Significant Down-Regulation of "Biological Adhesion" Genes in Porcine Oocytes after IVM

Global N6-methyladenosine methylation analysis reveals the positive correlation between m6A modification and mRNA abundance during Apostichopus japonicus disease development

N⁶-methyladenosine (m⁶A), the most abundant epitranscriptomic modification in eukaryotic messenger RNA (mRNA), plays important roles in regulation of gene expression for fundamental biological processes and diverse physiological functions, including combating with pathogen infection. Here, we were first profile transcriptome-wide m⁶A sequencing in four stages of skin ulceration syndrome-diseased Apostichopus japonicus following Vibrio splendidus infection, including Control (healthy), Early (small ulcer), Later (extensive ulcer), and Resistant (no ulcer) groups. Our results revealed that three experimental groups were all extensively methylated by m⁶A and the proportion of the m⁶A modified genes were also significantly increased to 28.90% (Early), 27.97% (Later), and 29.98% (Resistant) when compared with Control group (15.15%), indicating m⁶A modification could be induced by V. splendidus infection. Intriguingly, we discovered a positive correlation between the m⁶A methylation level and mRNA abundance, indicating a positive regulatory role of m⁶A in sea cucumber gene expression during V. splendidus infection. Moreover, genes with specific and differentially expressed m⁶A methylation in Later group were both enriched in cell adhesion, while Early and Resistant groups were both mainly involved in DNA conformation change and chromosome organization when compared with Control, suggesting the higher-methylated m⁶A might serve as "conformational marker" and associated to the initiation of related anti-disease genes transcription in order to improve disease resistance of sea cucumber. Subsequently, we selected the pivotal genes enriched in cell adhesion pathway and found that the IggFc-binding protein (FcGBP) and Fibrocystin-L both had higher levels of m⁶A methylation and higher level of mRNA expressions in Later group. Conversely, Fibrinogen C domain-containing protein 1 (F1BCD1) gene presented as an antibacterial role in sea cucumber and showed higher mRNA expression and higher m⁶A methylation in Resistant group and lower mRNA level in Later group. The levels of m⁶A methylation and mRNA abundance of FcGBP and F1BCD1 genes indicates disease occurrence or disease resistant were also verified by MeRIP-qPCR. Overall, our study presents the first comprehensive characterize of dynamic m⁶A methylation modification in the different stages of disease in sea cucumber. These data provide an invaluable resource for future studies of function and biological significance of m⁶A in mRNA in marine invertebrates.

Vitrification of bovine germinal vesicle oocytes significantly decreased the methylation level of their in vitro derived MII oocytes

CONTEXT

The vitrification of oocytes is important for the conservation of animals, and the effect of vitrification on methylation patterns of bovine oocytes remains unclear.

AIMS

This article aims to investigate the effect of vitrification on the DNA methylation patterns on vitrified GV oocytes and their in vitro derived MII oocytes.

METHODS

5-MeC staining and single-cell whole genome bisulphite sequencing (SC-WGBS) were utilised to analyse fresh GV oocytes (F_GV group), MII oocytes (F_MII group), vitrified GV oocytes (V_GV group) and their in vitro derived MII oocytes (V_MII group).

KEY RESULTS

Results of both 5-MeC staining and SC-WGBS showed that no significant difference was found between the F_GV group and the V_GV group, while the methylation level of the V_MII group was significantly lower than that of the F_MII group. Moreover, supplementation of 2μM resveratrol (Res) in IVM medium significantly improved maturation and development ability of vitrified GV oocytes by restoring their DNA methylation levels.

CONCLUSION

In conclusion, vitrification of bovine GV oocytes significantly decreased the DNA methylation level of their in vitro derived MII oocytes, and 2μM Res improved their development ability by restoring DNA methylation level.

IMPLICATIONS

Our results provide an efficient approach to improve the maturation and fertilisation ability of vitrified GV oocytes.

Genome-wide identification m6A modified circRNAs revealed their key roles in skin ulceration syndrome disease development in Apostichopus japonicus

Circular RNAs (circRNAs) are novel endogenous non-coding RNAs (ncRNAs) and can be acted as competing endogenous RNAs (ceRNAs) to regulate microRNA (miRNA) and downstream gene expression. Recently, m⁶A modification has been found in circRNA, and m⁶A circRNAs also play important roles in various biological processes and a variety of diseases. Our previous study had been demonstrated that circRNAs were differentially expressed in skin ulceration syndrome (SUS) diseased sea cucumber Apostichopus japonicus. However, whether the function of circRNAs are dependent on m⁶A levels are largely unknown. Here, we firstly investigated the genome-wide map of m⁶A circRNAs in sea cucumbers with different stages of Vibrio splendidus challenge, that's Control group, SUS-diseased group, and SUS-resistant group. MeRIP-seq revealed that m⁶A abundances were enriched in circRNAs in all three groups, especially for SUS-resistant group. Among them, more than 62% of modified circRNAs harbor only a single m⁶A peak and about 55% of m⁶A sites in circRNAs were derived from sense overlapping in each group. After V. splendidus infection, we found that most of m⁶A peaks in circRNAs were upregulated and less were downregulated in both SUS-diseased and SUS-resistant groups when compared with Control. Furthermore, GO analysis indicated that the host genes of circRNAs with dysregulated m⁶A peaks in SUS-diseased and SUS-resistant groups were both mainly enriched in the adhesion pathway. More importantly, we discovered that more than 50% m⁶A circRNAs showed a positive correlation between the circRNAs expression and m⁶A methylation levels both in SUS-diseased and SUS-resistant groups. Therefore, a core circRNA-miRNA-mRNA (ceRNA) network whether influenced by m⁶A modification was constructed based on conjoint analysis. Our results indicated that several selected m⁶A circRNAs bind with miRNAs were mainly targeting to ubiquitylation system and adhesion pathway. What's more, three candidate m⁶A circRNAs and three target genes were validated by MeRIP-qPCR and qPCR, whose m⁶A levels in circRNA and mRNA expressions were consistent with disease occurrence or disease resistance. All of our current findings suggested that m⁶A circRNAs could play important roles during pathogen infection and might be served as a new molecular biomarker in SUS disease diagnose of A. japonicus.

Metabolism-associated genome-wide epigenetic changes in bovine oocytes during early lactation

Dietary intake in early lactating cows is outmatched by milk production. These cows experience a negative energy balance, resulting in a distinct blood metabolism and poor reproductive function due to impaired ovulation and increased embryo loss. We hypothesize that oocytes from lactating cows undergoing transient metabolic stress exhibit a different epigenetic profile crucial for developmental competence. To investigate this, we collected oocytes from metabolically-profiled cows at early- and mid-postpartum stages and characterized their epigenetic landscape compared with control heifers using whole-genome bisulfite sequencing. Early-postpartum cows were metabolically deficient with a significantly lower energy balance and significantly higher concentrations of non-esterified fatty acids and beta-hydroxybutyrate than mid-postpartum animals and control heifers. Accordingly, 32,990 early-postpartum-specific differentially methylated regions (DMRs) were found in genes involved in metabolic pathways, carbon metabolism, and fatty acid metabolism, likely descriptive of the epigenetic regulation of metabolism in early-postpartum oocytes. DMRs found overlapping CpG islands and exons of imprinted genes such as MEST and GNAS in early-postpartum oocytes suggest that early lactation metabolic stress may affect imprint acquisition, which could explain the embryo loss. This whole-genome approach introduces potential candidate genes governing the link between metabolic stress and the reproductive outcome of oocytes.

Changes in Ovarian and Uterine Morphology and Estrous Cycle in CD-1 Mice After Vanadium Inhalation

Vanadium is a metal present in particulate matter and its reprotoxic effects have been demonstrated in males and pregnant females in animal models. However, the effects of this metal on the reproductive organs of nonpregnant females have not been sufficiently studied. In a vanadium inhalation model in nonpregnant female mice, we found anestrous and estrous cycle irregularity, as well as low serum concentrations of 17β-estradiol and progesterone. A decrease in the diameter of secondary and preovulatory follicles, as well as a thickening of the myometrium and endometrial stroma, was observed in the vanadium-treated mice. There was no difference against the control group with respect to the presence of the estrogen receptor α in the uterus of the animals during the estrous stage. Our results indicate that when vanadium is administered by inhalation, effects are observed on the female reproductive organs and the production of female sex hormones.

Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers (Bos indicus L.)

High fertility and early puberty in Bos indicus heifers are desirable and genetically correlated traits in beef production. The hypothalamus-pituitary-ovarian (HPO) axis synthesizes steroid hormones, which contribute to the shift from the pre-pubertal state into the post-pubertal state and influence subsequent fertility. Understanding variations in abundance of proteins that govern steroid synthesis and ovarian signaling pathways remains crucial to understanding puberty and fertility. We used whole ovaries of six pre-pubertal and six post-pubertal Brahman heifers to conduct differential abundance analyses of protein profiles between the two physiological states. Extracted proteins were digested into peptides followed by identification and quantification with massspectrometry (MS) by sequential window acquisition of all instances of theoretical fragment ion mass spectrometry (SWATH-MS). MS and statistical analysis identified 566 significantly differentially abundant (DA) proteins (adjusted p < 0.05), which were then analyzed for gene ontology and pathway enrichment. Our data indicated an up-regulation of steroidogenic proteins contributing to progesterone synthesis at luteal phase post-puberty. Proteins related to progesterone signaling, TGF-β, retinoic acid, extracellular matrix, cytoskeleton, and pleiotrophin signaling were DA in this study. The DA proteins probably relate to the formation and function of the corpus luteum, which is only present after ovulation, post-puberty. Some DA proteins might also be related to granulosa cells signaling, which regulates oocyte maturation or arrest in ovaries prior to ovulation. Ten DA proteins were coded by genes previously associated with reproductive traits according to the animal quantitative trait loci (QTL) database. In conclusion, the DA proteins and their pathways were related to ovarian activity in Bos indicus cattle. The genes that code for these proteins may explain some known QTLs and could be targeted in future genetic studies.

Transcriptome analysis of porcine immature oocytes and surrounding cumulus cells after vitrification and in vitro maturation

Cryopreservation impairs oocyte quality, which may be associated with abnormal gene expression. Currently, alteration of mRNA levels in vitrified porcine oocytes has not been well characterized. The aim of this study was to analyze transcriptome profiles with RNA sequencing (RNA-seq) in porcine immature oocytes and their surrounding cumulus cells (CCs) after vitrification and in vitro maturation (IVM). There were 19 upregulated and 18 downregulated genes differentially expressed in vitrified oocytes, with no significant GO enrichment or KEGG pathway identified for these genes. In addition, CCs derived from vitrified oocytes had 40 significantly upregulated and 100 significantly downregulated genes. In total, 7 GO terms were significantly enriched in molecular function and biological process, and only MAPK signaling pathway reached significant enrichment based on KEGG analysis. Moreover, selected differentially expressed genes had similar expression patterns through comparison between results from qRT-PCR and RNA-Seq. In conclusion, our data provided detailed information on mRNA transcriptomes in porcine immature oocytes and CCs after vitrification and IVM, which offered now insights regarding reduced developmental potential of the vitrified oocytes.

Response to abiotic and organic substances stimulation belongs to ontologic groups significantly up-regulated in porcine immature oocytes

The efficiency of the process of obtaining mature oocytes, and then of porcine embryos in vitro depends on many factors and requires meeting many conditions. These include selection of morphologically appropriate oocytes, selection of appropriate medium components, as well as a number of abiotic factors (appropriate microenvironment during in vitro culture).

Oocytes were taken from 45 pubertal crossbred Landrace gilts. The BCB test was carried out. BCB + oocytes were divided into two groups: “before IVM” and “after IVM”. “Before IVM” oocytes were subjected to molecular analyzes immediately after collection, while “after IVM” oocytes underwent in vitro maturation and then the second BCB test. Oocytes that remained BCB+ after the second test were used for molecular analyzes using Affymetrix expression microarrays.

A group of genes responsible for response to organic substance and response to abiotic stimulus, which underwent significant changes (decrease) was discovered after oocyte in vitro maturation. Genes such as MM, PLDP, SERPINH, MYOF, DHX9, HSPA5, VCP, KIT, SERPINH1, PLD1, and VCP showed the largest decrease after the culture period. The levels of these genes were therefore elevated in oocytes before the in vitro maturation process.

In conclusion, a number of organic and abiotic factors have an impact on the process of the oocyte in vitro maturation. The presented results confirm the literature data in which the low efficiency of obtaining mature oocytes in in vitro conditions is mentioned, which further impacts the amount of viable embryos obtained.

Expression Changes in Fatty acid Metabolic Processrelated Genes in Porcine Oocytes During in Vitro Maturation

Mammalian oocytes undergo compound processes of nuclear and cytoplasmic maturation that allow them to reach MII stage. Only fully mature, oocyte can be successfully fertilized by a single spermatozoon. Fatty acids, apart from their role in cellular metabolism, inflammation and tissue development, have positive and detrimental effects on oocyte maturation, fertilization, blastocyst cleavage rate and embryo development in mammals. Using microarrays, we have analyzed the expression changes in fatty acids- -related genes during in vitro maturation of porcine oocytes. The oocytes were recovered from ovaries of 45 pubertal crossbred Landrace gilts and subsequently subjected to BCB test. For further analyses, only granulosa cell-free BCB+ oocytes were used and divided into two groups. The first one, described as “before IVM”, was directly exposed to molecular assays, the second one, described as “after IVM”, was first in vitro matured and then subjected to a second BCB test. Oocytes, if classified as BCB+, were then passed to corresponding molecular analyses. We found significant down-regulation of genes involved in fatty acid metabolic process, such as: ACSL6, EPHX2, FADS2, PTGES, TPI1, TBXAS1, NDUFAB1, MIF, ACADSB and DECR1 in porcine oocytes analyzed after IVM, in comparison to those analyzed before IVM. In conclusion, apart from poor data available concerning analyzed genes in relation to reproductive events, significant changes in their expression point to their potential role as an oocyte developmental competence markers in pigs. Introducing molecular diagnostics of oocytes could be the prospective tool for selection of best gametes, leading to improved outcomes of in vitro fertilization.