The hnRNP RALY regulates transcription and cell proliferation by modulating the expression of specific factors including the proliferation marker E2F1

Abstract

The heterogeneous nuclear ribonucleoproteins (hnRNP) form a large family of RNA-binding proteins that exert numerous functions in RNA metabolism. RALY is a member of the hnRNP family that binds poly-U-rich elements within several RNAs and regulates the expression of specific transcripts. RALY is up-regulated in different types of cancer, and its down-regulation impairs cell cycle progression. However, the RALY's role in regulating RNA levels remains elusive. Here, we show that numerous genes coding for factors involved in transcription and cell cycle regulation exhibit an altered expression in RALY-down-regulated HeLa cells, consequently causing impairments in transcription, cell proliferation, and cell cycle progression. Interestingly, by comparing the list of RALY targets with the list of genes affected by RALY down-regulation, we found an enrichment of RALY mRNA targets in the down-regulated genes upon RALY silencing. The affected genes include the E2F transcription factor family. Given its role as proliferation-promoting transcription factor, we focused on E2F1. We demonstrate that mRNA stability and E2F1 protein levels are reduced in cells lacking RALY expression. Finally, we also show that RALY interacts with transcriptionally active chromatin in both an RNA-dependent and -independent manner and that this association is abolished in the absence of active transcription. Taken together, our results highlight the importance of RALY as an indirect regulator of transcription and cell cycle progression through the regulation of specific mRNA targets, thus strengthening the possibility of a direct gene expression regulation exerted by RALY.

Long noncoding RNA EMS connects c-Myc to cell cycle control and tumorigenesis

“…RALY belongs to the heterogeneous nuclear ribonucleoprotein family that binds to poly-U elements within several RNAs (64,65). It has been recently shown that RALY is able to stabilize E2F1 mRNA by binding to its 3′-UTR (48). Here, we identify EMS as a RALY binding partner.…”

“…Because many lncRNAs exert their functions through interaction with their target proteins (47), we hypothesized that EMS could regulate E2F1 mRNA stability in a similar manner. It has been recently shown that the heterogeneous nuclear ribonucleoprotein RALY, a poly-U binding protein, is able to stabilize E2F1 mRNA by binding to its 3′-untranscribed region (UTR) (48). Analysis of the EMS sequence revealed that EMS contains a poly-U stretch with 22 uridines (SI Appendix, Fig.…”

DNA Conformation Regulates Gene Expression: The MYC Promoter and Beyond

“…Namely, hnRNP LL was observed to interact with the single‐stranded DNA i‐motif of the BLC2 promoter sequence to stimulate transcription in a DNA conformation‐dependent manner . In HeLa cells, hnRNP RALY can bind chromatin, via both RNA‐dependent and independent mechanisms, to regulate cell cycle signatures and proliferation . Moreover, the purine‐rich element binding protein (Pur) family is a highly conserved group of proteins with a variety of functions, including regulation of RNA transport and translation, and transcriptional regulation of genes including MYC through binding and remodeling of single stranded DNA .…”

“…[119] In HeLa cells, hnRNP RALY can bind chromatin, via both RNA-dependent and independent mechanisms, to regulate cell cycle signatures and proliferation. [120] Moreover, the purine-rich element binding protein (Pur) family is a highly conserved group of proteins with a variety of functions, including regulation of RNA transport and translation, and transcriptional regulation of genes including MYC through binding and remodeling of single stranded DNA. [121][122][123][124] In Drosophila, regulation of MYC transcription by the RNA-binding protein B52 has been reported, [125] although it is unclear whether this occurs as a result of direct interaction with single-stranded DNA in the promoter.…”

Overexpression of RALY promotes migration and predicts poor prognosis in hepatocellular carcinoma

“…RALY is a member of the heterogeneous nuclear ribo-nucleoprotein family that binds poly-U-rich elements within several RNAs and regulates the expression of specific transcripts. Previous studies have shown that RALY is upregulated in different types of cancer, 6 – 8 , 19 and its downregulation impairs cell cycle progression. 19 A recent study demonstrated that RALY can promote invasiveness in breast cancer cells; additionally, RALY expression is increased in breast tumors, which correlates with decreased patient survival.…”