hens. Twelve candiate genes, linked to calcium remodeling, were identified by gene function analysis and validated using qPCR. MEPE, CALCB, OTOP2, STC2 and ATP2C2 were confirmed to be highly expressed in laying hens as compared to molting and non-laying hens. RNA-seq and qPCR data for relative gene expression were highly correlated (R2 =0.99). Conclusions: Our study reports the expression of four novel genes that are speculated to transport calcium ions across the uterine epithellium for eggshell mineralization. These genes can be used as quantitative basis of selecting hens with an improved eggshell quality.
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Project description:Comparing cumulus and granulosa cells from human individual pre-ovulatory follicles after controlled ovarian stimulation
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Project description:Previous work has suggested that the hormones testosterone and corticosterone influence the process of meiotic segregation in the ovarian follicles of laying hens, ultimately influencing whether the resulting egg produces a male or female chick. We tested whether treatment with testosterone and/or corticosterone stimulated changes in the expression of genes that may influence the process of meiotic segregation as a next step towards understanding the mechanism by which these hormones may play a role in sex ratio adjustment in birds.
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Project description:In this study, RNA-Seq technology was adopted to investigate the differences in expression profiles of the hepatic lipid metabolism-related genes and the associated pathways between juvenile and laying hens. RNA-Seq analysis was carried out to estimate total RNA harvested from the liver of juvenile hens (n = 3) and laying hens (n = 3). Compared with juvenile hens, 2574 differentially expressed (DE) genes (1487 down and 1087 up) with P ⤠0.05 were obtained, and 955 of these genes were significantly DE (SDE) at a false discovery rate (FDR) of 0.05 and fold-change ⥠2 in laying hens. There were 198 SDE novel genes (107 down-regulated and 91 up-regulated) (FDR ⤠0.05) that were obtained from the transcriptome, and most of them were highly expressed. Moreover, 332 SDE isoforms were identified. Gene Ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that SDE genes were significantly associated with steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ⤠0.05). The top significantly enriched GO terms included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction suggesting the principal lipogenesis in the liver of laying hens. This study suggests that the major changes at the level of transcriptome in laying hen liver are closely related to fat metabolism. Some highly differentially expressed uncharacterized novel genes and alternative splicing isoforms detected might also take part in lipid metabolism, though it needs investigation. Therefore, this study provides valuable information of mRNA of chicken liver, and deeper functional investigations on the mRNAs could help explore or provide new insights into molecular networks of lipid metabolism in chicken liver. The liver expression profile of juvenile hens and laying hens were generated by RNA-seq.
2016-01-08 | E-GEOD-70010 | biostudies-arrayexpress
Project description:In this study, RNA-Seq technology was adopted to investigate the differences in expression profiles of the hepatic lipid metabolism-related genes and the associated pathways between juvenile and laying hens. RNA-Seq analysis was carried out to estimate total RNA harvested from the liver of juvenile hens (n = 3) and laying hens (n = 3). Compared with juvenile hens, 2574 differentially expressed (DE) genes (1487 down and 1087 up) with P ≤ 0.05 were obtained, and 955 of these genes were significantly DE (SDE) at a false discovery rate (FDR) of 0.05 and fold-change ≥ 2 in laying hens. There were 198 SDE novel genes (107 down-regulated and 91 up-regulated) (FDR ≤ 0.05) that were obtained from the transcriptome, and most of them were highly expressed. Moreover, 332 SDE isoforms were identified. Gene Ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that SDE genes were significantly associated with steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ≤ 0.05). The top significantly enriched GO terms included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction suggesting the principal lipogenesis in the liver of laying hens. This study suggests that the major changes at the level of transcriptome in laying hen liver are closely related to fat metabolism. Some highly differentially expressed uncharacterized novel genes and alternative splicing isoforms detected might also take part in lipid metabolism, though it needs investigation. Therefore, this study provides valuable information of mRNA of chicken liver, and deeper functional investigations on the mRNAs could help explore or provide new insights into molecular networks of lipid metabolism in chicken liver.
2016-01-08 | GSE70010 | GEO