Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors

Abstract

Embryonic development relies on activating and repressing regulatory influences that are faithfully integrated at the core promoter of individual genes. In vertebrates, the basal machinery recognizing the core promoter includes TATA-binding protein (TBP) and two TBP-related factors. In Xenopus embryos, the three TBP family factors are all essential for development and are required for expression of distinct subsets of genes. Here, we report on a non-canonical TBP family-insensitive (TFI) mechanism of transcription initiation that involves mesoderm and organizer gene expression. Using TBP family single- and triple-knockdown experiments, α-amanitin treatment, transcriptome profiling and chromatin immunoprecipitation, we found that TFI gene expression cannot be explained by functional redundancy, is supported by active transcription and shows normal recruitment of the initiating form of RNA polymerase II to the promoter. Strikingly, recruitment of Gcn5 (also known as Kat2a), a co-activator that has been implicated in transcription initiation, to TFI gene promoters is increased upon depletion of TBP family factors. TFI genes are part of a densely connected TBP family-insensitive T-box-Otx2-Gsc interaction network. The results indicate that this network of genes bound by Vegt, Eomes, Otx2 and Gsc utilizes a novel, flexible and non-canonical mechanism of transcription that does not require TBP or TBP-related factors.

Arid3a regulates nephric tubule regeneration via evolutionarily conserved regeneration signal-response enhancers

“…ChIP was performed as described previously (Gazdag et al, 2016). Myc-Xtr.arid3a -, Xtr.Arid3b -, and mouse kdm4a mRNA-injected embryos were collected at stages 35/36 and subjected to ChIP using Dynabeads Protein A (Dynabeads, Great Neck, NY, USA).…”

Using Xenopus to understand human disease and developmental disorders

“…For example, investigations of the molecular regulation of the cell cycle continue to use Xenopus oocytes, eggs and embryos as a major model (Malhotra, Vinod, Mansfeld, Stemmann, & Mayer, ; Sabherwal, Thuret, Lea, Stanley, & Papalopulu, ; Sanuki et al, ). Xenopus also has greatly enhanced our understanding of DNA replication and repair (Kalb, Mallery, Larkin, Huang, & Hiom, ; Long, Joukov, Budzowska, & Walter, ; Räschle et al, ; Shintomi, Takahashi, & Hirano, ; Zhang et al, ), and the mechanisms of genome organization, transcriptional regulation, and epigenetics (Belikov, Berg, & Wrange, ; Bogdanović et al, ; Buisine et al, ; Gazdag, Jacobi, van Kruijsbergen, Weeks, & Veenstra, ; Gao et al, ; Hontelez et al, ; Owens et al, ; Tamaoki et al, ; Wang et al, ; Wen, Fu, Guo, Chen, & Shi, ). Numerous studies in Xenopus elucidate mechanisms of morphogenesis and organogenesis ( Agricola et al, ; Bestman, Huang, Lee‐Osbourne, Cheung, & Cline, ; Metikala, Neuhaus, & Hollemann, ; Mimoto, Kwon, Green, Goldman, & Christian, ; Nie & Bronner, ; Okada, Wen, Miller, Su, & Shi, ; Ossipova et al, ; Tanizaki, Ishida‐Iwata, Obuchi‐Shimoji, & Kato, ).…”

“…, and the mechanisms of genome organization, transcriptional regulation, and epigenetics (Belikov, Berg, & Wrange, 2016;Bogdanović et al, 2016;Buisine et al, 2015;Gazdag, Jacobi, van Kruijsbergen, Weeks, & Veenstra, 2016;Gao et al, 2016;Hontelez et al, 2015;Owens et al, 2016;Tamaoki et al, 2016;Wang et al, 2014;Wen, Fu, Guo, Chen, & Shi, 2015). Numerous studies in Xenopus elucidate mechanisms of morphogenesis and organogenesis (Agricola et al, 2016;Bestman, Huang, Lee-Osbourne, Cheung, & Cline, 2015;Metikala, Neuhaus, & Hollemann, 2016;Mimoto, Kwon, Green, Goldman, & Christian, 2015;Nie & Bronner, 2015;Okada, Wen, Miller, Su, & Shi, 2015;Ossipova et al, 2015;Tanizaki, Ishida-Iwata, Obuchi-Shimoji, & Kato, 2015).…”

Evolution of Diverse Strategies for Promoter Regulation

“…Notably, the complexity of promoter architecture increases when viewed in eukaryotes that are complex multicellular organisms compared with single-cell organisms (prokaryotes and eukaryotes), with tissuespecific promoter regulation becoming critical in the former category. Various examples have also been identified for TBP-independent transcription in eukaryotes (e.g., [19]). Such transcription processes clearly have sequence and structural requirements, but these differ from examples described here and are beyond the remit of this review.…”