Cold exposure impacts DNA methylation patterns in cattle sperm
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA923667 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23075469_1.fastq.gz | Fastqsanger.gz | |||
| SRR23075469_2.fastq.gz | Fastqsanger.gz | |||
| SRR23075470_1.fastq.gz | Fastqsanger.gz | |||
| SRR23075470_2.fastq.gz | Fastqsanger.gz | |||
| SRR23075471_1.fastq.gz | Fastqsanger.gz |
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Project description:Epigenetic markers, such as DNA methylation, in sperm plays crucial roles in spermatogenesis and fertilization, and a portion of methylation escape the early embryonic genome-wide DNA demethylation and affect later growth and development of offspring. DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. The effects of this cold exposure on the methylation dynamics of bovine sperm remain unexamined. Methylation profiles of sperm, collected from bulls during summer and winter seasons were analyzed by Whole Genome Bisulfite Sequencing (WGBS). Cold exposure during winter does not have a significant effect on the global methylation level, it altered the methylation levels at certain genomic loci and genes that may impact the maintenance of methylation status of imprinted genes and other loci, which may impact the development and growth of offspring.
2024-01-31 | GSE222863 | GEO
Project description:While cold stress has been shown to seriously impact cattle industry, there are only a few reports investigating the effect of cold stress on cattle. Whether severe cold stress results in alterations in gene expression and affects molecular genetic mechanisms remains unknown. We used microarrays to analyze the alterations in gene expression in peripheral blood samples in response to cold exposure and identified differentially regulated genes.
2016-04-02 | GSE79827 | GEO
Project description:While cold stress has been shown to seriously impact cattle industry, there are only a few reports investigating the effect of cold stress on cattle. Whether severe cold stress results in alterations in gene expression and affects molecular genetic mechanisms remains unknown. We used microarrays to analyze the alterations in gene expression in peripheral blood samples in response to cold exposure and identified differentially regulated genes. This study was performed on 30 healthy Sanhe heifers with similar genetic backgrounds, weight, and age. In order to induce cold stress, the cattle were transferred outdoor and were exposed to a temperature of -32°C for 3 hours followed by housing in cowshed at 5°C for 15 hours. Blood samples with EDTA were collected from each animal before and after the cold exposure. After total RNA was isolated from blood cells, six RNA samples (three derived before and three after the cold exposure), were collected from three animals randomly selected from the 30 healthy heifers for gene expression profiling in response to severe cold stress.
2016-04-02 | E-GEOD-79827 | biostudies-arrayexpress
Project description:Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the RRBS technology.
2018-05-03 | GSE102169 | GEO
Project description:Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the MeDIP-chip technology (methylated DNA immunoprecipitation followed by microarray hybridation).
2018-05-03 | GSE102960 | GEO
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.
2024-02-16 | GSE225705 | GEO
Project description:RNA molecules within ejaculated sperm can be characterized through whole transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses using RNA-Sequencing (RNA-Seq) technology. Low mapping rates observed during data processing were mainly attributed to the presence of ribosomal RNA and bacteria in sperm samples which led to a reduced sequencing depth or library size. To explore the possibility that unmapped reads could be associated with bacteria, we then identified bacteria-associated transcripts within RNA-Seq data derived from bovine and equine sperm cell preparations. This analysis revealed bacterial species that may closely interact with sperm and potentially influence male fertility. Identifying these potentially pathogenic or beneficial species and understanding how they may affect sperm quality in each species could be paramount to assess the breeding capacity of livestock.
2024-09-30 | GSE249884 | GEO
Project description:Light quantity impacts early response to cold and cold acclimation in young leaves of Arabidopsis
| PRJNA1169808 | ENA
Project description:Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperms through comparison with three bovine somatic tissues (mammary grand, brain and blood). Large differences between cattle sperms and somatic tissues were observed in the methylation patterns.
2018-03-08 | GSE106538 | GEO
Project description:There is growing evidence that paternal pre-conception cigarette smoke (CS) exposure is associated with increased risk of behavioral disorders and cancer in offspring. To characterize the effects of CS exposure on the sperm epigenome and offspring neurodevelopment, we investigated the impact of pre-conception paternal CS exposure on mouse sperm DNA methylation and gene expression in offspring. We further investigated the role of oxidative stress on sperm epigenetic changes using a mouse model (Nrf-/-) with impaired antioxidant capacity. Lastly, we evaluated the capacity for sperm DNA methylation to recover following removal of CS for 1-5 spermatogenic cycles (28-171 days). We found that smoking significantly impacts sperm DNA methylation as well as DNA methylation and gene expression in offspring. These changes were largely recapitulated in Nrf-/- mice independent of smoke exposure. Recovery experiments indicated that about half of differentially methylated regions returned to normal within 28 days of removal from smoke, however additional recovery following longer periods was not observed. Thus, we present strong evidence that cigarette smoke exposure induces paternally mediated, heritable epigenetic changes. Parallel studies performed in Nrf-/- mice provide evidence for oxidative stress as the predominant underlying mechanism for smoke-induced epigenetic changes to sperm as well as changes in the offspring of smoke-exposed sires. Lastly, recovery experiments indicate that while many epigenetic changes are corrected following removal from smoke exposure, aberrant methylation persists at a significant number of regions even after five spermatogenic cycles
2020-05-06 | GSE133739 | GEO