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PLoS One 2023 Jan 01;186:e0287858. doi: 10.1371/journal.pone.0287858.
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Metamorphic gene regulation programs in Xenopus tropicalis tadpole brain.

Raj S , Sifuentes CJ , Kyono Y , Denver RJ .

Amphibian metamorphosis is controlled by thyroid hormone (TH), which binds TH receptors (TRs) to regulate gene expression programs that underlie morphogenesis. Gene expression screens using tissues from premetamorphic tadpoles treated with TH identified some TH target genes, but few studies have analyzed genome-wide changes in gene regulation during spontaneous metamorphosis. We analyzed RNA sequencing data at four developmental stages from the beginning to the end of spontaneous metamorphosis, conducted on the neuroendocrine centers of Xenopus tropicalis tadpole brain. We also conducted chromatin immunoprecipitation sequencing (ChIP-seq) for TRs, and we compared gene expression changes during metamorphosis with those induced by exogenous TH. The mRNA levels of 26% of protein coding genes changed during metamorphosis; about half were upregulated and half downregulated. Twenty four percent of genes whose mRNA levels changed during metamorphosis had TR ChIP-seq peaks. Genes involved with neural cell differentiation, cell physiology, synaptogenesis and cell-cell signaling were upregulated, while genes involved with cell cycle, protein synthesis, and neural stem/progenitor cell homeostasis were downregulated. There is a shift from building neural structures early in the metamorphic process, to the differentiation and maturation of neural cells and neural signaling pathways characteristic of the adult frog brain. Only half of the genes modulated by treatment of premetamorphic tadpoles with TH for 16 h changed expression during metamorphosis; these represented 33% of the genes whose mRNA levels changed during metamorphosis. Taken together, our results provide a foundation for understanding the molecular basis for metamorphosis of tadpole brain, and they highlight potential caveats for interpreting gene regulation changes in premetamorphic tadpoles induced by exogenous TH.

PubMed ID: 37384728
PMC ID: PMC10310023
Article link: PLoS One

Species referenced: Xenopus tropicalis Xenopus laevis
Genes referenced: aurka aurkb avp bmp1 calm1 camk1d cdc16 cdc27 cdk14 cdk15 cdk17 cdk5r2 cdkl5 cdkn1a chrm2 dio3 dock3 e2f5 eef1a1 eef1a1o eef1b2 eif3d eif3e esr1 fabp2 gadd45g gal.1 galr1 gnrh1 gnrhr2 grin3b hba1 hbg1 hes4 hes5.3 hes5.4 hes6.2 hsd17b6 igfbp2 inhbb ins klf9 maoa mbp mc4r myc nacc1 nes neurod6 notch1 nr3c2 p2rx5 p2ry1 prl.1 rgcc riox2 rpl3 rpl9 rps19 scn5a snap25 snap91 sstr2 star tet2 tet3 thibz thrb trpm8 vim
GO keywords: Wnt signaling pathway [+]

Article Images: [+] show captions
References [+] :
Abu-Jamous, Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data. 2018, Pubmed