Elucidating the functions of virally encoded elements

An important step in studying viral infection like any other biological process is to establish the identity of the proteins that are expressed during the process. Using suites of ribosome profiling based techniques and analysis in conjunction with mass-spectrometry we identified several hundred previously unidentified viral open reading frames. Importantly, widespread translation outside of annotated protein-coding genes was also found in many organisms including mammalian cells.  The outstanding challenge now is to define the functions of these newly identified translation events. We are using the highly manipulatable viral system to elucidate the function of few promising candidates and we use systematic approaches to examine viral short ORFs functions

Unraveling cellular gene expression regulation during viral infection

Viruses are by definition fully dependent on the cellular translation machinery, and develop diverse mechanisms to co-opt it for their own benefit. Unlike many viruses, HCMV does not suppress the host translation machinery, and the extent to which translation machinery contributes to the overall pattern of viral replication and pathogenesis remained elusive. By simultaneously examining the changes in transcription and translation along HCMV infection, using ribosome profiling and RNA-seq, we uncover diverse and dynamic translational regulation for subsets of host genes. Although ribosome profiling provides precise and quantitative analysis of genes that are translationally regulated, our molecular understanding of this type of regulation is still at its infancy. We  develop approaches that will allow better  understanding of this regulation.

Decoding the latent state of infection

Primary infection with HCMV results in the establishment of a lifelong infection, which is aided by the ability of HCMV to undergo a latent infection. Reactivation from viral latency causes serious disease in immunocompromised individuals, underscoring the need to better understand the latency state. Although there are a few well-characterized latent transcripts, the full transcriptional program during latency is still unclear. We tackle the issue of latency by taking advantage of single cell RNA-seq technology.

Elucidating the functions of human cytomegalovirus encoded lincRNAs

Although viruses are known for their compact genomes and HCMV hardly contains intergenic regions, four HCMV encoded lincRNAs have been recently identified. Interestingly, these virally encoded lincRNAs comprise over 60% of expressed viral RNA and are highly conserved suggesting an important role in viral pathogenesis. Nonetheless the functions of these highly expressed viral transcripts are largely unknown. We aim to elucidate HCMV’s lincRNAs function  by combination of genome- wide and gene specific approaches.