Direct contributions of Otx2 as a positional tag to global gene regulation in the head organizer in Xenopus embryos Yuuri Yasuoka1, Yutaka Suzuki2, Shuji Takahashi3, Norihiro Sudou1, Yoshikazu Haramoto4, Makoto Asashima4, Sumio Sugano2, and Masanori Taira1 1Dept of Biol Sci, Grad Sch of Sci; 2Dept of Med Genome Sci, Grad Sch of Front Sci; 3Div of Life Sci, College of Arts and Sci, Univ. of Tokyo; 4SCRC, Nat Inst of Adv Industrial Sci and Tech, Japan Bilaterians use the homeodomain protein Otx to form the head, but how its positional information is utilized remains uncertain. In vertebrates, both Otx2 and the LIM homeodomain protein Lim1/Lhx1 are required for head formation, but the regulatory principles underlying Lim1 and Otx2 functions in the head organizer remain unsolved. In this talk, I present our recent data using ChIP-seq analysis, showing that Otx2, Lim1, the coactivator p300, and the corepressor TLE/Groucho colocalize on cis-regulatory modules (CRMs) of thousands of genes including most ‘head-organizer’ genes and even most ‘non-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 functions as a ‘positional tag’ for a number of genes, in which Otx2 not only activates head-organizer genes in association with Lim1 but also 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. Our ‘positional tag hypothesis’ provides the idea that positional information conducts ‘distributive regulation’ of many genes, resulting in regional identity by the summation of these individual responses, which is contrast to ‘top-down control’ as the top of regulatory hierarchy defining regional identity. Based on these data, we are also analyzing histone modifications, H3K4me1 and H3K27Ac, for enhancer markers in comparison with Otx2/Lim1/TLE-bound CRM types and expression profiles, which will be discussed in the end of my talk.

Direct contributions of Otx2 as a positional tag to global gene regulation in the head organizer in Xenopus embryos

Yuuri Yasuoka1, Yutaka Suzuki2, Shuji Takahashi3, Norihiro Sudou1, Yoshikazu Haramoto4, Makoto Asashima4, Sumio Sugano2, and Masanori Taira1

1Dept of Biol Sci, Grad Sch of Sci; 2Dept of Med Genome Sci, Grad Sch of Front Sci; 3Div of Life Sci, College of Arts and Sci, Univ. of Tokyo; 4SCRC, Nat Inst of Adv Industrial Sci and Tech, Japan

Bilaterians use the homeodomain protein Otx to form the head, but how its positional information is utilized remains uncertain. In vertebrates, both Otx2 and the LIM homeodomain protein Lim1/Lhx1 are required for head formation, but the regulatory principles underlying Lim1 and Otx2 functions in the head organizer remain unsolved. In this talk, I present our recent data using ChIP-seq analysis, showing that Otx2, Lim1, the coactivator p300, and the corepressor TLE/Groucho colocalize on cis-regulatory modules (CRMs) of thousands of genes including most ‘head-organizer’ genes and even most ‘non-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 functions as a ‘positional tag’ for a number of genes, in which Otx2 not only activates head-organizer genes in association with Lim1 but also 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. Our ‘positional tag hypothesis’ provides the idea that positional information conducts ‘distributive regulation’ of many genes, resulting in regional identity by the summation of these individual responses, which is contrast to ‘top-down control’ as the top of regulatory hierarchy defining regional identity. Based on these data, we are also analyzing histone modifications, H3K4me1 and H3K27Ac, for enhancer markers in comparison with Otx2/Lim1/TLE-bound CRM types and expression profiles, which will be discussed in the end of my talk.