Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation

Translational regulation plays a critical role during the oocyte-to-embryo transition (OET) and zygotic genome activation (ZGA). Here, we integrated ultra-low-input ribosome profiling (Ribo-lite) with messenger RNA sequencing to co-profile the translatome and transcriptome in human oocytes and early embryos. Comparison with mouse counterparts identified widespread differentially translated gene functioning in epigenetic reprogramming, transposon defense, and small RNA biogenesis, in part driven by species-specific regulatory elements in 3′ untranslated regions. Moreover, PRD-like homeobox transcription factors, including TPRXL, TPRX1, and TPRX2, are highly translated around ZGA. TPRX1/2/L knockdown leads to defective ZGA and preimplantation development. Ectopically expressed TPRXs bind and activate key ZGA genes in human embryonic stem cells. These data reveal the conservation and divergence of translation landscapes during OET and identify critical regulators of human ZGA. Description Waking up the genome in human embryos How zygotic genome activation (ZGA), the first gene expression event in life, is started in human remains poorly understood. ZGA depends on translational activities at the preceding stages. Zou et al. profiled the translatome and transcriptome from the same samples of human oocytes and early embryos. Comparison with corresponding data from mice revealed both conserved and human-specific translational activities during the oocyte-to-embryo transition. The authors identified the TPRX transcription factor family, which includes TPRXL, a maternally inherited factor, and TPRX1/2, two early transcribed transcription factors after fertilization, as being critical regulators for ZGA and embryonic development in humans. —DJ TPRXs are key transcription factors regulating the first transcription event of life in human oocytes and early embryos. INTRODUCTION During the mammalian oocyte-to-embryo transition (OET), translation plays a critical role in regulating meiotic resumption, zygotic genome activation (ZGA), and early embryonic development. ZGA marks the first transcription event in a new life and the onset of the embryonic program. However, how mammalian ZGA is initiated remains poorly understood. For example, although key ZGA transcription factors (TFs) have been well characterized in other species such as zebrafish and fly, which TFs control human ZGA remains elusive. RATIONALE Studying the translatomes in human oocytes and early embryos is critical for understanding their posttranscriptional regulation during human OET and identifying candidate ZGA regulators. In particular, the TFs regulating ZGA are expected to arise either from translation of oocyte-inherited transcripts or from transcription during the early phase of ZGA, and their motifs should be enriched at enhancers and promoters of ZGA genes. However, translatome profiling in human oocytes and early embryos is severely hindered by the scarcity of research materials. Therefore, we sought to first profile the translatomes and transcriptomes from the same low-input samples of human oocytes and early embryos using an ultrasensitive method. Combined with analyses of the assay for transposase-accessible chromatin sequencing (ATAC-seq) datasets in human early embryos that we reported previously, candidate TFs for human ZGA were then identified. Their potential roles in genome activation and early development were assessed by gene knockdown in human embryos and overexpression analyses in human embryonic stem cells (hESCs). RESULTS By combining the ultrasensitive Ribo-lite (ligation-free, ultra-low-input, and enhanced Ribo-seq) with Smart-seq2 in a method we call Ribo-RNA-lite (R2-lite), we jointly profiled the translatome and transcriptome across eight stages of human oocytes and early embryos. Through comparison with their counterparts in mouse, we found not only genes with conserved translational activities but also widespread, differentially translated genes functioning in epigenetic reprogramming, transposon defense, and small RNA biogenesis. Species-specific translation is in part driven by different configurations of regulatory elements such as cytoplasmic polyadenylation element (CPE) and polyadenylation signal site (PAS) in the 3′ untranslated regions (3′UTRs). Using the R2-lite data, we found that a group of PRD-like homeobox TFs became highly translated before or during ZGA, with their motifs enriched in distal open chromatin regions (putative enhancers) near activated genes upon ZGA. These TFs include TPRXL, which is encoded by a CPE-containing maternal transcript subjected to translation up-regulation upon meiotic resumption, and TPRX1/2, which are expressed during the early phase of ZGA (minor ZGA). The joint knockdown of TPRX1/2/L [TPRX triple KD (TKD)] led to severe defects in development and ZGA. About 31% of ZGA genes that preferentially contain PRD-like TF-binding motifs at promoters and nearby putative enhancers were down-regulated in TPRX TKD embryos. These TPRX target genes include ZSCAN4, DUXB, DUXA, NANOGNB, DPPA4, GATA6, DPRX, ARGFX, RBP7, and KLF5, many of which encode key transcription regulators. Finally, ectopically expressed TPRXs could bind and activate a subset of ZGA genes in hESCs. CONCLUSION Here, we charted the translational landscapes during the human OET. Comparison of data in mouse identified widespread differentially translated genes, in part driven by species-specific configuration of key regulatory elements in the 3′UTRs. This dataset further identified a group of PRD-like homeobox TFs, including TPRXL, TPRX1, and TPRX2, that are highly translated around ZGA. TPRXs are required for proper ZGA and preimplantation development and are also sufficient to activate key ZGA genes when ectopically expressed in hESCs. Therefore, these data not only reveal the conservation and divergence of translational regulation during OET but also identify critical TF regulators of human ZGA. Translatome-transcriptome co-profiling in human oocytes and early embryos reveals key human ZGA factors. The translatome and transcriptome were co-profiled in human oocytes and early embryos. Comparison with mouse reveals widespread species-specific translation from oocytes (full-grown oocytes depicted) to embryos, in part driven by distinct configurations of regulatory elements in 3′UTRs, including CPEs. The TPRX family TFs TPRXL/1/2 are highly translated around ZGA and are identified as critical regulators of human ZGA.