FUNCTIONAL AND MOLECULAR CHARACTERIZATION OF THE CYTOMEGALOVIRUS LINC RNA4.9

The majority of the human genome does not code for proteins yet is actively transcribed. A subset of non-coding transcripts which has gained much interest over the past decade is long (>200 nt) intergenic non-coding RNAs (lincRNAs). Over 8000 lincRNAs have been identified in human cells. LincRNAs are associated with diverse physiological and pathological conditions, yet the mechanism of action of most lincRNAs remains enigmatic.

Human cytomegalovirus (HCMV) is the largest human virus with a DNA genome of 235kb. Viruses are known for their extremely compact genomes and HCMV hardly contains intergenic regions. Nonetheless, four lincRNAs have been identified in the HCMV genome: RNA2.7 (β2.7), RNA1.2, RNA4.9 and RNA5.0 (numbers representing their mature form length in kb). Interestingly, while HCMV lincRNAs encoding genes occupy only ~6% of the viral genome, lincRNAs comprise over 60% of expressed viral transcripts. The functions of these highly expressed viral transcripts are largely unknown. Here we show that HCMV linc RNA4.9 localizes to the viral nuclear replication compartment suggesting a role in viral DNA replication. Interestingly, RNA4.9 does not show complete co-localization with nascent viral DNA or with the viral DNA polymerase. Moreover, the localization of RNA4.9 to sub-nuclear domains precedes that of the viral DNA polymerase and is maintained when viral DNA synthesis is blocked. The possible function and mechanism of action of RNA4.9 is discussed.