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

Area of Science:

• Developmental Biology
• Genomics
• Transcriptomics

Background:

• Previous short-read sequencing of the preimplantation mouse embryo transcriptome offered limited coverage and accuracy.
• Understanding the full complexity of early embryonic gene expression is crucial for developmental biology.

Purpose of the Study:

• To generate a more complete and precise transcriptome of the preimplantation mouse embryo.
• To identify novel transcripts and splicing isoforms using advanced sequencing techniques.

Main Methods:

• Utilized low-cell number Smart-seq2 method for long-read sequencing of the preimplantation mouse embryo transcriptome.
• Combined long-read and short-read sequencing data for comprehensive analysis.
• Investigated the functional impact of novel transcripts through depletion studies.

Main Results:

• Identified 2280 potential novel transcripts and 6289 novel splicing isoforms.
• Novel transcripts and isoforms showed enrichment for active promoter modification (H3K4me3).
• Discovered a novel Kdm4dl isoform and a noncoding gene (XLOC_004958), both critical for blastocyst development upon depletion.

Conclusions:

• The study provides a high-resolution and more precise transcriptome map of early mouse embryogenesis.
• Novel transcripts and isoforms play significant roles in blastocyst development.
• This work enhances the annotation of the preimplantation mouse embryo transcriptome.