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Sci Rep 2017 Jul 25;71:6414. doi: 10.1038/s41598-017-06679-x.
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Genome-wide identification of thyroid hormone receptor targets in the remodeling intestine during Xenopus tropicalis metamorphosis.

Fu L , Das B , Matsuura K , Fujimoto K , Heimeier RA , Shi YB .

Thyroid hormone (T3) affects development and metabolism in vertebrates. We have been studying intestinal remodeling during T3-dependent Xenopus metamorphosis as a model for organ maturation and formation of adult organ-specific stem cells during vertebrate postembryonic development, a period characterized by high levels of plasma T3. T3 is believed to affect development by regulating target gene transcription through T3 receptors (TRs). While many T3 response genes have been identified in different animal species, few have been shown to be direct target genes in vivo, especially during development. Here we generated a set of genomic microarray chips covering about 8000 bp flanking the predicted transcription start sites in Xenopus tropicalis for genome wide identification of TR binding sites. By using the intestine of premetamorphic tadpoles treated with or without T3 and for chromatin immunoprecipitation assays with these chips, we determined the genome-wide binding of TR in the control and T3-treated tadpole intestine. We further validated TR binding in vivo and analyzed the regulation of selected genes. We thus identified 278 candidate direct TR target genes. We further provided evidence that these genes are regulated by T3 and likely involved in the T3-induced formation of adult intestinal stem cells during metamorphosis.

PubMed ID: 28743885
PMC ID: PMC5527017
Article link: Sci Rep

Species referenced: Xenopus tropicalis
Genes referenced: abhd11 actg1 acvr1b acy1.1 afg2a akap9 aldh2 ankrd17 anp32a apmapl arhgap18 arpp19 asah2 atad2b atosa babam2 bend7 bnip3 bpnt2 brd1 btg3 c1h14orf119 ca2 camk2g capza2 ccdc136 ccnf ccnj cdc14b cebpa celf4 cers2 ciapin1 cited4 cndp1 commd5 cops5 creld2 csnk1g3 ctu1 cul4a cyct cyp20a1 cyp4b1.5 dbp decr1 dhcr24 dll1 dot1l dpy19l4 dtx2 dusp6 dydc1 echdc2 efnb2 eif2s1 eif5 etfb etnppl fbxo6 fhod1 flvcr2 foxo3 foxo6 gadd45g galnt2 gata6 gatm gca ghsr gmppa gpat4 gpatch8 gsdme gtdc1 h2ac21 h2az1 h3-3b hadhb haghl hal.2 hbp1 hmgn1 hnf1b hook1 hoxa4 hoxd13 hps5 hyal1 idh1 idh2 ier5 igfbp1 ikzf2 il4i1 inpp5j insig1 irf2bpl isoc1 ivd junb jup KIAA0232 klf11 klf9 letmd1 lgals4.1 lonrf1 mark3 mbd3 mettl1 MGC75872 MGC89226 mhc1a mindy2 mospd2 mpc1 mplkip mrpl46 mrps30 mtfp1 mtmr14 mtrf1 myo19 myo5c n4bp1 narf ncbp2 ndufa3 nfib nfil3 nr4a1 nrg1 ntm nudt4 oaz1 ociad2 pafah1b1 pcca pdlim5 pex11a pgpep1 pias3 pim3 pla2g6 plcb2 plcxd2 plekhg1 pm20d2 pmpcb polr2e ppm1a ppm1b ppp1cc ppp1r11 prkaa1 prtfdc1 psmc6 ptch1 pum2 rabl2b ranbp9 rcbtb2 rhou rps2 runx1t1 rxrb sae1 sdha sec24d sema3b sema4g setd1a setd1b sgms1 sh3rf3 siah1 ski slc25a1 slc25a23 slc25a43 slc25a48 slc2a11 slc2a2 slc3a2 smarcc2 sox4 spag7 sptlc1 stk10 syap1 tfg tgfa thra thrb timm23 tiparp tmem130 tmem185a tmem241 tmem243 tmem67 tnfrsf10b tor2a triap1 trib2 trim63 trpm1 uba52 ubxn2a ufm1 ugp2 uqcrq urod vdac2 vgll1 vmo1 washc5 xpnpep2 xrcc3 zfp36 zmym2 znf420 znf706 znf827

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References [+] :
Amano, Isolation of genes involved in intestinal remodeling during anuran metamorphosis. 1998, Pubmed, Xenbase