Determination of single embryo sex in Macaca mulatta and Mus musculus RNA-Seq transcriptome profiles

Sexing of cattle embryos using RNA-sequencing data or polymerase chain reaction based on a complete sequence of cattle chromosome Y

When necessary, RNA-sequencing data or polymerase chain reaction (PCR) assays can be used to determine the presence of the chromosome Y (ChrY) in samples. This information allows for biological variation due to sexual dimorphism to be studied. A prime example is when researchers conduct RNA-sequencing of single embryos, or conceptuses, prior to the development of gonads. A recent publication of a complete sequence of the ChrY has removed limitations for the development of these procedures in cattle, otherwise imposed by the absence of a ChrY in the reference genome. Using the sequence of the cattle ChrY and transcriptome data, we conducted a systematic search for genes in the ChrY that are exclusively expressed in male tissues. The genes ENSBIXG00000029763, ENSBIXG00000029774, ENSBIXG00000029788, and ENSBIXG00000029892 were consistently expressed across male tissues and lowly expressed or absent in female samples. We observed that the cumulative values of counts per million were 2688-fold greater in males than the equivalent values in female samples. Thus, we deemed these genes suitable for the sexing of samples using RNA-sequencing data. We successfully used this set of genes to infer the sex of 22 cattle blastocysts (8 females and 14 males). Additionally, the completed sequence of the cattle ChrY has segments in the male-specific region that are not repeated. We designed a pair of oligonucleotides that targets one of these non-repeated regions in the male-specific sequence of the ChrY. Using this pair of oligonucleotides, in a multiplexed PCR assay with oligonucleotides that anneal to an autosome chromosome, we accurately identified the sex of cattle blastocysts. We developed efficient procedures for the sexing of samples in cattle using either transcriptome data or their DNA. The procedures using RNA-sequencing will greatly benefit researchers who work with samples limited in cell numbers which are only sufficient to produce transcriptome data. The oligonucleotides used for the accurate sexing of samples using PCR are transferable to other cattle tissue samples.

Differential expression analysis of sugar accumulation-related genes during chestnut nut development

The chestnuts of Castanea mollissima Bl. are an important food crop in China, and have high nutritional content. To understand the pattern of sugar accumulation during chestnut nut development, the related enzyme gene regulatory pathways, and the molecular regulatory mechanisms of chestnut sugar biosynthesis metabolism, two chestnut varieties with different sugar content, namely Chengbu Youzhu (hereinafter referred to as CBYZ) and AnYou No. 1 (hereinafter referred to as AY01), were selected for investigation. Total sugar and starch content, and the activity of enzymes related to sugar accumulation, were measured in the nuts of the two chestnut varieties 10 days after flowering (DAF), 20 DAF, 30 DAF, 40 DAF, 50 DAF, 60 DAF, 70 DAF, 80 DAF, and 90 DAF. Changes in starch, straight-chain starch, and branched-chain starch content, and sucrose-phosphate synthase, soluble starch synthase, and granule-bound starch synthase enzyme activities were consistent with one-another. A total of 24 differentially expressed genes between the two varieties were associated with sugar biosynthesis and metabolism at three key stages (30, 60, and 90 DAF) of sugar accumulation. Further analysis showing upregulation of the expression of starch-related genes, such as β-amylase, GYS, and INV indicated that these genes were not actively expressed in AY01, resulting in slow accumulation of starch and reduced sugar content. By contrast, the downregulation of the expression of genes, such as PGK and MDH1, indicated that these genes were actively expressed in low-sugar chestnuts, resulting in the rapid fermentation of sugars. A link between gene up- or down-regulation during different developmental stages of chestnut and the effect of their expression on sugar content were established by KEGG pathway enrichment analysis. These findings provide further insights into the mechanism of sugar biosynthesis in chestnuts.

Allele-specific expression analysis reveals conserved and unique features of preimplantation development in equine ICSI embryos

Embryonic genome activation and dosage compensation are major genetic events in early development. Combined analysis of single embryo RNA-seq data and parental genome sequencing was used to evaluate parental contributions to early development and investigate X-chromosome dynamics. In addition, we evaluated dimorphism in gene expression between male and female embryos. Evaluation of parent-specific gene expression revealed a minor increase in paternal expression at the 4-cell stage that increased at the 8-cell stage. We also detected eight genes with allelic expression bias that may have an important role in early development, notably NANOGNB. The main actor in X-chromosome inactivation, XIST, was significantly upregulated at the 8-cell, morula, and blastocyst stages in female embryos, with high expression at the latter. Sexual dimorphism in gene expression was identified at all stages, with strong representation of the X-chromosome in females from the 16-cell to the blastocyst stage. Female embryos showed biparental X-chromosome expression at all stages after the 4-cell stage, demonstrating the absence of imprinted X-inactivation at the embryo level. The analysis of gene dosage showed incomplete dosage compensation (0.5 < X:A < 1) in MII oocytes and embryos up to the 4-cell stage, an increase of the X:A ratio at the 16-cell and morula stages after genome activation, and a decrease of the X:A ratio at the blastocyst stage, which might be associated with the beginning of X-chromosome inactivation. This study represents the first critical analysis of parent- and sex-specific gene expression in early equine embryos produced in vitro.

Temporal patterns of gene regulation and upstream regulators contributing to major developmental transitions during Rhesus macaque preimplantation development

The preimplantation period of life in mammals encompasses a tremendous amount of restructuring and remodeling of the embryonic genome and reprogramming of gene expression. These vast changes support metabolic activation and cellular processes that drive early cleavage divisions and enable the creation of the earliest primitive cell lineages. A major question in mammalian embryology is how such vast, sweeping changes in gene expression are orchestrated, so that changes in gene expression are exactly appropriate to meet the developmental needs of the embryo over time. Using the rhesus macaque as an experimentally tractable model species closely related to the human, we combined high quality RNA-seq libraries, in-depth sequencing and advanced systems analysis to discover the underlying mechanisms that drive major changes in gene regulation during preimplantation development. We identified the major changes in mRNA population and the biological pathways and processes impacted by those changes. Most importantly, we identified 24 key upstream regulators that are themselves modulated during development and that are associated with the regulation of over 1000 downstream genes. Through their roles in extensive gene networks, these 24 upstream regulators are situated to either drive major changes in target gene expression or modify the cellular environment in which other genes function, thereby directing major developmental transitions in the preimplantation embryo. The data presented here highlight some of the specific molecular features that likely drive preimplantation development in a nonhuman primate species and provides an extensive database for novel hypothesis-driven studies.