[PRESS RELEASE 2012-06-12] By combining high throughput sequencing, bioinformatics and specific experimental verifications, groups at Stockholm University, Science for Life Laboratory and the Royal Institute of Technology, have shed light on the impact that specific nucleotide base changing, so-called A-to-I RNA editing, of particular small RNA structures has on regulatory non-coding RNA during brain development
Small stretches of about 22 nt non-coding RNA, so-called microRNA or miRNA, are important for gene regulation through its binding to coding RNA sequences. “By combining different methods for RNA sequencing with new bioinformatics tools we could find novel sites of nucleotide base exchange, so-called editing”, says Jens Lagergren, Professor at the Royal Institute of Technology and group leader at SciLifeLab Stockholm. He further explains that “an increase in editing of miRNAs during mouse brain development adds to the complexity of the regulation”.
High throughput RNA sequencing (RNA-Seq) was performed to search for known and novel sites of adenosine to inosine (A-to-I) miRNA editing that have altered levels of editing during brain development. Mouse brain tissue from three different stages of the mouse brain development; embryonic day 15, postnatal day 2 and postnatal day 21, was studied. High throughput RNA-Seq analysis was primarily performed using the SOLiD system and complemented with Illumina miRNA reads.
To increase the specificity of the sequence analysis a new filter, the K-safety filter was developed. Including pre-processing and stringent data filtering as well as comparing different sequencing methods, eight editing candidates were identified. Six of these eight candidates have an increased ratio of editing through development.
The most noticeable editing events found in this study occurred in the short part of the miRNA sequence that is necessary for correct target binding. Editing was found to increase from embryonic to adult brain and thereby changing the target binding ability of the miRNAs. One example of this is the novel candidate miR-381 that is thought to target Pum2, which is involved in the regulation of neural development. As editing of miR-381 increases during development, the expression of Pum2 increases and this leads to a downregulation of dendrite outgrowth.
Ylva Ekdahl, Hossein Shahrabi Farahani, Mikaela Behm, Jens Lagergren, and Marie Öhman. (2012) “A-to-I editing of microRNAs in the mammalian brain increase during development”. Genome Res. gr.131912.111 Published in Advance May 29, 2012,doi:10.1101/gr.131912.111
The Science for Life Laboratory is a joint effort between four Swedish universities, Karolinska Institute, The Royal Institute of Technology (KTH), Stockholm University and Uppsala University, to build an infrastructure for high-throughput research in the areas of health and environment. This center was started in 2010.