HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Icahn School of Medicine, United States
- Icahn School of Medicine at Mount Sinai, United States
- IIGM (Italian Institute for Genomic Medicine), Italy
- Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- University of Toronto, Canada
- NYU, United States
- Italian Institute for Genomic Medicine, Italy
- Max Delbruck Center for Molecular Medicine, Germany
- H Lee Moffitt Cancer Center and Research Institute;, United States
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore., Singapore
Abstract
High spliceosome activity is a dependency for cancer cells, making them more vulnerable to perturbation of the splicing machinery compared to normal cells. To identify splicing factors important for prostate cancer (PCa) fitness, we performed pooled shRNA screens in vitro and in vivo. Our screens identified HNRNPM as a regulator of PCa cell growth. RNA- and eCLIP-sequencing identified HNRNPM binding to transcripts of key homeostatic genes. HNRNPM binding to its targets prevents aberrant exon inclusion and back-splicing events. In both linear and circular mis-spliced transcripts, HNRNPM preferentially binds to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM dependent linear splicing events using splice-switching-antisense-oligonucleotides (SSOs) was sufficient to inhibit PCa cell growth. This suggests that PCa dependence on HNRNPM is likely a result of mis-splicing of key homeostatic coding and non-coding genes. Our results have further been confirmed in other solid tumors. Taken together, our data reveal a role for HNRNPM in supporting cancer cell fitness. Inhibition of HNRNPM activity is therefore a potential therapeutic strategy in suppressing growth of PCa and other solid tumors.
Data availability
All data needed to evaluate the conclusions in this study are present in the paper and/or its Supplementary Materials. eCLIP and RNA-Sequencing data supporting the findings of this study have been deposited into the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus under accessions GSE113786.
Article and author information
Author details
Salvatore Oliviero
Funding
National Cancer Institute (R01CA197910)
- David Mulholland
National Medical Research Council (NMRC/OFIRG/0032/2017)
- Dave Keng Boon Wee
- Ernesto Guccione
National Research Foundation Singapore (NRF-CRP17-2017-06)
- Dave Keng Boon Wee
- Ernesto Guccione
National Cancer Institute (R01CA249204)
- Ernesto Guccione
ISMMS
- Ernesto Guccione
Melanoma Research Alliance (MRA Team Science Award)
- Eva Hernando
- Ernesto Guccione
Lee Kuan Postdoctural Fellowship
- Simin Zheng
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Ho et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness
eLife 10:e59654.
https://doi.org/10.7554/eLife.59654
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Enhancers and promoters are classically considered to be bound by a small set of transcription factors (TFs) in a sequence-specific manner. This assumption has come under increasing skepticism as the datasets of ChIP-seq assays of TFs have expanded. In particular, high-occupancy target (HOT) loci attract hundreds of TFs with often no detectable correlation between ChIP-seq peaks and DNA-binding motif presence. Here, we used a set of 1003 TF ChIP-seq datasets (HepG2, K562, H1) to analyze the patterns of ChIP-seq peak co-occurrence in combination with functional genomics datasets. We identified 43,891 HOT loci forming at the promoter (53%) and enhancer (47%) regions. HOT promoters regulate housekeeping genes, whereas HOT enhancers are involved in tissue-specific process regulation. HOT loci form the foundation of human super-enhancers and evolve under strong negative selection, with some of these loci being located in ultraconserved regions. Sequence-based classification analysis of HOT loci suggested that their formation is driven by the sequence features, and the density of mapped ChIP-seq peaks across TF-bound loci correlates with sequence features and the expression level of flanking genes. Based on the affinities to bind to promoters and enhancers we detected five distinct clusters of TFs that form the core of the HOT loci. We report an abundance of HOT loci in the human genome and a commitment of 51% of all TF ChIP-seq binding events to HOT locus formation thus challenging the classical model of enhancer activity and propose a model of HOT locus formation based on the existence of large transcriptional condensates.
