DcpS is a transcript-specific modulator of RNA in mammalian cells

Abstract

The scavenger decapping enzyme DcpS is a multifunctional protein initially identified by its property to hydrolyze the resulting cap structure following 3 ′ end mRNA decay. In Saccharomyces cerevisiae, the DcpS homolog Dcs1 is an obligate cofactor for the 5 ′ -3 ′ exoribonuclease Xrn1 while the Caenorhabditis elegans homolog Dcs-1, facilitates Xrn1 mediated microRNA turnover. In both cases, this function is independent of the decapping activity. Whether DcpS and its decapping activity can affect mRNA steady state or stability in mammalian cells remains unknown. We sought to determine DcpS target genes in mammalian cells using a cell-permeable DcpS inhibitor compound, RG3039 initially developed for therapeutic treatment of spinal muscular atrophy. Global mRNA levels were examined following DcpS decapping inhibition with RG3039. The steady-state levels of 222 RNAs were altered upon RG3039 treatment. Of a subset selected for validation, two transcripts that appear to be long noncoding RNAs HS370762 and BC011766, were dependent on DcpS and its scavenger decapping catalytic activity and referred to as DcpS-responsive noncoding transcripts (DRNT) 1 and 2, respectively. Interestingly, only the increase in DRNT1 transcript was accompanied with an increase of its RNA stability and this increase was dependent on both DcpS and Xrn1. Importantly, unlike in yeast where the DcpS homolog is an obligate cofactor for Xrn1, stability of additional Xrn1 dependent RNAs were not altered by a reduction in DcpS levels. Collectively, our data demonstrate that DcpS in conjunction with Xrn1 has the potential to regulate RNA stability in a transcript-selective manner in mammalian cells.

The human decapping scavenger enzyme DcpS modulates microRNA turnover

“…We further validated the effect of the inhibition of DcpS on miRNA levels by performing TaqMan quantitative PCR assays for a representative number of affected miRNAs ( Figure S3 ). To confirm that the increased miRNA levels upon DcpS inhibition are not caused by a modification of transcripts levels as recently reported for a subset of RNAs 16 , we measured the levels of a primary miRNA molecule coding for six different miRNAs (the miR-17 ~ 92 cluster) including miR-17, miR-19b and miR-20a, three miRNAs that are significantly increased in treated cells. Using quantitative PCR, we did not detect any significant changes in the level of the primary molecule between control DMSO and DcpS inhibitor treated cells ( Figure S4A ).…”

In vitro and in vivo effects of 2,4 diaminoquinazoline inhibitors of the decapping scavenger enzyme DcpS: Context-specific modulation of SMN transcript levels

“…A number of gene transcripts have been observed to change in response to DAQ-DcpSi [ 22 ]. Thus we sought to determine whether some of these were responsive to DcpS inhibition per se or some other effect(s) of these compounds unrelated to DcpS.…”

“…Testing the DcpS-sensitive transcripts reported by Zhou et al . (2015) [ 22 ], the pattern of changes in Dolichyl-Phosphate Mannosyltransferase Subunit 3( DPM3 ) and Progestin and AdipoQ Receptor Family Member 8 ( PAQR8 ) was consistent with their being DcpS-sensitive genes, both qualitatively (same direction of change as induced by pharmacological DcpS inhibition) and quantitatively (because the degree of modulation was related to the degree of DcpS knockdown). The lack of effect in clone 70 suggests that greater than 50% loss of DcpS activity is required to cause a change in either DPM3 or PAQR8 .…”

Small Molecules in Development for the Treatment of Spinal Muscular Atrophy

“…Thus, small molecules in the quazoline series, such as 17 , appear to stabilize RNA levels through inhibition of DcpS. 94 …”