Discovering the Function of Ultra-Conserved “Poison Exons” Through a CRISPR-Based Tool
Scientists at Seattle’s Fred Hutchinson Cancer Research Centre have used a CRISPR-based tool to identify the role of ultra-conserved elements in DNA in blocking the growth of tumour cells and keeping healthy cells growing. Published in Nature Genetics, the research found the importance of these ultra-conserved elements that have remained identical between species, such as humans and mice, over millions of years and showed how essential they are in maintaining a healthy cell.
When the first human genome was fully sequenced in 2003, these ultra-conserved elements drew interest, but not many studies to date have showed exactly how essential they are in regulating a cell.
This new study looked a sections of DNA called “poison exons” which regulate the activity of cells by shutting off the production of particular proteins. This means when undesirable proteins are being made, they can halt its production and ensure the cells are kept on the right track.
Previous studies have knocked out these poison exons one by one to identify any effect, but not much was found. The team at the Fred Hutchinson Cancer Research Centre used a wider approach by applying a CRISPR gene-editing enzyme along with guide-RNA molecules that could hunt down and snip out hundreds of poisons exons at once from the genomes of humans, mice and rats. They called this technique “paired guide RNAs for alternative exon removal” – pgFARM.
The team identified 465 poison exons that were highly conserved between species, and another 91 poison exons that were not so highly conserved. Many of the poison exons were found to perform the same function, which explained why in older studies where poison exons were knocked out one by one, there seemed to be no effect. When knocking out several poison exons at the same time in this study, cells were found to die.
To further understand the role poison exons have on maintaining a healthy cell, the team used lung tumours in live mice and identified many poison exons that are essential for normal cell growth, with some even having “clinically relevant” tumour-suppressing effects. They were found to lie within genes for RNA splicing factors and up-regulate the genes that govern RNA splicing, an important part of the protein-making machinery in a cell. The team suggested that a potential role for these poison exons could be to control RNA-splicing factors that could promote tumour growth and rein them in.
The team’s next steps include determining whether any of these ultra-conserved poison exons are important for early embryonic development, which would show exactly how essential they are to cell development. Understanding the mysteries of ultra-conserved elements could possibly lead to new targets in cancer treatment, and help scientists understand the exact importance of these elements that have remained unchanged over millions of years.