SUMMARY
One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the mid-blastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation, and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal and BMP signaling together generate most of the spatio-temporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.
Footnotes
Key changes to manuscript: Page 1, lines 29-33: We have replaced some references. We previously cited work on the DUX transcription factors, which are part of the first wave of zygotic transcription in mammals (De Iaco et al., 2017; Hendrickson et al., 2017; Whiddon et al., 2017). The maternal factors Dppa2 and Dppa4 have recently been shown to control transcription of the DUX genes, and we now refer to this work (De Iaco et al., 2019; Eckersley-Maslin et al., 2019). Page 2, lines 41-44: We have added more references to original and more up-to-date publications on RNA profiling to identify major waves of gene transcription in mouse and human embryos (Bolton et al., 1984 and Vanessa et al., 2011). Pages 4-5, lines 157-162: We have extended our analysis of the maternal contribution to zygotic gene expression. Page 5, lines 194-196: We have reanalyzed the morphological defects caused by the combined loss of Wnt and BMP signaling. Page 8, lines 309-311: We acknowledge the work of Chen et al. (2013). This study used ChIP-Seq at two developmental stages, pre-MBT (nuclear cycles 8-12) and MBT (nuclear cycles 13-14), to detect the progression of zygotic genome activation in Drosophila. Page 8, lines 314-319: We mention more studies that recorded changes to chromatin accessibility (Liu et al., 2018; Lu et al., 2016; Wu et al., 2016) and spatial chromatin organisation (Du et al., 2017; Flyamer et al., 2017) during the maternal-to-zygotic transition. Page 8, lines 324-327: We refer here to studies of temporal gene expression across MBT that are indicative of a gradual activation of the zygotic genome commencing before MBT in Drosophila, zebrafish and frogs (Ali-Murthy et al., 2013; Collart et al., 2014; Mathavan et al., 2005; Owens et al., 2017; Tan et al., 2013). Page 9, lines 344-348: We have updated the list of studies exploring transcriptional condensates (Boija et al., 2018; Chong et al., 2018; Sabari et al., 2018; Shrinivas et al., 2018). Page 10, lines 361-365: We have introduced references to key studies about the regulation of Wnt, Nodal and BMP signaling (Faure et al., 2000; Gentsch et al., 2018b; Heasman, 2006; Jones et al., 1995; Larabell et al., 1997; Schohl and Fagotto, 2002; Tao et al., 2005; Yang et al., 2002). Page 10, lines 372-375: We have summarised published work (Harvey et al., 2010), which corroborates our observations that several signals can be integrated at the chromatin level.