During the maternal-to-zygotic transition (MZT), maternal transcriptome should be degraded, and replaced by zygotic transcripts in a highly coordinated manner. As transcription is silenced in early stages, transcriptome is regulated by cytoplasmic polyadenylation and RNA decay. We recently developed a new high-throughput sequencing technique, coined TAIL-seq, that profiles the poly(A) length and 3′-end modifications. TAIL-seq enables us to monitor the dynamics of adenylation, deadenylation and nucleotide tagging to the 3′-end of maternal RNAs with single-nucleotide resolution at genomic scale.
In this study, we apply TAIL-seq to early stage embryos of zebrafish to reveal how the RNA regulatory mechanisms influence the transcriptome. Our data confirm that poly(A) tails of most mRNAs elongate shortly after fertilization until the middle of the MZT, while a smaller group of transcripts escapes from this regulation. Surprisingly, most maternal RNAs acquire U tails in addition to poly(A) tails during the MZT. This phenomenon is observed in mouse and Xenopus laevis embryos, as well.
We identify Zcchc6 (also known as TUT7) and Zcchc11 (also known as TUT4) as the enzymes responsible for uridylation with further TAIL-seq experiments using morpholino-mediated knockdown. The maternal RNA clearance in zebrafish is significantly delayed during the MZT when Zcchc6 and Zcchc11 are knocked down, indicating that uridylation facilitates mRNA decay. Furthermore, the depletion of those enzymes delays the progression to gastrula in both zebrafish and Xenopus laevis. Thus, uridylation is indispensable for early embryogenesis.
We previously showed that human orthologs of Zcchc6 and Zcchc11 are pivotal to uridylation of messenger RNAs for their decay, and prefer short poly(A) tails. Our current data suggest that Zcchc6 and Zcchc11 contribute to selective clearance of molecules with short poly(A) tails. Indeed, maternal RNAs with shorter poly(A) tails elude the degradation in the MZT when the expression of Zcchc6 and Zcchc11 proteins are repressed.
In conclusion, Zcchc6 and Zcchc11 add uridine tails to short poly(A) tails in the vertebrate MZT, which is essential for the precise regulations of maternal factor expression in the early embryogenesis.