Genes are transcribed from DNA into RNA, which is then processed in various ways before being translated into proteins. RNA molecules get edited or spliced, and certain sequences might be removed before the final messenger RNA (mRNA) molecule is created. Splice sites are places in genes where that editing occurs. Some genes have alternative splice sites, which can lead to the production of multiple different mRNA transcripts from one sequence of DNA. Some versatile genes might encode for a few different proteins based on their splice sites. But many times, alternative splice events create mRNA products that are not functional or useful to the cell; those transcripts are typically degraded and eliminated. Alternative splicing also has to be regulated, so that potentially deleterious transcripts aren't floating around the cell.
Researchers have now found, however, that during a crucial stage of development, the regulation of alternative splicing goes wild. Reporting in Science, investigators studied the very early developmental stages of human, mouse, and cow embryos, focusing on a period known as zygotic genome activation (ZGA). During this time, the organism is making a transition; it is switching its reliance from mRNA transcripts leftover from the maternal egg cell, and beginning to express the genes in its own genome. In humans, that happens at the 8-cell stage, while in mice, it happens at the 2-cell stage.
In this study, the researchers examined all of the mRNA transcripts present in zygotes at this point to create a splicing event atlas. The diversity among mRNA transcripts was found to be higher at this time than in any other cell type that's ever been studied, the researchers noted. Once the zygotes moved on to their next stage of development, this diversity was dramatically reduced, and returned to a more average level.
The study authors said that the regulation of splicing temporarily fails at a critical stage of development, when the embryo begins to make its own mRNA and proteins. They suggested that this is purposeful, and protects the embryo.
“We think this happens because there are instructions in our genome that tell a few genes to not do their job at that developmental stage,” said senior study author and ICREA Research Professor Manuel Irimia. "The embryo cells mess up their splicing on purpose and they do so for a functional reason."
They researchers also found that the response to DNA damage was unusually slow as well during this time point; the loss of splicing control impacted DNA damage response proteins, destroying them.
"As embryos activate their genome for the first time and start to transcribe, there may be trade-offs involved in order to avoid developmental failure,” suggested co-first study author Dr. Barbara Pernaute, a postdoctoral researcher at the CRG.