HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells

Abstract

Although antisense transcription is a widespread event in the mammalian genome, double-stranded RNA (dsRNA) formation between sense and antisense transcripts is very rare and mechanisms that control dsRNA remain unknown. By characterizing the FGF-2 regulated transcriptome in normal and cancer cells, we identified sense and antisense transcripts IER3 and IER3-AS1 that play a critical role in FGF-2 controlled oncogenic pathways. We show that IER3 and IER3-AS1 regulate each other’s transcription through HnRNPK-mediated post-transcriptional regulation. HnRNPK controls the mRNA stability and colocalization of IER3 and IER3-AS1. HnRNPK interaction with IER3 and IER3-AS1 determines their oncogenic functions by maintaining them in a single-stranded form. hnRNPK depletion neutralizes their oncogenic functions through promoting dsRNA formation and cytoplasmic accumulation. Intriguingly, hnRNPK loss-of-function and gain-of-function experiments reveal its role in maintaining global single- and double-stranded RNA. Thus, our data unveil the critical role of HnRNPK in maintaining single-stranded RNAs and their physiological functions by blocking RNA-RNA interactions.

LncRNA ELF3-AS1 inhibits gastric cancer by forming a negative feedback loop with SNAI2 and regulates ELF3 mRNA stability via interacting with ILF2/ILF3 complex

“…Besides, the ILF2/ILF3 complex could dynamically regulate the dsRNA stability of ELF3-AS1 and ELF3 (Fig 9B), suggesting ILF2/ ILF3 complex may play a critical role in modulating dsRNA stability. Interestingly, a recent publication by Mahale and colleagues provided very similar evidence for the role of antisense RNA (IER3-AS1) and sense RNA (IER3 ) [35]. Based on RNA-seq analysis, they found that activation of FGF2/FGFR signaling greatly enhanced the mRNA levels of IER3 and IER3-AS1.…”

“…Based on RNA-seq analysis, they found that activation of FGF2/FGFR signaling greatly enhanced the mRNA levels of IER3 and IER3-AS1. IER3 and IER3-AS1 formed RNA duplex and regulated their mRNA stability each other by interacting with HNRNPK protein [35].…”

PITAR, a DNA damage-inducible Cancer/Testis long noncoding RNA, inactivates p53 by binding and stabilizing TRIM28 mRNA

“…Independent validation of ChIRP RNA with RT-qPCR showed an efficient pulldown of PITAR by PITAR-specific probes compared to LacZ (Control) probes ( Figure 4A ). Noncoding RNAs interact with target mRNAs through direct or indirect RNA-RNA interactions (Faghihi et al ., 2008; Gong and Maquat, 2011; Kretz et al ., 2012; Engreitz et al ., 2014; Mahale et al ., 2022a). Enrichment of TRIM28 mRNA in the PITAR ChIRP pull-down indicates the presence of potential TRIM28 mRNA: PITAR lncRNA interactions.…”

“…The copyright holder for this preprint this version posted April 12, 2023. ; https://doi.org/10.1101/2023.04.11.536370 doi: bioRxiv preprint described earlier (Mahale et al, 2022). RNA probes specific to PITAR and TRIM28 were designed by ACD's made-to-order probes service.…”

“…No. 323100) from Advanced Cell Diagnostics (ACD), which was described earlier (Mahale et al, 2022). RNA probes specific to PITAR and TRIM28 were designed by ACD's made-to-order probes service.…”