ENAapplication/xmlftp.sra.ebi.ac.uk/vol1/fastq/DRR001/DRR001819/DRR001819.fastq.gzprimaryOK2000000GenomicsLaboratory of Molecular Biology, Department of Biological Sciences, Graduate School of Science, The University of Tokyohttps://www.ebi.ac.uk/ena/browser/view/PRJDB2825Xenopus tropicalisIn vertebrates, homeodomain proteins Otx2 and Lim1/Lhx1 are required for head formation, but the regulatory principles underlying their functions in the head organizer remain unsolved. Here we show using ChIP-seq analysis that Otx2, Lim1, the coactivator p300 and the corepressor TLE/Groucho colocalize on cis-regulatory modules (CRMs) of thousands of genes including almost all ‘head-organizer’ genes in the Xenopus tropicalis gastrula. Comprehensive analysis of CRMs with RNA-seq data revealed that Lim1/Otx2-bound CRMs co-localizing with TLE rather than p300 are strongly associated with region/tissue-specific genes. Together with reporter analyses, our data suggest that Otx2 activates head-organizer genes with Lim1 and represses non-head-organizer genes with transcriptional repressors such as Goosecoid. Thus, it is likely that each of thousands of genes interprets Otx2 as a ‘positional tag’ to determine its expression in the head organizer, corroborating the idea that positional information directly contributes “massively parallel (distributive) gene regulation” rather than “hierarchal top-down gene control.” This general principle of gene regulation by region/tissue specific transcription factors may underlie the extraordinary diversities of morphologies in animals.ENAMotch A, LIP4, A430090G16, Materials, BcDNA:GH12350, determination, protanomaly, region or site annotation, MCG10, protan series, Gene, Dlim1, CBP/p300, lim-1, RSTS2, l(3)04539, dmCBP, CG15321, p300 HAT, C819, DmelCG7467, CG15319, red colour blindness, p300, Whole Transcriptome Shotgun Sequencing, DmelCG15319, CG11354, Crbp, dKAT3, partial, Notch 1 extracellular truncation, portion of tissue, MCOPS5, l(3)j9C3, colorblindness, positional, LIM-1, Protan defect, red color blindness, Notch 1, Genetic, 5'-cAMP response element binding protein binding, red colorblindness, EIF4EL1, protan, 5' cAMP response element binding protein binding, RTS, CREB binding, Tissue, xlim-1, 3', Notch 1 intracellular domain, protan type, anon-WO0172774.126, l(3)00090, en(lz)4F/4H, Lim, Nej, site, PAG, associated, NICD, CG1435, dLim1, data, BcDNA:GH04929, protan defect, 5'-cyclophosphate response element binding protein binding, Protanopia, anon-WO03040301.89, cyclic AMP response element binding protein binding, KAT3B, lim1, KAT3A, RNA-seq, CG7467, dlim-1, Cistrons, eld, RSTS, chemical analysis, CBP_, sequence, tissue portion, Genetic Materials, simple tissue, dlim1, region, partial achromatopsia, EIF4E1, p300/CBP, l(1)G0112, dCBP, l(1)G0350, l(1)G0470, DmelCG11354, DmelCG1435, positional polypeptide feature, CBP, Cbp, Nejire, protanopia, Dmel_CG15321, NEXT, mT14, EIF4F, AUTS19, A730011L11, Osa, OSA, primary structure of sequence macromolecule, LIM1, DOID:13910, Lim1, BcDNA.GH12350, nej CBP, E(E2F)3C, Material, anon-WO0147981.11, cbp, anon-WO0118547.314, Cistron, assay, Genetic Material., CPHD6, adenosine 3', CG10760Silurana tropicalis., tropical clawed frog, western clawed frog, Xenopus laevis tropicalis, Xenopus (Silurana) tropicalis, Xenopus tropicalis0.00.00.00.00.00falseXenopus tropicalisComprehensive analysis of CRMs with RNA-seq data revealed that Lim1/Otx2-bound CRMs co-localizing with TLE rather than p300 are strongly associated with region/tissue-specific genes.2022-05-112014-06-01PRJDB28258364