Figure 4. Classification of genes based on timing of transcriptional initiation during early embryogenesis.
Using single-embryo RNA-seq data from our group (Lott et al., 2011), we identified three broad classes of genes: those at high levels in the earliest embryos (‘maternal’ genes), those not present in the earliest embryos, but transcribed prior to or during mitotic cycle 14 (‘zygotic’), and those not present through cycle 14 (‘silent’). We further divided the zygotic genes into four different groups based on their onset of zygotic expression—‘Early’ genes with onset of expression around mitotic cycles 10–11, ‘Mid’ genes at cycles 12–13, ‘Late’ genes at early cycle 14, and ‘Later’ zygotic genes whose onset of expression was during late cycle 14. Post-MBT polII ChIP data (Chen et al., 2013) was used to define two maternal groups of genes—those bound by polII in the embryo (‘Mat/Zyg’ genes), and those that are strictly maternally deposited (‘Mat-only’ genes). (A) Heatmap showing the expression levels for all groups at 8 timepoints (from cycle 10 through 14D) across the MZT (Lott et al., 2011). (B) Heatmaps showing RNA polymerase II ChIP-seq signals (Chen et al., 2013) around the transcription start sites (±1.5 kb) of the genes in each category for three developmental time points, pre-MBT (left), MBT (middle), and post-MBT (right) embryos. Genes within each group were ordered based on cycle 14 RNA polymerase II signals (genes with the highest signal are on top).