High-resolution analysis of gene activity during the Xenopus mid-blastula transition

Abstract

The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here, we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilisation wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the seventh cleavage and extending beyond the MBT at the twelfth cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal mRNAs that are deadenylated shortly after fertilisation, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organisation of gene regulatory networks in the early Xenopus embryo.

Regulation of zygotic genome activation and DNA damage checkpoint acquisition at the mid-blastula transition

“…Indeed, analyses of RNA synthesis and large-scale gene expression have found zygotic gene expression in Drosophila, Xenopus and zebrafish well before the MBT. 1,[4][5][6]45,46 Additionally, gene expression profiling data from haploid and diploid Drosophila embryos suggest more complex regulation of zygotic transcription, with distinct subsets of zygotic transcripts that depend either on time or on the N:C ratio. 1 Our studies also provide insight into cell cycle remodeling at the MBT.…”

New insights into the maternal to zygotic transition

“…Thus, of the 286 X. tropicalis genes thought to be polyadenylated within three hours of fertilisation, 254 (89%) were also classified by Aanes et al (2011) as being maternal transcripts subject to polyadenylation in zebrafish (Aanes et al, 2011;Collart et al, 2014). As in the zebrafish, the products of polyadenylated maternal mRNAs in X. tropicalis are necessary for the proper activation of zygotic transcription: treatment of embryos with cordycepin, which blocks polyadenylation, prevented the normal activation of many, but not all, zygotically activated genes.…”

“…been identified and the Xenopus orthologue of pou5f1 (Oct91) cannot be detected maternally (Collart et al, 2014). Of the Sox genes, Sox1 and Sox2 were both detected at low levels maternally before being strongly activated at around the time of the MBT, and only Sox3 has significant levels of maternal transcripts in X. tropicalis.…”

“…Genes activated during the MZT and their participation in a gene regulatory network Similar to the studies discussed above, sequencing-based methods have been used to study the onset of transcription in X. tropicalis, with samples taken for RNA sequencing at intervals of 30 min from fertilisation, through the MBT and up to the early gastrula stage (Collart et al, 2014). This high-resolution study allows one to infer with more confidence the structure of gene regulatory networks in the embryo as well as to make comparisons with other species.…”

Single‐Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16‐Cell Frog (Xenopus) Embryo

“…Proteins that were identified or quantified during this work compare favorably to transcripts that were recently identified in the early developing embryo using next‐generation sequencing technologies 28, 29. Table S6 tabulates 998 transcripts for which we have manually confirmed the corresponding transcript in the published mRNA datasets.…”