X Chromosome Dosage Compensation

We are fascinated by Ohno’s Hypothesis of sex chromosome evolution and dosage compensation which suggests that the single X-chromosome in male is transcriptionally up-regulated to equalize its gene dosage to autosomes (A). Subsequently, X chromosome inactivation (XCI) is emerged in female to achieve dosage compensation between sexes and between X and A.

Whether this hypothesis is true in mammals is still highly controversial with much international debate. However, most studies were conducted in humans, mice or other model organisms. Therefore, we decided to test Ohno’s hypothesis in domestic species to enable cross-species comparison. Using RNA-seq datasets, we defined the first comprehensive profile of X-chromosome up-regulation (X-to-Autosome ratio) dynamics during early embryonic development and in somatic tissues in cattle and sheep. We also identified “dosage-sensitive” genes that require complete dosage compensation.

Genomic Imprinting

We used sheep model to study the effects of maternal diets on genomic imprinting patterns and genes expression. We first identified informative single nucleotide polymorphisms (SNPs) to trace all genes’ parental origins, and then tested for their allelic expression biases.

In total, we identified 13 novel imprinted genes in sheep and validated seven genes by independent methods. Moreover, we also characterized four novel imprinted clusters.

Although the maternal nutrition did not seem to change the genomic imprinting patterns, we found that maternal nutrition significantly altered imprinted gene expression levels, revealing that gene expression and genomic imprinting are regulated through different epigenetic mechanisms.

These results demonstrated that there is a trans-generational effect of maternal diet on fetal development on the epigenetic level and stressed the importance of a balanced diet during pregnancy. Further research should focus on parental effects of fetal epigenetic regulation and development.

Epigenetic Dynamics in Embryos

We initiated a collaborative research project to profile the methylome in bovine single pre-implantation embryos using RNA-seq, reduced representative bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (WGBS).

We found that after fertilization, the major wave of genome-wide DNA demethylation was complete at the 8-cell stage when de novo methylation became prominent. Sperm and oocytes had numerous differentially methylated regions (DMRs) which were enriched in intergenic regions. DMRs were also identified between in vivo and in vitro matured oocytes.

This is the first comprehensive analysis of the global dynamics of DNA methylation in bovine gametes and single early embryos. Our work provided new insight into the epigenetics of embryos produced by assisted reproduction such as in vitro fertilization as well as models for human early embryos for which studies on in vivo development are extremely limited. Future research should focus on define biomarkers that could be used to improve in vitro matured oocytes and embryos.

Zygotic Genome Activation

The process of ZGA is essential in all metazoans but remains poorly understood. Moreover, very little is known about how multiple pioneer TFs regulate zygotic genome activation (ZGA) in any organism. To define the underlying mechanism of early transcription factors regulating ZGA and chromatin remodeling in early embryos, we have employed diverse techniques including: classical genetics, functional genomics, chromatin mapping, bioinformatics and microscopy.

We identify the GA-binding factor CLAMP as a novel pioneer factor in fruit fly embryogenesis.  We combine diverse genomic, biochemical, and computational approaches to demonstrate: 1) CLAMP is a novel pioneer factor that binds to nucleosomal DNA, activates zygotic transcription, and increases chromatin accessibility at targeted loci; 2) CLAMP and Zelda function cooperatively at promoters of other essential TFs; 3) When Zelda is bound at a locus but does not open chromatin, CLAMP can open the chromatin to facilitate Zelda binding.  Overall, we determine that CLAMP is an essential pioneer factor that functions with Zelda to regulate fruit fly zygotic genome activation.