Being a young scientist, I take a lot of ‘science’ for granted. Weve ‘always’ had PCR. Weve ‘always’ had restriction enzymes. We ‘always’ knew HIV-1 is a retrovirus, and uses CD4 and CCR5/CXCR4 to infect cells. Weve ‘always’ known that retroviruses are important for the evolution of life on this planet. We ‘always’ knew about micro-RNA and the RNA silencing machinery.
So its wonderful fun to read papers written before we knew X, Y, Z– watching the discoveries take place. Considering my last entry was about how much you totally dont want ERVs to be functional, I thought Id write about a real world example about how retroviral promoters can be an ‘alternate’ promoter for a ‘normal’ gene, and end up causing cancer.
A long time ago, in the before times, a group was studying how infection with Avian Leukosis Virus lead to cancer. ALV is a bird retrovirus that comes in both endogenous and exogenous flavors, which has actually caused a lot of trouble in the past (endogenous ALV rearranging with exogenous ALV lead to a really bad ALV epidemic in the 1990s).
They found that ALV really liked to insert upstream of a gene they called ‘bic’ (B cell Integration Cluster, bic). When B-cells were infected with ALV, the retroviral promoter acted as an alternate promoter for bic, and bic was way, way upregulated in cancerous cells. They looked in lots of different b-cell lymphomas, and they found the same thing– an ALV insertion somewhere upstream of bic, lots of bic.
So they played around with the bic transcripts, figuring they had discovered a new oncogene… but they noticed something odd… The bic RNA didnt code for a protein. There werent any open reading frames.
In this paper, it was awesome to see the researchers reason this out. Bic is processed, but no gene. Is it a pseudogene? Hmm, no, doesnt have the genetic characteristics of a pseudogene. And its super cell specific, no way is it a pseudogene. Maybe with ribosomal frame-shifts, theres something there? No, too many stop codons. Maybe it just works as an RNA? The secondary structure is really complex– Maybe the RNA does something on its own?