With terabytes of data streaming off sequencers nowadays, there’s heaps of data available that is begging to be mined. You don’t always have to run your own wet lab experiments either, if you know where to look. We know most bosses or PIs out there will probably resist cutting you loose to Starbuck’s to “crunch data” on your MacBook, so ease their concerns by pointing them to some recent work in Genome Research. A team of scientists from Uppsala University in Sweden mined publicly available data sets, and revealed that nucleosomes and their histone modifications are positioned within exons to epigenetically control mRNA splicing.
The Uppsala group studying genome regulation looked at nucleosome position in relation to genomic features other than the traditional TSS. The team aligned, annotated, and heat-mapped data from whatever genome-wide studies they could get their hands on until they got their results (We’re sure this took more than just a laptop and coffee shop Wi-Fi!). Some of the Swedish team’s key findings were:
- Nucleosomes have defined, well conserved positions at exons, regardless of transcription level. “We were quite surprised to see that nucleosomes have a better defined position over internal exons than at the TSS. Even more surprising was that this packaging of the genome has been conserved since C. elegans…” author Claes Wadelius commented.
- Histone marks on these nucleosomes regulate exon expression and are involved in mRNA splicing. “The nucleosomes over the exons have different epigenetic modifications depending on whether they are used in the mRNA produced by the gene, or not. In other words there is an epigenetic control of splicing.” explained Wadelius.
It’s uncertain what discoveries are still hidden in some sequencer’s hard drive but Dr. Wadelius feels “certain that we will discover other connections between additional histone modifications and molecular function.” We say, keep up the good work!
Read all of the details in Genome Research, August 2009