Poster Presentation 40th Annual Lorne Genome Conference 2019

Novel mechanism for stem-cell specific miRNA regulation in development and disease (#239)

Madara Ratnadiwakara 1 2 , Helen E Abud 3 4 , Thierry Jarde 1 3 4 , Karen Oliva 5 , Rebekah Engel 5 , Paul J McMurrick 5 , Minna-Liisa Anko 1 2
  1. Hudson Institute of Medical Research, Clayton, VIC, Australia
  2. Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
  3. Department of Anatomy and Developmental Biology , Monash University, Clayton, VIC 3800, Australia
  4. Cancer Program , Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia
  5. Cabrini Monash University Department of Surgery, Cabrini Health, Malvern, VIC 3144, Australia

MicroRNAs (miRNAs) regulate gene expression post-transcriptionally by fine-tuning mRNA levels and translation. miRNA biogenesis is tightly regulated to maintain specific miRNA expression patterns in different tissues and developmental stages, misexpression leading to pathological conditions. Although the RNA binding proteins (RBPs) Drosha, DGCR8 and Dicer are the essential components of the miRNA processing pathway, multiple other RBPs have recently been identified as critical regulators of miRNA biogenesis. The CNNC motif bound by the splicing factor SRSF3 has been shown to specify pri-miRNA hairpins and in vitro studies have demonstrated SRSF3 enhancing pri-miRNA processing in a CNNC dependant manner. However, the in vivo functional relevance of SRSF3 activity in miRNA processing has remained unexplored. Our analysis of SRSF3 binding sites in embryonic stem cells (ESCs) identified SRSF3 binding at the CNNC motif in miRNAs located in polycistronic miRNA clusters. We demonstrate that SRSF3 depletion in ESCs leads to reduced levels of mature miRNAs without affecting pri-miRNA levels, suggesting a role of SRSF3 in the nuclear processing step. Interestingly, the processing of specific miRNAs within miRNA clusters is individually regulated, leading to differential expression of mature miRNAs derived from the same pri-miRNA. In particular miRNAs with CNNC motifs within a specific distance from the 3’end of the mature miRNA are selectively regulated by SRSF3.

Furthermore, SRSF3 is frequently overexpressed in tumour cells and misexpression of miRNAs is a characteristic of many cancers. The gene expression analysis in colorectal cancer patient samples confirmed that the same SRSF3 mediated mechanism of miRNA regulation operates in cancer. Intriguingly, the analysis of the mRNA targets of the SRSF3 regulated miRNAs and their functional studies demonstrated that SRSF3 confers some of its ESCs/cancer cell-specific properties through the regulation of miRNAs, uncovering an additional layer in the complex cell/tissue-specific regulation of miRNAs.