Identification of adenovirus-encoded small RNAs by deep RNA sequencing

• Discovery of novel adenovirus-encoded small RNAs by using deep sequencing.
• Nineteen small RNAs of 25–35 nucleotides in length were considered to be most significant.
• These small RNAs were mapped to the region of the viral genome encoding the VA RNA I and II genes.
• They displayed different expression profiles during the course of the infection.
• Potential cellular targets of these small RNAs are predicted using bioinformatics tools.

Using deep RNA sequencing, we have studied the expression of adenovirus-encoded small RNAs at different times after infection. Nineteen small RNAs which comprised more than 1% of the total pool of small RNAs at least one time point were identified. These small RNAs were between 25 and 35 nucleotides long and mapped in the region of the VA RNAI and RNAII genes. However, the overlap was incomplete and some contained a few extra nucleotides at the 3' end. This finding together with the observation that some of the small RNAs were detected before VA RNA expression had started might indicate that they are derived from other precursors than VA RNAI and II. Interestingly, the small RNAs displayed different expression profiles during the course of the infection suggesting that they have different functions. An effort was made to identify their mRNA targets by using computer prediction and deep cDNA sequencing. The most significant targets for the earliest small RNAs were genes involved in signaling pathways.