Return to search results Title: Nascent transcriptome of Xenopus laevis embryos at mid-blastula transition (MBT) stages

Summary

To validate that EU-RNA imaging provides a direct readout of wide-spread zygotic transcription, we sought to identify the nascent transcriptome using RNA-seq. We micoinjected 5-ethynyl uridine (EU) into 1-cell Xenopus embryos, isolated total RNA from embryos at mid-blastula transition (MBT), biotinylated EU-RNA and purified it to generate cDNA libraries for sequencing. Total RNA from normal embyros were used as control. We found over 25,000 nascent genes in this EU-RNA dataset at mid-ZGA. The nascent transcriptome dataset captures nearly 90% of the transcripts present in the whole-embryo dataset and with similar or better read-depth, indicating that our EU-RNA imaging is truly representative of wide-spread zygotic transcription. Furthermore, of the known zygotic genes that are most highly induced at MBT, we detected all of them and at much higher levels than in the whole-embryo dataset. These results show that our labeling captures the nascent zygotic transcriptome. We found ~ 4-fold higher sensitivity for nascent transcripts in the EU-RNA dataset compared to the whole embryo dataset, and as excepted we did not detect thousands of maternal-only transcripts in the nascent dataset. Together, these results suggest that EU-labeling provides a visual readout of bona fide nascent zygotic transcripts.

Contributors: Matthew Good, Hui Chen, Matthew Good

Experiment Type: Duplicates for nascent EU-RNA from EU-injected embryos and total RNA from normal embryos, respectively

Experiment Reagents: 5-Ethynyluridine.


Article: XB-ART-56041, PubMed

Source: NCBI GEO, Xenbase Download

Sample	View		GSMs	Assay Type
WE - NF9 GSM3832851  GSM3832852  RNA-Seq [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9      WE + 5-EU - NF9 DEG GSM3832849  GSM3832850  RNA-Seq [-] [+] Background: Xla.Outbred Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area chemical 5-Ethynyluridine NF stage 1 zygote Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9

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