Cairns Lab - RNA Modifications

In addition to epigenetics, we are working on understanding the epitranscriptome—modifications placed on noncoding RNAs that affect their function.

RNA Pol II Enhancer-Binding Factors

Most noncoding RNAs are transcribed by RNA Polymerase III. We previously determined the entire RNA Pol III transcriptome in human cells and revealed the close collaboration between RNA Pol II (which transcribes mRNAs) enhancer-binding factors and Pol III.

Enhancer-binding factors open up the chromatin to allow Pol III access to Pol III genes, which reside in these enhancers (Oler et al., Nature Str. Mol Biol. 2010).

Locations of RNA Modifications

We then developed an effective method to determine the locations of one of the most prevalent RNA modifications (cytosine methylation; Khoddami and Cairns, Nature Biotechnology 2013).

Modifications at Base-Pair Resolution

We have recently developed additional methods to profile additional major modifications at base-pair resolution, in collaboration with Cynthia Burrows lab (University of Utah) (Khoddami et al., in preparation).