ABSTRACT
Alternative splicing (AS) and alternative promoter (AP) usage expand the repertories of mammalian transcriptome profiles and thus diversify gene functions. However, our knowledge about the extent and functions of AS and AP usage in mouse early embryogenesis remains elusive. Here, by performing whole-transcriptome splicing profiling with high-throughput next generation sequencing, we report that AS extensively occurs in embryonic day (E) 7.5 mouse primary germ layers, and may be involved in multiple developmental processes. In addition, numerous RNA splicing factors are differentially expressed and alternatively spliced across the three germ layers, implying the potential importance of AS machinery in shaping early embryogenesis. Notably, AP usage is remarkably frequent at this stage, accounting for more than one quarter (430/1,648) of the total significantly different AS events. Genes generating the 430 AP events participate in numerous biological processes, and include important regulators essential for mouse early embryogenesis, suggesting that AP usage is widely used and might be relevant to mouse germ layer specification. Our data underline the potential significance of AP usage in mouse gastrulation, providing a rich data source and opening another dimension for understanding the regulatory mechanisms of mammalian early development.
Footnotes
Competing interests
The authors declare no competing or financial interests.
Author contributions
Conceptualization: X.L., Z.-A.Z., Z.Y., L.L.; Methodology: X.L., Z.-A.Z., X.W., W.D.; Validation: X.L.; Formal analysis: X.L., Z.-A.Z., Z.Y., L.L.; Investigation: X.L.; Data curation: X.L., Z.-A.Z., X.W., X.Z., Y.Z.; Writing - original draft: X.L.; Writing - review & editing: X.L., L.L.; Supervision: Z.Y., L.L.; Project administration: X.Z.; Funding acquisition: Z.Y., L.L.
Funding
The work was funded by the National Key R&D Program of China [2017YFC1001401], the National Natural Science Foundation of China [31771633], the Beijing Municipal Natural Science Foundation [5162005], and the Beijing Municipal Education Commission [KM20171002001].
Data availability
Raw data from RNA-seq and Microarray are available at Gene Expression Omnibus, under accession number GSE111957.
Supplementary information
Supplementary information available online at http://bio.biologists.org/lookup/doi/10.1242/bio.032508.supplemental
- Received January 9, 2018.
- Accepted January 31, 2018.
- © 2018. Published by The Company of Biologists Ltd
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
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