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Dev Biol 2017 Jun 15;4262:301-324. doi: 10.1016/j.ydbio.2016.09.017.
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Conservatism and variability of gene expression profiles among homeologous transcription factors in Xenopus laevis.

Watanabe M , Yasuoka Y , Mawaribuchi S , Kuretani A , Ito M , Kondo M , Ochi H , Ogino H , Fukui A , Taira M , Kinoshita T .

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.

PubMed ID: 27810169
Article link: Dev Biol

Species referenced: Xenopus tropicalis Xenopus laevis
Genes referenced: alx1 arx bix1.1 bmal2 brms1l clock cry1 cry2 crygdl.43 ctc1 dmrt1 drgx eomes foxa1 foxa2 foxd3 foxg1 foxh1 foxh1.2 foxj2 foxm1 foxn1 foxn3 foxp4 foxr1 gata1 gata2 gata3 gata4 glis1 grm6 gsc gsc2 hbox10 hes1 hes2 hes3 hes4 hes5 hes5.10 hes5.4 hes5.5 hes5.6 hes5.7 hes5.8 hes5.9 hes6.1 hes7.1 id4 impdh1 isl2 isx lhx2 lhx3 lhx5 lhx9 lmx1b lmx1b.2 mbip mipol1 mix1 mixer nkx1-2 nkx2-1 nkx2-3 nkx2-6 nkx2-8 nkx3-1 nkx3-3 nkx6-1 nkx6-2 npas2 nudt9 otx1 otx2 pax1 pax2 pax3 pax4 pax5 pax6 pax7 pax8 pax9 pdcl3 per1 per2 per3 phox2a pitx1 pitx2 pou1f1 pou5f3 pou6f1 pou6f2 prrx1 prrx2 rax rlim rpl31 sebox slc25a21 snd1 sox12 sox13 sox14 sox17a sox18 sox2 sox21 sox6 ssbp3 sstr1 tbx1 tbx6 tbx6r tcf19 tef vamp1 vamp2 ventx1 ventx1.2 ventx2 ventx2.2 ventx3 ventx3.2

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