TRANSCRIPTIONAL MULTIPOTENCY IN EARLY EMBRYO

In embryo stages, larvae and adult-differentiated red spherules, proximal and distal TREs are detected by Precision Run-On Sequencing (PRO-seq), which maps genome-wide the location of paused or elongating RNA polymerase Pol II at base pair resolution, thus enabling the genome-wide location of TRE transcription start sites along with their proximal pause and pause-release rates. In parallel, TRE accessibility is estimated by ATAC-seq. Our analysis identifies surprisingly early and widespread TRE accessibility in four-cell cleavage embryos that is not necessarily associated with concurrent or subsequent transcription. TRE transcriptional differences identified by PRO-seq provide more contrast among embryonic stages than ATAC-seq accessibility differences, in agreement with the excess of accessible but inactive TREs during embryogenesis. Global TRE accessibility reaches a maximum around the late blastula stage, which coincides with the consolidation of major embryo regionalization and peak histone variant H2A.Z expression. A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during embryogenesis. Our analysis also reveals that a large number of distal TREs become transcriptionally disengaged during developmental progression, in support of an early Pol II paused model for developmental gene regulation that eventually resolves in prompt transcriptional activation or permanent silencing. Thus, developmental potency in early embryos may be facilitated by widespread incipient accessibility and transcriptional pause at developmental TREs.