Integration of whole-genome DNA methylation data with RNA sequencing data to identify markers for bull fertility
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ABSTRACT:
ORGANISM(S): Bos taurus
PROVIDER: GSE142472 | GEO | 2019/12/21
REPOSITORIES: GEO
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Project description:Purpose: Screening the sperm sncRNAs that are responsible for dairy cattle fertility is of great interest, however, exploring the fertility-associated sncRNAs in sperm and linking them with the epigenetic inheritance in bovine has not been performed yet. Here in this study, we hypothesized that some sncRNAs in bovine sperm have a great potential to be linked with direct and immediate bull fertility data and could later influence the embryo and possibly impacting the daughter fertility. Methods: 12 bovine cryopreserved semen (high bull fertility, n=3 VS low bull fertility, n=3; high daughter fertility, n=3 vs low daughter fertility, n=3) that came from a pre-filtered 100 bull list (Figure 1) had been selected to extract total sperm RNA, the somatic cell lysis buffer had been added during the RNA extraction process to avoid the somatic cell pollution. The maternal and other confounding factors had been taken into consideration during the calculation of the phenotype criteria index.After the library construction, the library size that was smaller than 200 base pairs (adapter size around 125 nt) had been cut and sent for next-generation sequencing Results: bull fertility and daughter fertility related sncRNAs had been identified. Conclusions: providing promising epigenetic biomarker for cattle fertility improvement in the future, although these small non-coding RNAs need to be validated in larger sample sizes before being used as biomarkers.
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Project description:The aim of this study was to examine the effect of sire fertility status on conceptus-induced changes in the endometrial transcriptome. Holstein Friesian bulls (3 High fertility, HF, 3 Low fertility, LF) were selected from the Irish national population of AI bulls (minimum of 500 inseminations/bull) based on adjusted fertility scores (HF: +4.37% and LF: -12.7%; mean = 0%). To generate elongated conceptuses, Day 7 blastocysts produced in vitro using sperm from these six bulls were transferred in groups of 5-10 to synchronized heifers (n=7 heifers per bull; total 42 heifers). Conceptuses were recovered following slaughter on Day 15 (recovery rate: HF 59.4% vs. LF 45.0%; P<0.05). In parallel, Day 15 endometrial explants were recovered from synchronized cyclic heifers (n=4). Explants from each heifer were co-cultured for 6 h in RPMI medium with (i) nothing, control (ii) 100 ng/ml ovine recombinant interferon tau (IFNT) (iii) a single conceptus from each high fertility bull, or (iv) a single conceptus from each low fertility bull. To minimize variation, explants from the same uterus were used across all treatments, replicated across 4 heifers. After 6 h, explants were snap frozen and stored at -80°C. Extracted mRNA was subjected to RNA-seq (Illumina NextSeq 500) and the resulting data were analyzed through a bioinformatic pipeline with R software.
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Project description:Integration of whole-genome DNA methylation data with RNA sequencing data to identify markers for bull fertility
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Project description:high daughter fertility and low daughter fertility bulls were screened from the private bull database and then identify the sperm-derived DMR and DMC that associated with daughter fertility via whole genome methylation sequencing
2023-08-23 | GSE211926 | GEO
Project description:Prediction of male or semen fertility potential remains a persistent challenge that has yet to be fully resolved. This work analyzed several in vitro parameters and proteome of spermatozoa in bulls cataloged as high (HF; n=5) and low field (LF; n=5) fertility after more than a thousand artificial inseminations. Sperm motility was evaluated by Computer-Assisted Sperm Analysis. Sperm viability, mitochondrial membrane potential (MMP), and reactive oxygen species (mROS) of spermatozoa were assessed by flow cytometry. Proteome was evaluated by SWATH-MS procedure. Spermatozoa of HF bulls showed significantly higher total motility than the LF group (41.4% vs. 29.7%). Rates of healthy sperm (live, high MMP, and low mROS) for HF and LF bull groups were 49% and 43%, respectively (p > 0.05). Spermatozoa of HF bulls showed higher presence of differentially abundant proteins (DAPs) related to both energy production (COX7C), mainly OXPHOS pathway, and to the development of structures linked with the motility process (TPPP2, SSMEM1 and SPAG16). Furthermore, we observed that EQTN, together with other DAPs related to the interaction with the oocyte, were overrepresented in HF bull spermatozoa. The biological processes related to protein processing, catabolism, and protein folding were found to be overrepresented in LF bull sperm in which the HSP90AA1 chaperone was identified as the most DAP
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Project description:The objective of the study was to identify the fertility-associated metabolites in bovine spermatozoa using liquid chromatography-mass spectrometry (LC-MS). Six Holstein Friesian crossbred bulls (three high-fertile and three low-fertile bulls) were the experimental animals. Sperm proteins were isolated and protein-normalized samples were processed for metabolite extraction and subjected to LC-MS/MS analysis. Mass spectrometry data were processed using iMETQ software and metabolites were identified using Human Metabolome DataBase while, Metaboanalyst 4.0 tool was used for statistical and pathway analysis. A total of 3,704 metabolites belonging to various chemical classes were identified in bull spermatozoa. After sorting out exogenous metabolites, 56 metabolites were observed common to both the groups while 44 and 35 metabolites were found unique to high- and low-fertile spermatozoa, respectively. Among the common metabolites, concentrations of 19 metabolites were higher in high-fertile compared to low-fertile spermatozoa (fold change > 1.00). Spermatozoa metabolites with variable importance in projections score of more than 1.5 included hypotaurine, d-cysteine, selenocystine. In addition, metabolites such as spermine and l-cysteine were identified exclusively in high-fertile spermatozoa. Collectively, the present study established the metabolic profile of bovine spermatozoa and identified the metabolomic differences between spermatozoa from high- and low-fertile bulls. Among the sperm metabolites, hypotaurine, selenocysteine, l-malic acid, d-cysteine, and chondroitin 4-sulfate hold the potential to be recognized as fertility-associated metabolites.
2021-12-07 | MTBLS1071 | MetaboLights
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Project description:Assisted reproduction technologies (ART) and high selection pressure observed in the dairy industry are leading towards the use of younger females for reproduction purpose, reducing the interval between generations. This situation might have an impact on 10 young Holstein cows were used 3 times each at different ages for ovarian stimulation protocols and oocyte collections (at 8, 11 and 14 months). These oocytes were then fertilized in vitro with adult bull semen, generating 3 lots of embryos per animal.
2016-08-11 | E-GEOD-85437 | biostudies-arrayexpress
Project description:Despite passing routine laboratory tests for semen quality, bulls used in artificial insemination (AI) can exhibit a significant variation in fertility. During fertility analysis, a subfertile bull with a low pregnancy rate of 10% was identified. To fully characterize the phenotype, a range of in vitro, in vivo and molecular assays were carried out. Additionally, knockout mice were generated to investigate the function of the identified mutated gene. Sperm from the subfertile bull exhibited reduced motility and severely reduced caffeine-induced hyperactivation compared to control bulls of proven fertility. Ability to penetrate the zona pellucida, cleavage rate, cleavage kinetics, and blastocyst yield after IVF or AI were significantly lower than in control bulls. Whole-genome sequencing and RNA sequencing of testis revealed a critical mutation in AK9 that affect splicing, shaping the majority of AK9 transcripts that leads to a premature termination codon and a severely truncated protein. Transgenic mice deficient in AK9 were generated, resulting in the production of immotile sperm that were unable to fertilize the oocyte. These sperm exhibited abnormalities, including a low ATP concentration. RNA-seq analysis of testis revealed differential gene expression of components of the axoneme and sperm flagella, as well as steroid metabolic processes. Sperm ultrastructural analysis showed a higher percentage of sperm with abnormal flagella. The infertility produced by AK9 mutant bull and in AK9 deficient mice indicates the essential metabolic role of AK9 in sperm motility and/or hyperactivation, which in turn affects sperm binding and penetration of the zona pellucida.
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