Novel functions for Sm-class RNAs in the regulation of gene expression

Summary
The overarching goal of my laboratory is to define the functions and mechanisms of a group of non-
coding RNAs (ncRNAs): the small nuclear, U-rich RNAs (snRNAs). Cellular snRNAs associate with Sm proteins
to form ribonucleoprotein particles (RNPs) that are essential components of cellular machineries responsible for
the precursor messenger RNA (pre-mRNA) processing steps of splicing and 3¢-end formation, and their
perturbation underlies several diseases. Recent research from my lab and others suggests that this group of
ncRNAs is more functionally diverse than previously thought and that the canonical functions of snRNAs in
splicing and 3¢-end processing constitute only the tip of the iceberg.
Using Herpesvirus saimiri (HVS) as a model system, we recently showed that snRNAs perform functions
beyond pre-mRNA processing. This primate g-herpesvirus expresses seven snRNAs in latently infected cells
called HSURs (Herpesvirus saimiri U-rich RNAs). We have focused on two of these ncRNAs, HSURs 1 and 2,
because they are the most highly conserved HSURs among different HVS groups and the only two expressed
by the related Herpesvirus ateles. HSUR1 and HSUR2 basepair with host microRNAs (miRNAs) and target one
miRNA, miR-27, for degradation. Work from our laboratory showed that HSUR2 also basepairs with host mRNAs
and links bound miRNAs with specific mRNAs to destabilize them. This constitutes the first example of an snRNA
function after pre-mRNA processing. We also developed iRICC, a technique to determine RNA binding partners
of a single RNA of interest and the sequences mediating RNA-RNA interactions in vivo. Using iRICC we showed
that HSUR2 binding sites reside mostly in the 3¢ untranslated regions (3¢UTRs) of target mRNAs. We also
showed that HSUR2 does not present a “seed” or specialized region that is used to interact with most targets,
but rather acts as a flexible adaptor that interacts through different base-pairing arrangements with different
mRNAs. iRICC revealed that HSUR1 profusely binds to coding sequences in addition to 3¢UTRs of target
mRNAs. These findings suggest that HSUR1 might regulate host gene expression through mechanisms different
from those employed by HSUR2. Finally, we have also developed an approach for identifying low-abundance
snRNAs and discovered that mammalian cells express previously uncharacterized snRNAs.
We will use a combination of genetic, genome-wide, molecular biology and biochemical approaches to
further characterize mechanical aspects of HSUR1 and HSUR2 function and to functionally characterize novel
cellular snRNAs. This work will advance our understanding of the mechanisms underlying the regulation of
gene expression by this class on ncRNAs during viral infection. It will also illuminate novel mechanisms of
gene regulation in the broad range of eukaryotes that express snRNAs.

Grant Number: 5R35GM144241-05
NIH Institute/Center: NIH
Principal Investigator: Demian Cazalla