Brenda L. Bass, PhD, Endowed Chair

Distinguished Professor of Biochemistry

Emma Eccles Jones Medical Sciences Building

15 N Medical Drive East, Room 4100

Campus Phone: (801) 581-4884

Email: bbass@biochem.utah.edu

The Bass Lab

My laboratory continues our research towards the goal of understanding the biological functions of double-stranded RNA (dsRNA). These functions are mediated by proteins that bind dsRNA, called dsRNA binding proteins (dsRBPs). Because of the structure of dsRNA, dsRBPs will recognize any dsRNA, irrespective of its sequence. A long-standing hypothesis in our laboratory is that different dsRNA-mediated pathways required in animals will be affected by multiple dsRBPs, and thus, will intersect and affect each other. As described below, progress in the past year supports this hypothesis (Project 1). Because dsRBPs will bind each other’s dsRNA substrates, they have evolved other mechanisms to gain specificity, and our studies of the past year offer one way this can happen (Project 2). Finally, a year ago I was honored to receive the NIH Director’s Pioneer award to test the idea that long dsRNA has unrecognized functions in signaling stress, innate immunity and aging, and during the past year we have been extremely excited to begin to get results from this project (Project 3).

Project 1:Adenosine deaminases that act on RNA (ADARs) are dsRBPs that target dsRNA in living cells to change its sequence. Since DNA passes its genetic information directly to RNA, by changing an RNA's sequence, ADARs indirectly alter genetic information. ADARs are particularly important in the nervous system where they diversify genetic information to allow complex processes such as learning and memory. In humans, ADARs are linked to longevity, and aberrant levels of editing are associated with neurological disease and cancer. While these are established functions of ADARs, because they bind any dsRNA, in theory the enzymes should be able to affect any pathway that involves dsRNA. In fact, in the past year we have definitively shown that ADARs can target dsRNA that is processed by another dsRBP called Dicer1, which cleaves long dsRNA to make shorter dsRNAs called small interfering RNAs (siRNAs) and microRNAs (miRNAs). We found that while editing in these small RNAs is rare, at least 40% of miRNAs have altered levels in strains of the model organism C. elegans that contain a deletion in one of their ADAR genes. About 40% of siRNAs derived from endogenous genes (endo-siRNAs) also have altered levels in at least one mutant strain, including 63% of Dicer-dependent endo-siRNAs. Our data indicate ADARs, through both direct and indirect mechanisms, are important for maintaining wildtype levels of many small RNAs in C. elegans.

Project 2: The specific sequence change made by an ADAR is the “editing” of the nucleoside called adenosine, to create an inosine (A-to-I). The extent an adenosine is “edited” depends on the identity of neighboring nucleosides. For example, human ADAR2 (hADAR2) has 5’ and 3’ neighbor preferences, but which amino acids in the hADAR2 protein mediate these preferences, 2 and by what mechanism, is unknown. We performed a screen in yeast to identify mutations in the hADAR2 catalytic domain that allow editing of an adenosine within a disfavored context. Binding affinity, catalytic rate, base-flipping and preferences were monitored to understand effects of the mutations on ADAR reactivity. Our data provide the first information on the amino acids important for preferences, and point to a conserved loop as being of key importance. Our studies set the stage for understanding the basis of altered editing levels in disease and developing therapeutic reagents.

Project 3: Over the years research in my laboratory has hinted that cells have a characteristic dsRNA:dsRBP ratio, and that aberrations from this ratio signals responses such as innate immunity, stress and aging. One way to alter the dsRNA:dsRBP ratio in cells would be to induce expression of cellular dsRNAs. While viruses produce dsRNA, the traditional view is that long dsRNA is rare among endogenous transcripts. However, we previously reported a C. elegans long noncoding dsRNA (rncs-1) that is induced by the lack of food; our recent studies indicate there are hundreds of other C. elegans dsRNAs, albeit how they are regulated is unclear, and we are actively pursuing this question.

Certain mammalian dsRBPs are activated by viral dsRNA. Since dsRBPs bind to dsRNA of any sequence, these proteins may also bind cellular dsRNA, possibly leading to an aberrant immune response. In fact, the dsRBP PKR, which binds viral dsRNA to trigger a host response to viral infection, is also activated when mice are fed a high-fat diet. We hypothesize it is endogenous dsRNA that activates PKR under this metabolic stress. To test this we incubated mouse cells with or without palmitic acid (PA) to mimic a high-fat or regular diet, respectively, and isolated and characterized RNAs bound to the PKR in the cells. Interestingly, >40% of the isolated RNAs are non-coding RNAs, and current efforts are focused on characterizing these RNAs.

Honors: 2011 NIH Director’s Pioneer Award 2011 AAAS fellow (elected)

1. Warf, M.B., Shepherd, B.A., Johnson, W.E., and Bass, B.L. (2012). Effects of ADARs on small RNA processing pathways in C. elegans. Genome research 22, 1488-1498.