Identification of novel oocyte and granulosa cell markers

Genome-wide association study on milk production and somatic cell score for Thai dairy cattle using weighted single-step approach with random regression test-day model

Genome-wide association studies are a powerful tool to identify genomic regions and variants associated with phenotypes. However, only limited mutual confirmation from different studies is available. The objectives of this study were to identify genomic regions as well as genes and pathways associated with the first-lactation milk, fat, protein, and total solid yields; fat, protein, and total solid percentage; and somatic cell score (SCS) in a Thai dairy cattle population. Effects of SNPs were estimated by a weighted single-step GWAS, which back-solved the genomic breeding values predicted using single-step genomic BLUP (ssGBLUP) fitting a single-trait random regression test-day model. Genomic regions that explained at least 0.5% of the total genetic variance were selected for further analyses of candidate genes. Despite the small number of genotyped animals, genomic predictions led to an improvement in the accuracy over the traditional BLUP. Genomic predictions using weighted ssGBLUP were slightly better than the ssGBLUP. The genomic regions associated with milk production traits contained 210 candidate genes on 19 chromosomes [Bos taurus autosome (BTA) 1 to 7, 9, 11 to 16, 20 to 21, 26 to 27 and 29], whereas 21 candidate genes on 3 chromosomes (BTA 11, 16, and 21) were associated with SCS. Many genomic regions explained a small fraction of the genetic variance, indicating polygenic inheritance of the studied traits. Several candidate genes coincided with previous reports for milk production traits in Holstein cattle, especially a large region of genes on BTA14. We identified 141 and 5 novel genes related to milk production and SCS, respectively. These novel genes were also found to be functionally related to heat tolerance (e.g., SLC45A2, IRAG1, and LOC101902172), longevity (e.g., SYT10 and LOC101903327), and fertility (e.g., PAG1). These findings may be attributed to indirect selection in our population. Identified biological networks including intracellular cell transportation and protein catabolism implicate milk production, whereas the immunological pathways such as lymphocyte activation are closely related to SCS. Further studies are required to validate our findings before exploiting them in genomic selection.

Ectopic expression of CGG-repeats alters ovarian response to gonadotropins and leads to infertility in a murine FMR1 premutation model

Women heterozygous for an expansion of CGG repeats in the 5'UTR of FMR1 risk developing fragile X-associated primary ovarian insufficiency (FXPOI) and/or tremor and ataxia syndrome (FXTAS). We show that expanded CGGs, independent of FMR1, are sufficient to drive ovarian insufficiency and that expression of CGG-containing mRNAs alone or in conjunction with a polyglycine-containing peptide translated from these RNAs contribute to dysfunction. Heterozygous females from two mouse lines expressing either CGG RNA-only (RNA-only) or CGG RNA and the polyglycine product FMRpolyG (FMRpolyG+RNA) were used to assess ovarian function in aging animals. The expression of FMRpolyG+RNA led to early cessation of breeding, ovulation and transcriptomic changes affecting cholesterol and steroid hormone biosynthesis. Females expressing CGG RNA-only did not exhibit decreased progeny during natural breeding, but their ovarian transcriptomes were enriched for alterations in cholesterol and lipid biosynthesis. The enrichment of CGG RNA-only ovaries for differentially expressed genes related to cholesterol processing provided a link to the ovarian cysts observed in both CGG-expressing lines. Early changes in transcriptome profiles led us to measure ovarian function in prepubertal females that revealed deficiencies in ovulatory responses to gonadotropins. These include impairments in cumulus expansion and resumption of oocyte meiosis, as well as reduced ovulated oocyte number. Cumulatively, we demonstrated the sufficiency of ectopically expressed CGG repeats to lead to ovarian insufficiency and that co-expression of CGG-RNA and FMRpolyG lead to premature cessation of breeding. However, the expression of CGG RNA-alone was sufficient to lead to ovarian dysfunction by impairing responses to hormonal stimulation.

Forecasting early onset diminished ovarian reserve for young reproductive age women

PURPOSE

To investigate the biological networks associated with DOR in young women and the subsequent molecular impact on preimplantation embryos.

METHODS

Whole peripheral blood was collected from patients: young women presenting with diminished ovarian reserve (DOR) and age-matched young women with normal ovarian reserve. Maternal exome sequencing was performed on the NovaSEQ 6000 and sequencing validation was completed using Taqman® SNP Genotyping Assays. Blastocyst global methylome and transcriptome sequencing were also analyzed.

RESULTS

Exome sequencing revealed 730 significant DNA variants observed exclusively in the young DOR patients. Bioinformatic analysis revealed a significant impact to the Glucocorticoid receptor (GR) signaling pathway and each young DOR female had an average of 6.2 deleterious DNA variants within this pathway. Additional stratification based on patient age resulted in a cut-off at 31 years for young DOR discrimination. Embryonic global methylome sequencing resulted in only a very small number of total CpG sites with methylation alterations (1,775; 0.015% of total) in the DOR group. Additionally, there was no co-localization between these limited number of altered CpG sites and significant variants, genes, or pathways. RNA sequencing also resulted in no biologically significant transcription changes between DOR blastocysts and controls.

CONCLUSION

GR signaling DNA variants were observed in women with early-onset DOR potentially compromising oocyte production and quality. However, no significant downstream effects on biological processes appear to impact the resulting blastocyst. The ability to forecast premature DOR for young women may allow for earlier identification and clinical intervention for this patient population.

Effects of Zinc Supplementation During In Vitro Maturation on Meiotic Maturation of Oocytes and Developmental Capacity in Yak

Zinc (Zn) is an essential trace element that is required during mammalian developmental processes. The objective of this study was to investigate the effects of Zn supplementation during in vitro maturation (IVM) on the developmental capacity of yak (Bos grunniens) oocytes. Cumulus expansion, nuclear maturation, intracellular glutathione (GSH), reactive oxygen species (ROS) levels, superoxide dismutase (SOD) activity, subsequent embryonic development, and the expression of Zn transporters (ZnTs) and Zrt and Irt-like proteins (ZiPs) were evaluated. The Zn concentrations in yak plasma and follicular fluid were 0.740 ± 0.012 and 0.382 ± 0.009 μg/mL, respectively. The cumulus expansion did not show significant differences in COCs after matured with or without Zn supplementation (P > 0.05). The intracellular GSH was higher in oocytes matured with 1 or 2 mg/L Zn than in control group (0 mg/L) (P < 0.05). However, ROS levels of oocytes matured with 1 or 2 mg/L Zn were reduced significantly compared with the control and 0.5 mg/L groups (P < 0.05). The SOD activity was increased significantly after Zn supplementation. The cleavage rate was not significantly different after Zn supplementation (P > 0.05). Percentages of matured oocytes that developed into the blastocyst stage after IVF were 47.9, 50.5, 60.4, and 58.9% for 0, 0.5, 1, and 2 mg/L Zn groups, respectively. Gene expression analysis revealed that the expression patterns associated with Zn were changed after Zn supplementation. In conclusion, Zn supplementation to IVM improved yak oocyte maturation and subsequent development by increasing GSH and SOD activity, decreasing ROS in oocytes.

A whole genome sequence association study for puberty in a large Duroc × Erhualian F2 population

A large proportion of gilts and sows are culled from reproduction populations because of anestrus and pubertal reproductive failure. Selecting early onset of puberty gilts has a favorable effect on sows' reproductivity. However, age at puberty is hard to be routinely measured in commercial herds. With molecular genetic predictors, identifying individuals that have a propensity for early onset of puberty can be simplified. We previously performed genome scanning and a genome-wide association study for puberty in an F2 resource population using 183 microsatellites and 62 125 SNPs respectively. The detection power and resolution of identified quantitative trait loci were very low. Herein, we re-sequenced 19 founders of the F2 resource population in high coverage, and whole genome sequences of F2 individuals were imputed to perform an association study for reproductive traits. A total of 2339 SNPs associated with pubertal reproductive failure were identified in the region of 30.94-40.74 Mb on SSC7, with the top one, positioned at 33.36 Mb, explaining 16% of the phenotypic variances. We improved the magnitude of the P-value by 10E+5 to 10E+7 using the whole genome sequence rather than using low/middle density markers as in previous studies, and we narrowed down the QTL confidence interval to 5.25 Mb. Combining the annotation of gene function, RAB23 and BAK1 were perceived as the most compelling candidate genes. The identified loci may be useful in culling sows failing to show estrus by marker-assisted selection to increase reproductive efficiency of swine herds.

Stable reference genes in granulosa cells of bovine dominant follicles during follicular growth, FSH stimulation and maternal aging

The aim of the present study was to determine a set of reference genes in granulosa cells of dominant follicles that are suitable for relative gene expression analyses during maternal and follicular aging. Granulosa cells of growing and preovulatory dominant follicles were collected from aged and young cows (maternal aging study) and from FSH-stimulated follicles developing under different durations of FSH treatment (follicular aging study). The mRNA levels of the two commonly used reference genes (GAPDH, ACTB) and four novel genes (UBE2D2, EIF2B2, SF3A1, RNF20) were analysed using cycle threshold values. Results revealed that mRNA levels of GAPDH, ACTB, EIF2B2, RNF20, SF3A1 and UBE2D2 were similar (P>0.05) between dominant follicle type, age and among follicles obtained after FSH-stimulation, but differed (P=0.005) due to mRNA processing (i.e. with versus without amplification). The stability of reference genes was analysed using GeNorm, DeltaCT and NormFinder programs and comprehensive ranking order was determined using RefFinder. The mRNA levels of GAPDH and ACTB were less stable than those of UBE2D2 and EIF2B2. The geometric mean of multiple genes (UBE2D2, EIF2B2, GAPDH and SF3A1) is a more appropriate reference control than the use of a single reference gene to compare relative gene expression among dominant and FSH-stimulated follicles during maternal and/or follicular aging studies.

Identification of a novel isoform of the leukemia-associated MLLT1 (ENL/LTG19) protein

Genome wide transcriptional profiles offer abundant information regarding mRNA levels in specific tissues, organs or developmental stages. Although these data sets do not offer spatial or cell type-specific information, they can be extremely useful for gene discovery when analyzed by the appropriate techniques. Previously, we proposed and validated the use of combinatorial dataset analysis techniques to identify novel genes required during pre-implantation development. Now we build upon this work to identify genes that have dynamic expression during gametogenesis. Here we present detailed analysis of the expression pattern of leukemia-associated, myeloid/lymphoid or mixed-lineage leukemia; translocated to 1 (Mllt1) gene. We document a novel splice isoform of Mllt1 and confirm that both Mllt1 mRNA isoforms are translated. We provide data supporting that MLLT1 protein isoforms display distinct stage-specific expression during spermiogenesis and adult tissues. Finally, we evaluated genes neighboring the Mllt1 locus, and show dynamic stage specific expression patterns of other genes Catsperd, Prr22, Rfx2 and Slc25a41. We document testes expressed alternative isoforms of Prr22 and Rfx2. These results indicate that transcriptome data mining, combined with specific expression analysis provides a wealth of novel gene expression information.

Oocyte-cumulus cell interactions regulate free intracellular zinc in mouse oocytes

Zinc increases in the oocyte during maturation and is required for progression and completion of meiosis. The objective of this study was to determine whether cumulus cells regulate the levels of free intracellular zinc in the oocyte during maturation. In the cumulus-oocyte complex (COC) the relative level of free intracellular zinc was almost fourfold higher in cumulus cells compared with the resident germinal vesicle-stage oocyte. Removal of cumulus cells caused a fourfold increase in intracellular zinc in the oocyte by 1 h after cumulus cell removal, but subsequent coculture of denuded oocytes with COC decreased free intracellular zinc in the oocyte by 65%. Thus, cumulus cells suppress free intracellular zinc in the oocyte. The mRNA transcripts for the zinc transporter proteins Slc39a6, Slc39a8, Slc39a9, Slc39a10, Slc39a12, Slc30a2, Slc30a4, Slc30a5 and Slc30a8 mRNAs were higher in oocytes, while Slc39a1, Slc39a7, Slc39a13, Slc39a14, Slc30a6, Slc30a7 and Slc30a9 mRNAs were higher in cumulus cells. Thus a complex zinc transport network is present in the COC. Pretreatment with epidermal growth factor for 4 h abolished the ability of COCs to restrict free intracellular zinc in denuded oocytes. Coculture of denuded metaphase II oocytes with COC lowers free intracellular zinc in mature oocytes. Oocytes matured in vivo or oocytes from older mice had lower levels of free intracellular zinc than oocytes matured in vitro or from younger mice. Thus, a precise mechanism for regulating oocyte zinc homeostasis has been uncovered in the COC that is disrupted with increasing age or by removal of cumulus cells.

Competence of an artificial bent DNA as a transcriptional activator in mouse ES cells

Curved DNA structures with a left-handed superhelical conformation can activate eukaryotic transcription. However, their potency in transgene activation in embryonic stem (ES) cells has not been examined. T20 is an artificial curved DNA of 180 bp that serves as a transcriptional activator. We investigated the effect of T20 on transcription in mouse ES cell lines or hepatocytes differentiated from them. We established 10 sets of cell lines each harboring a single copy of the reporter construct. Each set comprised a T20-harboring cell line and a T20-less control cell line. Analyses showed that in ES cells and in hepatocytes originating from these cells, T20 both activated and repressed transcription in a manner that was dependent on the locus of reporter. The present and previous studies strongly suggest that in cells that have a strict gene regulation system, transcriptional activation by T20 occurs only in a transcriptionally active locus in the genome.