Transcription factor Wilms’ tumor 1 regulates developmental RNAs through 3′ UTR interaction

Abstract

Wilms' tumor 1 (WT1) is essential for the development and homeostasis of multiple mesodermal tissues. Despite evidence for post-transcriptional roles, no endogenous WT1 target RNAs exist. Using RNA immunoprecipitation and UV cross-linking, we show that WT1 binds preferentially to 3 ′ untranslated regions (UTRs) of developmental targets. These target mRNAs are down-regulated upon WT1 depletion in cell culture and developing kidney mesenchyme. Wt1 deletion leads to rapid turnover of specific mRNAs. WT1 regulates reporter gene expression through interaction with 3 ′ UTR-binding sites. Combining experimental and computational analyses, we propose that WT1 influences key developmental and disease processes in part through regulating mRNA turnover.

Tumour suppressor WT1 regulates the let-7-Igf1r axis in kidney mesenchyme

“…The transcription factor role of WT1 has been considered to be responsible for the cellular changes observed in WT. However, we have recently shown that WT1 is also a regulator of RNA stability and that its role in posttranscriptional regulation is equally important in development (Bharathavikru et al, 2017). We had also observed in this study that WT1 interacts with microRNAs.…”

“…WT1 interaction with both the pre-as well as the mature microRNA suggest that the WT1-RNA complex could be involved in either microRNA targeting or microRNA processing. Since in an earlier study, we used FLASH to identify WT1 interaction with RNA hybrids (Bharathavikru et al, 2017), showing preferential enrichment towards the 3' UTR of the transcript, we decided to assess if any significant WT1- Although microRNA-mRNA hybrids were identified, these did not show any change in expression; only a few were downregulated in expression (Table S1).…”

“…Hence, we decided to investigate whether there were any changes in miRNA levels in WT1 expressing cells. Since multiple let-7 microRNAs were found to interact with WT1 and let-7c was present in both RIP and FLASH datasets (Bharathavikru et al, 2017), it was selected as one of the representative microRNAs for most of the validation studies. Northern blotting analysis of cells where WT1 is depleted (Wt1 knockdown M15 cells or Wt1 knockout embryonic stem (ES) cells) showed a downregulation of mature miRNA let-7c levels (Panel I, Fig.…”

“…All these observations suggest that the dysregulation of the microRNA let-7 pathway and the downstream Igf1r modulation is one of the contributing causes of WT. Sequencing of Hybrids) and RNA immunoprecipitation (RIP), was done in mesonephric M15 cells (Bharathavikru et al, 2017). This showed different noncoding and small RNA subtypes, of which microRNA was one of the common enriched categories ( Fig.…”

DNA and RNA binding by the Wilms' tumour gene 1 (WT1) protein +KTS and −KTS isoforms—From initial observations to recent global genomic analyses

“…88,91 Recently, it was demonstrated by RNA immunoprecipitation that WT1 binds preferentially to secondary structures in 3′ untranslated regions in mRNAs, thus regulating their stability. 92 There is little consensus among investigators, however, as to which isoforms bind with higher affinity to RNA, some finding the KTS containing isoforms binding more strongly to RNA, 90 and others the −KTS isoforms, 91,93,94 whereas still others see RNA binding only by +KTS isoforms. 88 WT1+KTS has also been shown to control the translation of transcripts possessing a retained intron.…”