Dosage Compensation of the X Chromosomes in Bovine Germline, Early Embryos, and Somatic Tissues

Abstract

Dosage compensation of the mammalian X chromosome (X) was proposed by Susumu Ohno as a mechanism wherein the inactivation of one X in females would lead to doubling the expression of the other. This would resolve the dosage imbalance between eutherian females (XX) versus male (XY) and between a single active X versus autosome pairs (A). Expression ratio of X- and A-linked genes has been relatively well studied in humans and mice, despite controversial results over the existence of upregulation of X-linked genes. Here we report the first comprehensive test of Ohno’s hypothesis in bovine preattachment embryos, germline, and somatic tissues. Overall an incomplete dosage compensation (0.5 < X:A < 1) of expressed genes and an excess X dosage compensation (X:A > 1) of ubiquitously expressed “dosage-sensitive” genes were seen. No significant differences in X:A ratios were observed between bovine female and male somatic tissues, further supporting Ohno’s hypothesis. Interestingly, preimplantation embryos manifested a unique pattern of X dosage compensation dynamics. Specifically, X dosage decreased after fertilization, indicating that the sperm brings in an inactive X to the matured oocyte. Subsequently, the activation of the bovine embryonic genome enhanced expression of X-linked genes and increased the X dosage. As a result, an excess compensation was exhibited from the 8-cell stage to the compact morula stage. The X dosage peaked at the 16-cell stage and stabilized after the blastocyst stage. Together, our findings confirm Ohno’s hypothesis of X dosage compensation in the bovine and extend it by showing incomplete and over-compensation for expressed and “dosage-sensitive” genes, respectively.

TAF4b transcription networks regulating early oocyte differentiation

“…Boxplots of log2 fold change between the autosomes and X chromosomes used the output of DESeq2 as input, based on other publications comparing autosomal and X chromosome expression (Hirota et al 2018). The X:A ratio was calculated using pairwiseCI (v. 0.1.27), a bootstrapping R package, after filtering genes for an average TPM > 1 (Duan et al 2019b;Sangrithi et al 2017). The RXE was calculated using a custom R script based after filtering genes for an average TPM > 1 and adding pseudocounts for log transformation (log2(x+1)), based on other RXE publications (Duan et al 2019a;Jue et al 2013).…”

Conditional knockdown of transformer in sheep blow fly suggests a role in repression of dosage compensation and potential for population suppression

“…It is unclear why autosomal RNA levels are different between the strains but as a consequence all further statistical analyses were done on the normalized RNA levels within each strain or the XX/XY ratios between strains. Consequently, we next calculated the X:A ratio, the ratio of overall expression of the X chromosome to autosomes [ 35 , 36 ], for each sex for both strains. The X:A ratio was significantly higher for DR3#6; LctraIR7 XX than XY pupae ( P < 0.0001; Tukey’s HSD), consistent with hyperactivation of the X chromosome ( Fig 5C ).…”

TAF4b Transcriptional Regulation During Cellular Quiescence of Developing Prospermatogonia

“…For X chromosome analysis, boxplots of log2 fold change between the autosomes and X chromosomes used the output of DESeq2 as input, based on other publications comparing autosomal and X chromosome expression [47]. The X:A ratio was calculated using pairwiseCI (v. 0.1.27), a bootstrapping R package, after filtering genes for an average TPM > 1 [48,49]. The RXE was calculated using a custom R script based after filtering genes for an average TPM > 1 and adding pseudocounts for log transformation (log2(x+1)), based on other RXE publications [50,51].…”