Post‐transcriptional gene expression control by NANOS is up‐regulated and functionally important in pR b‐deficient cells

Abstract

Inactivation of the retinoblastoma tumor suppressor (pRb) is a common oncogenic event that alters the expression of genes important for cell cycle progression, senescence, and apoptosis. However, in many contexts, the properties of pRb-deficient cells are similar to wild-type cells suggesting there may be processes that counterbalance the transcriptional changes associated with pRb inactivation. Therefore, we have looked for sets of evolutionary conserved, functionally related genes that are direct targets of pRb/E2F proteins. We show that the expression of NANOS, a key facilitator of the Pumilio (PUM) post-transcriptional repressor complex, is directly repressed by pRb/E2F in flies and humans. In both species, NANOS expression increases following inactivation of pRb/RBF1 and becomes important for tissue homeostasis. By analyzing datasets from normal retinal tissue and pRb-null retinoblastomas, we find a strong enrichment for putative PUM substrates among genes de-regulated in tumors. These include pro-apoptotic genes that are transcriptionally down-regulated upon pRb loss, and we characterize two such candidates, MAP2K3 and MAP3K1, as direct PUM substrates. Our data suggest that NANOS increases in importance in pRb-deficient cells and helps to maintain homeostasis by repressing the translation of transcripts containing PUM Regulatory Elements (PRE).

Proteomic analysis of pRb loss highlights a signature of decreased mitochondrial oxidative phosphorylation

“…These changes show that Rb loss affects not only the level of RNAs but also the extent to which specific transcripts are actively translated. This agrees with previous work showing that translational regulation of specific E2F-driven mRNAs can prevent the aberrant appearance of the protein (Miles et al 2014).…”

“…This regulation is not well understood but is clearly of great significance. The miRNA network and RNA-binding proteins that increase in Rb/RB1 mutant cells and target cell cycle-regulated transcripts are likely to be involved (Miles et al 2014). It may also be relevant that p53, a tumor suppressor commonly inactivated with Rb (Cerami et al 2012), can regulate translation through modulation of mTOR (Loayza-Puch et al 2013).…”

“…Another line of investigation shows that the Nanos RNA-binding protein is up-regulated in RB1 mutant cells. Nanos/Pumilio complexes suppress protein synthesis via multiple mechanisms, and the 3 ′ untranslated region (UTR) sequences of many E2F-dependent mRNAs contain consensus binding sites for these proteins (Miles et al 2012(Miles et al , 2014. Pools of pRb have also been observed in the cytoplasm (Jiao et al 2006;Roth et al 2009) and at mitochondria (Hilgendorf et al 2013), suggesting that pRb likely has roles that extend beyond transcription.…”

Pumilio and nanos RNA-binding proteins counterbalance the transcriptional consequences of RB1 inactivation

“…3 Here, by comparing the classes of genes that are directly bound by RB/ E2F proteins in flies 4 and humans, and by examining the lists of genes that are deregulated by the loss of RB 5 or retinoblastoma-family protein 1 (Rbf1) (its Drosophila ortholog), we recently discovered an additional regulatory loop that helps cells cope with transcriptional changes associated with RB loss. 6 Our results show that, in addition to the standard E2F target genes involved in cell cycle progression, members of the RB family and E2F family also control the expression of components of the Pumilio (Pum) post-transcriptional repressor complex. Pum proteins repress the translation of their substrates by binding to a Pumilio regulatory element (PRE: UGUAXAUA) within the 3 0 untranslated region (UTR) of mRNAs.…”

“…10 In both flies and human cells, inactivation of RB/Rbf1 increases the expression of the components of the Pum complex, most notably Nanos1/Nanos, and this increases the post-transcriptional repression mediated via PRE elements. 6 Informatics analysis of retinoblastoma tumors revealed that approximately 20% of the transcripts that have altered gene expression contain putative PREs in their 3 0 UTRs. Most of these upregulated genes are transcribed from E2F-responsive loci.…”