Abstract
The early embryonic genome exists in a dormant state following fertilization, and it then subsequently undergoes broad activation of zygotic transcription at the early stages of development. A major challenge is the detection of newly made zygotic transcripts and the determination of their activation onset time due to the presence of large and predominantly maternal pool of RNAs. Here we describe a detailed method to measure the zygotic transcription during zygotic genome activation (ZGA) of Xenopus early embryos using metabolic labeling of nascent transcripts with 5-ethynyl uridine (5-EU) followed by purifying and sequencing the nascent EU-RNAs (EU-RNA-seq). This method is highly sensitive in detecting early zygotic transcripts that are not detected by total RNA-seq and determines the actual onset time of transcriptional activation for zygotic genes. The method is applicable to a wide variety of embryonic model systems and has already afforded novel insights into gene regulation in early embryogenesis.