Conservatism and variability of gene expression profiles among homeologous transcription factors in Xenopus laevis

Abstract

Xenopus laevis has an allotetraploid genome of 3.1Gb, in contrast to the diploid genome of a closely related species, Xenopus tropicalis. Here, we identified 412 genes (189 homeolog pairs, one homeologous gene cluster pair, and 28 singletons) encoding transcription factors (TFs) in the X. laevis genome by comparing them with their orthologs from X. tropicalis. Those genes include the homeobox gene family (Mix/Bix, Lhx, Nkx, Paired, POU, and Vent), Sox, Fox, Pax, Dmrt, Hes, GATA, T-box, and some clock genes. Most homeolog pairs for TFs are retained in two X. laevis subgenomes, named L and S, at higher than average rates (87.1% vs 60.2%). Among the 28 singletons, 82.1% were deleted from chromosomes of the S subgenome, a rate similar to the genome-wide average (82.1% vs 74.6%). Interestingly, nkx2-1, nkx2-8, and pax9, which reside consecutively in a postulated functional gene cluster, were deleted from the S chromosome, suggesting cluster-level gene regulation. Transcriptome correlation analysis demonstrated that TF homeolog pairs tend to have more conservative developmental expression profiles than most other types of genes. In some cases, however, either of the homeologs may show strongly different spatio-temporal expression patterns, suggesting neofunctionalization, subfunctionalization, or nonfunctionalization after allotetraploidization. Analyses of otx1 suggests that homeologs with much lower expression levels have undergone greater amino acid sequence diversification. Our comprehensive study implies that TF homeologs are highly conservative after allotetraploidization, possibly because the DNA sequences that they bind were also duplicated, but in some cases, they differed in expression levels or became singletons due to dosage-sensitive regulation of their target genes.

Tissue-Specific Gene Inactivation inXenopus laevis: Knockout oflhx1in the Kidney with CRISPR/Cas9

“…Lhx1 protein was first detected in 1-cell embryos, with increased expression around gastrulation (stage 10-12) after the midblastula transition ( Figure 7B). Lhx1 levels decreased between stages 25 and 30 and increased during later tadpole stages (35-40), corresponding to previously published mRNA expression data (Taira et al 1992;Session et al 2016;Watanabe et al 2017) and the results seen in slc45a2 knockout embryos ( Figure 7A). Taken together, these data indicate that low levels of maternally loaded lhx1 RNA and/or Lhx1 protein may compensate for the genomic knockout during head formation, and that knockout of slc45a2 does not alter the embryo stage-specific Lhx1 expression pattern.…”

“…There are multiple potential explanations for this observation. Unlike morpholinos or dominant negative constructs, CRISPR should not affect maternal protein or RNA (Watanabe et al 2017). Prior studies suggest that CRISPR may not influence early Xenopus embryonic development due to unaffected maternal mRNA and protein deposits (Bhattacharya et al 2015).…”

A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs

“…In the two Xenopus species, the single mammalian gene encoding Mix-like 1 (Mixl1) is represented by mix1, mixer , and species-specific expansions and losses of genes referred to as bix [89]. …”

ADAMTS9, a member of the ADAMTS family, in Xenopus development

“…It is known that 92% of the genes are conserved between X. tropicalis and the subgenome L of X. laevis when only 68% are conserved between X. tropicalis and the subgenome S of X. laevis (Session et al, 2016). The Xenopus ADAMTS gene family have the following proportions: 100% are present in X. tropicalis and X. laevis subgenome L but only 63% are present in X. laevis subgenome S. Some of the ADAMTS genes used in this study are not located on chromosomes or have not been annotated thus these data can help improve the genome assembly by allocating ADAMTS genes into the correct chromosome (Watanabe et al, 2016). The phylogenetic study shows that the ADAMTS family is conserved between Xenopus, human and mouse suggesting possible conservation of their functions.…”