While cocktails and embryonic development usually don’t mix well, a cocktail of three transcription-activator-like effectors (TALEs) has just shaken up our understanding of the role LINE-1 retrotransposons during early embryonic development. LINE-1 activation had been considered a consequence of developmental processes, but now a talented team from the lab of Maria-Elena Torres-Padilla at the German Research Center for Environmental Health show that LINE-1 elements actively shape chromatin accessibility during early embryonic development.
After fertilization, the zygote undergoes dramatic epigenomic reprogramming to initiate embryonic development. DNA becomes exposed during this transformation to totipotency, allowing previously repressed LINE-1 retrotransposons get busy. To understand this process, the talented team made use of early mouse embryos, where custom RT-qPCR assays and RNA-FISH helped to demonstrate that LINE-1 elements are transcriptionally active during pre-implantation and that the highest levels occur at the 2-cell stage. Then the team sought to manipulate LINE-1 elements with a cocktail of three TALEs.
Here’s what they discovered when serving the TALE cocktail with a garnish of different effector domains:
- Microinjection of the cocktail with an activating VP64 domain prolongs LINE-1 activity past the 2-cell stage and results in developmental arrest
- The effects implicate LINE-1s at the chromatin level, rather than coding level, since pharmacologically inhibiting LINE-1’s reverse transcriptase does not rescue the phenotype and injecting LINE-1 mRNAs into non-manipulated embryos does not produce developmental arrest
- When expressed in zygotes directly following fertilization, the cocktail with a repressive KRAB domain also decreases the rate of development
- Injection of LINE-1 mRNA does not rescue the phenotype, which again implicates LINE-1s at the chromatin level
- Timing is everything, as expression in late 2-cell embryos does not produce a developmental phenotype, which suggests a function in zygotic genome activation (ZGA)
- RNA-Seq of embryos with either cocktail effector mix revealed that gene expression changes do not preferentially occur to genes in proximity of LINE-1s but rather that there are subtle and global changes in gene expression
- Finally, an imaging assay revealed that LINE-1 elements regulate global chromatin accessibility, where extended activation prevents the chromatin compaction required for later development and early silencing reduces chromatin accessibility
“We already knew LINE-1 elements to be highly expressed in early embryogenesis and so we wanted to know if this transcription is important in the events taking place in the early embryo”, senior author Maria Elena Torres-Padilla shares. First author Joanna Jachowicz continues, “We found that too much or too little LINE-1 expression caused development to come to a halt. This means that the precise timing and level of retrotransposon expression is critical for the development of the embryo.”
Torres-Padilla concludes, “These results identify a novel role for retrotransposons in shaping the chromatin ‘landscape’ necessary for the early developmental programme. It was previously assumed that the activation of retrotransposons was simply a side-effect of the chromatin remodelling occurring after fertilisation, a process termed epigenetic reprogramming. Our study demonstrates that LINE-1 elements have a specific role in regulating chromatin accessibility which in turn is necessary for the correct developmental programme to take place. This study is hugely significant in assigning a role to a large amount of the mammalian genome at the very earliest stages of life.”
Go read between the LINEs over at Nature Genetics, August 2017