Poster Presentation 50 Years Shine-Dalgarno Symposium 2023

Mechanisms producing novel polyadenylated isoforms of ncRNA RPPH1 (#103)

Kiarna Kavanagh-Beck 1 , Traude H Beilharz 1
  1. Monash University, Burwood, VIC, Australia

The lncRNA RPPH1 is normally produced by RNA polymerase III transcription without the addition of a polyA-tail. Surprisingly, the Beilharz lab has identified polyadenylated RPPH1 isoforms. The ratio of two polyadenylated isoforms is cancer cell line specific, and the MCF10A progression series revealed that an increase in the long polyadenylated RPPH1 isoform correlated with increasing metastatic potential. I investigated mechanisms regulating RPPH1 polyadenylation by performing CRISPR KOs of non-canonical post-transcriptional poly(A) polymerases as well as transcriptional inhibition by drug treatments.   This investigation revealed the short isoform depended on the non-canonical poly(A) polymerase PAPD5 and thus represents a decay intermediate. Whereas, transcriptional inhibition with actinomycin D rapidly reduced the long RPPH1 isoform which suggests its polyadenylation is linked to transcription. The 223bp RPPH1 promoter is shared with the RNA Polymerase II (RNAPII)-driven PARP2 gene. We hypothesised that a switch in RNAPII directionality generates the long polyadenylated RPPH1 and recruits the traditional 3’-end formation machinery to extend its poly(A)-tail. This idea was tested by use of a CDK9 inhibitor, AZ5576, to prevent RNAPII promoter-proximal pause release. Application of this inhibitor resulted in increased long polyadenylated RPPH1 isoform and decreased PARP2 expression. We propose that this is due to inhibitor induced RNAPII stalling within PARP2 that results in increased bidirectional RNAPII activity and aberrant RNAPII-mediated RPPH1 transcription. We theorise a shift toward RPPH1 long polyadenylated isoforms in cancer cells might reflect a global change in RNAPII activity that is particularly evident at this bidirectional promoter. Our research is still to uncover how this may be linked with the metastatic trajectory of tumours, but we are seeking to understand if the ratio of these adenylated RPPH1 isoforms might serve as functional cancer biomarkers. Current investigations aim to further explore alternative RPPH1 isoforms including long RPPH1 and circRPPH1 isoforms.

  1. Baer M, Nilsen TW, Costigan C, Altman S. Structure and transcription of a human gene for H1 RNA, the RNA component of human RNase P. Nucleic Acids Res. 1990;18(1):97-103.
  2. Saskia Gressel, Björn Schwalb, Tim Michael Decker, Weihua Qin, Heinrich Leonhardt, Dirk Eick, Patrick Cramer. CDK9-dependent RNA polymerase II pausing controls transcription initiation. eLife. 2017; 6: e29736