Poster abstracts

Poster number 49 submitted by Lisa Lojek

Decapping dependant decay regulates lncRNA regulation

Lisa Lojek (Center for RNA Biology, Case Western Reserve University), Sarah Geisler (Center for RNA Biology, Case Western Reserve University), Jeff Coller (Center for RNA Biology, Case Western Reserve University)

Abstract:
There has recently been an explosion of information in the field of noncoding RNAs (ncRNAs) regarding the various types and regulatory functions these ncRNAs have. However, one largely overlooked aspect of ncRNA biology is how the ncRNAs themselves are regulated. Current knowledge suggests that ncRNAs are similar to mRNAs in that they possess 5’ caps and 3’ poly-A tails. Since these features play important roles in mRNA decay, we were interested to see if mRNAs and ncRNAs are degraded by similar pathways. Decapping dependent 5’-to-3’ turnover is a major form of decay for mRNA transcripts. This process begins with removal of the poly-A tail followed by removal of the cap, by a conserved decapping enzyme, Dcp2p, which allows for exonucleolytic decay of transcripts. Dcp2p is a central component of not only primary but also secondary decay pathways; for this reason we investigated the role of the decapping enzyme on turnover of ncRNAs. We performed RNA-sequencing in yeast, and we identified over 100 long ncRNAs (lncRNAs) sensitive to Dcp2p. We first confirmed the enzymatic decapping activity of Dcp2p was responsible for turnover of lncRNA. We then tested a variety of proteins known to be active in various decay pathways and found that none of the other known Dcp2p cofactors were also involved in lncRNA turnover, with the exception of Rat1p (the nuclear exonuclease) and Xrn1p (the cytoplasmic exonuclease). Thus, this represents a completely novel decay pathway for these lncRNA. One third of the identified lncRNAs were associated with genes that were repressed under our growth conditions. Many of these inducible genes were part of larger metabolic pathways, for example four genes within the galactose response pathway had lncRNAs associated with them. Interestingly, we saw that presence of a lncRNA negatively influenced expression of the associated gene. Specifically, induction of GAL mRNA expression upon addition of galactose to the growth media was strongly impaired when the lncRNA could not be cleared from the cell. This led us to a model where presence of a lncRNA can act to suppress a locus, and that clearance of the lncRNA by Dcp2p can abrogate suppression. Since Dcp2p is a conserved enzyme, this may represent a fine tuning mechanism for transcription of normally repressed loci for many higher eukaryotes.

Keywords: non-coding RNA, decapping