High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing

Yunbo Qiao,Shisheng Huang,Qiuzhen Chen,Xiangyang Li,Wenjie Shu,Chao Ren,Xingchen Liu,Jianxiang Lin,Jie Yuan,Xiaochen Bo,Xingxu Huang,Zhen Liu,Susu Wu,Jiao Fan

doi:10.1038/s41467-020-16444-w

Abstract

The transcriptome of the preimplantation mouse embryo has been previously annotated by short-read sequencing, with limited coverage and accuracy. Here we utilize a low-cell number transcriptome based on the Smart-seq2 method to perform long-read sequencing. Our analysis describes additional novel transcripts and complexity of the preimplantation transcriptome, identifying 2280 potential novel transcripts from previously unannotated loci and 6289 novel splicing isoforms from previously annotated genes. Notably, these novel transcripts and isoforms with transcription start sites are enriched for an active promoter modification, H3K4me3. Moreover, we generate a more complete and precise transcriptome by combining long-read and short-read data during early embryogenesis. Based on this approach, we identify a previously undescribed isoform of Kdm4dl with a modified mRNA reading frame and a novel noncoding gene designated XLOC_004958. Depletion of Kdm4dl or XLOC_004958 led to abnormal blastocyst development. Thus, our data provide a high-resolution and more precise transcriptome during preimplantation mouse embryogenesis.

Highlights

The transcriptome of the preimplantation mouse embryo has been previously annotated by short-read sequencing, with limited coverage and accuracy
To characterize preimplantation embryo transcripts with more accurate information, we profiled the transcriptome using both long-read and short-read sequencing across mouse preimplantation developmental embryos derived from C57BL/6J × DBA/2 crosses (Fig. 1a)
We aimed to elucidating potential novel transcripts and strain-specific splicing isoforms as well as events involved in early embryogenesis

Summary

Introduction

The transcriptome of the preimplantation mouse embryo has been previously annotated by short-read sequencing, with limited coverage and accuracy. We generate a more complete and precise transcriptome by combining long-read and short-read data during early embryogenesis Based on this approach, we identify a previously undescribed isoform of Kdm4dl with a modified mRNA reading frame and a novel noncoding gene designated XLOC_004958. Even Dux, a previously wellaccepted ZGA factor[20], has recently been proposed to be a dispensable gene for this process[21] These findings drove us to identify novel transcripts and splicing variants involved in ZGA and preimplantation embryogenesis. We utilize the single-molecule real-time (SMRT) platform of Pacific Biosciences for full-length sequencing with high accuracy to improve the annotation of the mouse preimplantation transcriptome and generate a more accurately described transcriptome with additional novel transcripts and splicing isoforms. Our study provides an important resource for the high-resolution annotation of the transcriptome for interpreting early embryo development

Objectives

Methods

Results

Conclusion