TY - JOUR T1 - SLAMseq resolves the kinetics of maternal and zygotic gene expression in early zebrafish embryogenesis JF - bioRxiv DO - 10.1101/2022.06.01.494399 SP - 2022.06.01.494399 AU - Pooja Bhat AU - Luis E. Cabrera-Quio AU - Veronika A. Herzog AU - Nina Fasching AU - Andrea Pauli AU - Stefan L. Ameres Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/06/02/2022.06.01.494399.abstract N2 - The maternal-to-zygotic transition (MZT) is a key developmental process in metazoan embryos that involves the activation of zygotic transcription (ZGA) and degradation of maternal transcripts. We employed metabolic mRNA sequencing (SLAMseq) to deconvolute the compound embryonic transcriptome in zebrafish. While mitochondrial zygotic transcripts prevailed prior to MZT, we uncover the spurious transcription of hundreds of short and intron-poor nuclear genes as early as the 2-cell stage. Upon ZGA, most zygotic transcripts originate from thousands of maternal-zygotic (MZ) genes that are transcribed at rates comparable to those of hundreds of purely zygotic genes and replenish maternal mRNAs at distinct timescales. Rapid replacement of MZ transcripts involves transcript decay features unrelated to major maternal degradation pathways and promotes de novo synthesis of the core gene expression machinery by increasing poly(A)-tail length and translation efficiency. SLAMseq hence provides unprecedented insights into the timescales, molecular features and regulation of MZT during zebrafish embryogenesis.Competing Interest StatementVAH and SLA declare competing interest based on a granted patent related to SLAMseq. SLA is co-founder, advisor, and member of the board of QUANTRO Therapeutics GmbH. ER -