Oogenesis specific genes (Nobox,Oct4,Bmp15,Gdf9,Oogenesin1andOogenesin2) are differentially expressed during natural and gonadotropin-induced mouse follicular development

AbstractOvary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.

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Large-Scale Metadata Analysis of Ovary Based Multi-Omics Datasets for Understanding the Genes Regulating Litter Size

10.21203/rs.3.rs-22487/v1 ◽

2020 ◽

Author(s):

Ayyappa Kumar Sista Kameshwar ◽

Julang Li

Keyword(s):

Gene Expression ◽

Differentially Expressed Genes ◽

Litter Size ◽

Large Scale ◽

Expression Patterns ◽

Genetic Selection ◽

Follicular Development ◽

Oocyte Quality ◽

Differentially Expressed ◽

Metadata Analysis

Abstract Background : Litter size is a very important production index in the livestock industry, which is controlled by various complex physiological processes. To understand and reveal the common gene expression patterns involved in controlling prolificacy, we have performed a large-scale metadata analysis of five genome-wide transcriptome datasets of pig and sheep ovary samples obtained from high and low litter groups, respectively. We analyzed separately each transcriptome dataset using GeneSpring v14.8 software by implementing standard, generic analysis pipelines and further compared the list of most significant and differentially expressed genes obtained from each dataset to identify genes that are found to be common and significant across all the studies. Results : We have observed a total of 62 differentially expressed genes common among more than two gene expression datasets. The KEGG pathway analysis of most significant genes has shown that they are involved in metabolism, the biosynthesis of lipids, cholesterol and steroid hormones, immune system, cell growth and death, cancer-related pathways and signal transduction pathways. Of these 62 genes, we further narrowed the list to the 25 most significant genes by focusing on the ones with fold change >1.5 and p<0.05. These genes are CYP11A1, HSD17B2, STAR, SCARB1, IGSF8, MSMB, SERPINA1 , FAM46C, HEXA, PTTG1, TIMP1, FAM167B, CCNG1, FAXDC2, HMGCS1, L2HGDH, Lipin1, MME, MSMO1, PARM1, PTGFR, SLC22A4, SLC35F5, CCNA2, CENPU, CEP55, RASSF2, and SLC16A3 . Conclusions : Interestingly, comparing the list of genes with the list of genes obtained from our literature search analysis, we found only three genes in common. These genes are HEXA, PTTG1, and TIMP1. Our finding points to the potential of a few genes that may be important for ovarian follicular development and oocyte quality. Future studies revealing the function of these genes will further our understanding of how litter size is controlled in the ovary while also providing insight on genetic selection of high litter gilts.

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Exploring differentially expressed key genes related to development of follicle by RNA-seq in Peking ducks (Anas Platyrhynchos)

10.1101/483818 ◽

2018 ◽

Author(s):

Jindong Ren ◽

Changsen Sun ◽

Li Chen ◽

Jianhong Hu ◽

Xuetao Huang ◽

...

Keyword(s):

Expression Profiles ◽

Expression Patterns ◽

Follicular Development ◽

Egg Laying ◽

Differentially Expressed ◽

Transcriptional Analysis ◽

Follicle Development ◽

Hormone Synthesis ◽

Key Genes ◽

Reproductive Phases

AbstractDuck follicle enter different reproductive phases throughout life, and follicle gene expression patterns differ according to these phases. In particular, differentially expressed genes and related to development of follicle (mRNAs) play an important role to explore the key genes in this process; however, the expression profiles of these genes remain unclear. In this study, transcriptome sequencing was used to investigate the expression levels of duck ovarian genes, and comparative transcriptional analysis was carried out to identify differential genes, cluster them into groups and function identification. The results showed differential expression of 593 coding genes between young and laying ducks, and of 518 coding genes between laying and old ducks. In further GO analysis, 35 genes from the comparison bewtween old ducks and laying ducks have significant been changed involved in hormones related to follicle development. They include up-regulated genes StAR, CYP17, EPOX, 3β-HSD, CYP1B1 CYP19A1 and down-regulated genes SR-B1 in laying ducks hormone synthesis than old ducks. Among which EPOX is a key gene for time special highly expression during egg laying stage, and other key regulatory genes’ highly expression showed in young and laying stage and lower expression showing with follicular development stopping. Therefore, EPOX is key regulator for duck follicle development in laying period, when its expression level decrease 98% the follicular development will stopping in duck life cycle.

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Unraveling proteome changes and potential regulatory proteins of bovine follicular Granulosa cells by mass spectrometry and multi-omics analysis

Proteome Science ◽

10.1186/s12953-019-0152-1 ◽

2019 ◽

Vol 17 (1) ◽

Cited By ~ 1

Author(s):

Shuning Hou ◽

Qingling Hao ◽

Zhiwei Zhu ◽

Dongmei Xu ◽

Wenzhong Liu ◽

...

Keyword(s):

Mass Spectrometry ◽

Data Analysis ◽

Pathway Analysis ◽

Kegg Pathway ◽

Follicular Development ◽

Regulatory Proteins ◽

Differentially Expressed ◽

Omics Data ◽

Kegg Pathway Analysis ◽

Omics Data Analysis

Abstract Background In previous study, we performed next-gene sequencing to investigate the differentially expressed transcripts of bovine follicular granulosa cells (GCs) at dominant follicle (DF) and subordinate follicle (SF) stages during first follicular wave. Present study is designed to further identify the key regulatory proteins and signaling pathways associated with follicular development using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) and multi-omics data analysis approach. Methods DF and SF from three cattle were collected by daily ultrasonography. The GCs were isolated from each follicle, total proteins were digested by trypsin, and then proteomic analyzed via LC-MS/MS, respectively. Proteins identified were retrieved from Uniprot-COW fasta database, and differentially expressed proteins were used to functional enrichment and KEGG pathway analysis. Proteome data and transcriptome data obtained from previous studies were integrated. Results Total 3409 proteins were identified from 30,321 peptides (FDR ≤0.01) obtained from LC-MS/MS analysis and 259 of them were found to be differentially expressed at different stage of follicular development (fold Change > 2, P < 0.05). KEGG pathway analysis of proteome data revealed important signaling pathways associated with follicular development, multi-omics data analysis results showed 13 proteins were identified as being differentially expressed in DF versus SF. Conclusions This study represents the first investigation of transcriptome and proteome of bovine follicles and offers essential information for future investigation of DF and SF in cattle. It also will enrich the theory of animal follicular development.

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Transcriptomic and proteomic analyses between small yellow follicles and the smallest hierarchical follicles reveal a role of VLDLR in chicken follicle selection

10.21203/rs.2.17247/v1 ◽

2019 ◽

Author(s):

Qiuyue Chen ◽

Yiya Wang ◽

Zemin Liu ◽

Xiaoli Guo ◽

Yi Sun ◽

...

Keyword(s):

Laying Hens ◽

Follicular Development ◽

Differentially Expressed ◽

Integrated Analysis ◽

Functional Genes ◽

Differentially Expressed Proteins ◽

Important Process ◽

Laying Performance ◽

Follicle Selection

Abstract Background Follicle selection in chicken refers to the process of selecting one from a group of small yellow follicles (SY, 6-8mm in diameter) to enter the 12-15 mm hierarchical follicles (usually F6 follicles), which is a an important process affecting laying performance in the poultry industry. Although transcripromic analysis on chicken ovarian follicles was reported, integrated analysis on chicken follicles around selection by using both transcripromic and proteomic approaches was still lacking. In this study, we compared the proteomes and transcriptomes of SY and F6 follicles of laying hens and found some genes involved in chicken follicle selection.Results Transcriptomic analysis revealed 855 differentially expressed genes (DEGs) between SY follicles and F6 follicles of laying hens, among which 202 were upregulated and 653 were downregulated. Proteomic analysis revealed 259 differentially expressed proteins (DEPs), including 175 upregulated and 84 downregulated proteins. Among the identified DEGs and DEPs, the expression changes of seven genes including VLDLR1,WIF1, NGFR, AMH, BMP15, GDF6 and MMP13 , and nine proteins including VLDLR, VTG1, VTG3, PSCA, APOB, APOV1, F10, ZP2 and ZP3L2 were validated. In addition VLDLR expression was significantly down-regulated in F6 follicles compared with SY follicles, was signifcantly higher in the GCs than in the TCs and was stimulated by FSH in GCs of both hierarchical and prehierarchical follicles.Conclusions By comparing the proteomes and transcriptomes of SY follicles and F6 of laying hens, we identified some differentially expressed proteins/genes that might play certain roles in chicken follicle selection. These data may contribute to identification of the functional genes and proteins involved in chicken follicular development and selection.

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Identification of circular RNAs in the ovarian follicles of Meishan and Duroc sows during the follicular phase

Journal of Ovarian Research ◽

10.1186/s13048-020-00709-5 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Su Xie ◽

Mengxun Li ◽

Yansen Chen ◽

Yi Liu ◽

Lipeng Ma ◽

...

Keyword(s):

Follicular Development ◽

Ovarian Follicles ◽

Follicular Phase ◽

Differentially Expressed ◽

Circular Rnas ◽

Rna Seq ◽

Rt Pcr ◽

Reverse Transcription Pcr ◽

New Perspective

Abstract Circular RNAs (circRNAs) are a newly discovered class of endogenous non-coding RNAs that play an important role in growth and development by regulating gene expression and participating in a variety of biological processes. However, the role of circRNAs in porcine follicles remains unclear. Therefore, this study examined middle-sized ovarian follicles obtained from Meishan and Duroc sows at day 4 of the follicular phase. High-throughput RNA sequencing (RNA-seq) was utilized to construct circRNAs, and differential expression was identified. The findings were validated using reverse transcription PCR (RT-PCR) and DNA sequencing, GO and KEGG analyses were performed, and potential miRNA targets were identified. The RNA-seq identified a total of 15,866 circRNAs, with 244 differentially expressed in the Meishan relative to the Duroc (111 up-regulated and 133 down-regulated). The RT-PCR finding confirmed the RNA-seq results, and quantitative real-time PCR (qPCR) analysis examining a subset of the circRNAs showed that they are resistant to RNase R digestion. Bioinformatics analysis (GO and KEGG) showed that the host genes associated with the differentially expressed circRNAs are involved in reproduction and follicular development signaling pathways. Furthermore, many of the circRNAs were found to interact with miRNAs that are associated with follicular development. This study presents a new perspective for studying circRNAs and provides a valuable resource for further examination into the potential roles of circRNAs in porcine follicular development.

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Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep

Animals ◽

10.3390/ani11071863 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1863

Author(s):

Aiju Liu ◽

Xiaoyong Chen ◽

Menghe Liu ◽

Limeng Zhang ◽

Xiaofei Ma ◽

...

Keyword(s):

Litter Size ◽

Luteal Phase ◽

Production Efficiency ◽

Follicular Development ◽

Mapk Signaling ◽

Follicular Phase ◽

Differentially Expressed ◽

Low Fertility ◽

High Fecundity ◽

Phase Versus

Litter size is a considerable quality that determines the production efficiency of mutton sheep. Therefore, revealing the molecular regulation of high and low fertility may aid the breeding process to develop new varieties of mutton sheep. CircRNAs are the important factors regulating follicular development, but their mechanism role in the regulation of litter size in Hanper sheep is not clear. In the present study, ovarian tissues from the follicular (F) or luteal phase (L) of Hanper sheep that were either consecutive monotocous (M) or polytocous were collected. Then, we performed transcriptome sequencing to screen for differentially expressed circRNAs (DE-circRNAs) and elucidate their function. In total, 4256 circRNA derived from 2184 host genes were identified in which 183 (146 were upregulated, while 37 were downregulated) were differentially expressed in monotocous sheep in the follicular phase versus polytocous sheep in the follicular phase (MF vs. PF). Moreover, 34 circRNAs (14 were upregulated, while 20 were downregulated) were differentially expressed in monotocous sheep in the luteal phase versus polytocous sheep in the luteal sheep (ML vs. PL). This was achieved through DE-circRNAs function enrichment annotation analysis by GESA, GO, and KEGG, which function through the EGF-EGFR-RAS-JNK, TGF-β and thyroid hormone signaling pathway to affect the litter size of Hanper sheep in MF vs. PF and ML vs. PL. STEM results showed that MAPK signaling pathways play a key role in MF vs. PF and ML vs. PL. Through WGCNA analysis, AKT3 was a core gene in MF vs. PF and ML vs. PL. Moreover, competitive endogenous RNA (ceRNA) network analysis revealed the target binding sites for miRNA such as oar-miR-27a, oar-miR-16b, oar-miR-200a/b/c, oar-miR-181a, oar-miR-10a/b, and oar-miR-432 in the identified DE-cirRNAs.

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Plasma Protein Comparison between Dairy Cows with Inactive Ovaries and Estrus

Scientific Reports ◽

10.1038/s41598-019-49785-8 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Chang Zhao ◽

Shi Shu ◽

Yunlong Bai ◽

Dong Wang ◽

Cheng Xia ◽

...

Keyword(s):

Energy Balance ◽

Dairy Cows ◽

Ultrasound Examination ◽

Dairy Farm ◽

Follicular Development ◽

Negative Energy ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Differential Proteins ◽

Mixed Samples

Abstract To screen differentially expressed proteins in the blood dairy cows with inactive ovaries caused by a negative energy balance and to determine the roles of the identified proteins in the development of inactive ovaries.Holstein cows at 14 to 21 days postpartum in an intensive dairy farm were examined for their energy balance (EB) status by blood β-hydroxybutyrate (BHBA) and assigned to the inactive ovary (IO) group (n = 50) and the normal oestrus control (CON) group (n = 50) at 60 to 90 days postpartum by means of the oestrus manifestation, rectal examination and B-ultrasound examination. Fourteen differentially expressed proteins from 61 proteins in the plasma of dairy cows with IOs were identified by iTRAQ/LC-MS/MS and GO, KEGG, and PATHWAY analysis. Eleven expressed proteins were upregulated, and 3 expressed proteins were downregulated. Among the 10 differentially expressed proteins verified by Western blot or ELISA, the relative expression levels of ALDOB, IGFBP2, ITIH3 and LDHB in mixed samples and single samples were consistent with the proteomic protein results. PKM2, GPX3, ALDOB, RBP4 and AHSG were significantly different between the two groups (P < 0.05); APOA4 and SPAM1 were not significantly different (P > 0.05) but were still downregulated in the ovarian resting group. This study confirmed that 14 plasma differential proteins in the inactive ovaries of postpartum dairy cows were associated with follicular development, and these findings provide a foundation for further research on the mechanism and prevention of inactive ovaries in dairy cows.

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Screening and Identification of Differential Ovarian Proteins before and after Induced Ovulation via Seminal Plasma in Bactrian Camels

Animals ◽

10.3390/ani11123512 ◽

2021 ◽

Vol 11 (12) ◽

pp. 3512

Author(s):

Qi Wang ◽

Quanwei Zhang ◽

Yina Li ◽

Xingxu Zhao ◽

Yong Zhang

Keyword(s):

Hormone Secretion ◽

Follicular Development ◽

Differentially Expressed ◽

Proteomic Profiling ◽

Induced Ovulation ◽

Regulatory Processes ◽

Before And After ◽

Screening And Identification ◽

Bactrian Camels ◽

Neurochemical Signal

Camelidae are induced ovulators whose ovulation is tightly regulated by multiple factors. Understanding the biological mechanisms underlying follicular development, hormone secretion, and ovulation requires investigating the potential molecular pathways involved. However, little is known about these pathways in Bactrian camels. To screen and identify candidate biomarkers after inducing ovulation, this study performed comprehensive proteomic and molecular biological analyses of the ovaries from two camel groups (n = 6). We identified 5075 expressed ovarian proteins, of which 404 were differentially expressed (264 upregulated, 140 downregulated) (p < 0.05 or p < 0.01), in samples from plasma-induced versus control camels. Gene ontology annotation identified the potential functions of the differentially expressed proteins (DEPs). These results validated the differential expression for a subset of these proteins using Western blot (p < 0.05) and immunofluorescence staining. Three DEPs (FST, NR5A1, and PRL) were involved in neurochemical signal transduction, as well as endocrine and reproductive hormone regulatory processes. The Kyoto Encyclopedia of Genes and Genomes analysis indicated the involvement of several pathways, including the calcium, cAMP, gonadotropin-releasing hormone, MAPK, and neuroactive ligand–receptor signaling pathways, suggesting that induced ovulation depends on the hypothalamic–pituitary–ovarian axis. Identifying these candidate biomarkers enables a better understanding of Bactrian camel reproduction. Ovarian proteomic profiling and the measurement of selected proteins using more targeted methods is a promising approach for studying induced-ovulation mechanisms.

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Transcriptome analysis reveals that long noncoding RNAs contribute to developmental differences between medium-sized ovarian follicles of Meishan and Duroc sows

Scientific Reports ◽

10.1038/s41598-021-01817-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mengxun Li ◽

Yi Liu ◽

Su Xie ◽

Lipeng Ma ◽

Zhichao Zhao ◽

...

Keyword(s):

Signaling Pathway ◽

Litter Size ◽

Target Genes ◽

Hormone Secretion ◽

Follicular Development ◽

Akt Signaling ◽

Developmental Differences ◽

Differentially Expressed ◽

Akt Signaling Pathway ◽

Potential Target

AbstractOvulation rate is an extremely important factor affecting litter size in sows. It differs greatly among pig breeds with different genetic backgrounds. Long non-coding RNAs (lncRNAs) can regulate follicle development, granulosa cell growth, and hormone secretion, which in turn can affect sow litter size. In this study, we identified 3554 lncRNAs and 25,491 mRNAs in M2 follicles of Meishan and Duroc sows. The lncRNA sequence and open reading frame lengths were shorter than mRNAs, and lncRNAs had fewer exons, were less abundant, and more conserved than protein-coding RNAs. Furthermore, 201 lncRNAs were differentially expressed (DE) between breeds, and quantitative trait loci analysis of DE lncRNAs were performed. A total of 127 DE lncRNAs were identified in 119 reproduction trait-related loci. In addition, the potential target genes of lncRNAs in cis or trans configurations were predicted. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that some potential target genes were involved in follicular development and hormone secretion-related biological processes or pathways, such as progesterone biosynthetic process, estrogen metabolic process, ovarian steroidogenesis, and PI3K-Akt signaling pathway. Furthermore, we also screened 19 differentially expressed lncRNAs in the PI3K-Akt signaling pathway as candidates. This study provides new insights into the roles of lncRNAs in follicular growth and development in pigs.

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