RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia

Vasily V Grinev,Anita Van Oort,Farnaz Barneh,Sirintra Nakjang,Mojgan Reza,Constanze Bonifer,Hesta Mcneill,Job Smink,Richard Clough,Tatsiana V Ramanouskaya,Ilya M Ilyushonak,Michael Seyani,Natalia Martinez-Soria,Olaf Heidenreich,Salam A Assi

doi:10.1038/s41467-020-20848-z

Abstract

The fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of acute myeloid leukemia. Here we show that the RUNX1/RUNX1T1 oncogene is a regulator of alternative RNA splicing in leukemic cells. The comprehensive analysis of RUNX1/RUNX1T1-associated splicing events identifies two principal mechanisms that underlie the differential production of RNA isoforms: (i) RUNX1/RUNX1T1-mediated regulation of alternative transcription start site selection, and (ii) direct or indirect control of the expression of genes encoding splicing factors. The first mechanism leads to the expression of RNA isoforms with alternative structure of the 5’-UTR regions. The second mechanism generates alternative transcripts with new junctions between internal cassettes and constitutive exons. We also show that RUNX1/RUNX1T1-mediated differential splicing affects several functional groups of genes and produces proteins with unique conserved domain structures. In summary, this study reveals alternative splicing as an important component of transcriptome re-organization in leukemia by an aberrant transcriptional regulator.

Highlights

The fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of acute myeloid leukemia
Functional annotation by DAVID uncovered a highly significant enrichment of RUNX1/ RUNX1T1 binding at gene loci that are subject to alternative splicing and splice variants[24]
Gene set enrichment analysis (GSEA) suggests that knockdown of RUNX1/RUNX1T1 affects RNA binding proteins and snRNP assembly, and is associated with impaired mRNA processing and, in particular, splicing pathways (Fig. 1a; Supplementary Fig. 1b)[27]. These findings strongly suggest a regulatory role of this leukemic fusion protein in mRNA splicing and predict changes in splicing pattern in response to perturbing RUNX1/RUNX1T1 activity

Summary

Introduction

The fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of acute myeloid leukemia. The comprehensive analysis of RUNX1/RUNX1T1-associated splicing events identifies two principal mechanisms that underlie the differential production of RNA isoforms: (i) RUNX1/ RUNX1T1-mediated regulation of alternative transcription start site selection, and (ii) direct or indirect control of the expression of genes encoding splicing factors. A potential role of leukemic fusion genes encoding epigenetic modulators such as RUNX1/RUNX1T1 has not yet been established for the regulation of alternative splicing. To address this question, we performed perturbation experiments in t(8;21)-positive AML cells and examined the impact of RUNX1/RUNX1T1 knockdown on the gene expression and RNA splicing at a global level. Our modeling and experimental results indicate that oncoprotein-mediated differential splicing affects conserved domain structures in proteins, modulating leukemia-relevant processes such as nucleotide metabolism, cell adhesion and cell differentiation

Methods

Results

Conclusion