Title

p54nrb binds to hyper-edited Alu elements in vivo: A global analysis

Date of Completion

January 2008

Keywords

Biology, Molecular

Degree

Ph.D.

Abstract

Previous bioinformatic and biochemical studies have shown that ADAR RNA editing enzymes frequently convert adenosine nucleotides to inosines within inverted Alu elements located in human genes in the process of Alu hyper-editing. Separate studies have also shown that the human nuclear RNA binding protein p54nrb binds to hyper-edited RNAs and mediates their retention in the nucleus. The studies described herein provide new insight into the global cellular impact of the interaction of p54nrb with hyper-edited Alu elements. First, a bioinformatic survey of all human genes suggests that 55%–65% of all human genes may contain hyper-edited Alu elements, primarily within introns. The genes that contain inverted Alu elements are over 20-times longer, on average, than genes that lack Alu elements. Interestingly, chromosome 19 contains a relatively large number of short genes that contain a high percentage of Alu elements. In contrast, the Y chromosome contains a relatively low number of genes, many of which lack Alu elements. In addition, over 300 human genes contain inverted Alu elements within their 3'UTRs; a significant proportion of these genes are involved in the regulation of apoptosis and transcription, suggesting that p54nrb plays an active role in these processes. ^ These analyses also show that Alus alone have the proper bioinformatic profile to be transcriptome-wide targets of ADAR editing. Experimentally, p54nrb is shown to interact with a statistically-significant number of RNAs that contain hyper-edited Alu elements. Several important and previously unappreciated mechanisms of the regulation of hyper-editing are identified, including the importance of the amount of spacing between inverted Alu element pairs and the local distribution of Alu elements. Finally, it is shown that an ideal hyper-editing substrate that is capable of binding to p54nrb consists of a relatively long RNA molecule with a moderately large number of Alus which are found in inverted pairs spaced far apart from one another. Together, these two different approaches describe which human genes are capable of being edited by the ADAR enzymes and which are subsequently bound by the p54nrb nuclear retention complex. ^