Orthogonal proteomics methods to unravel the HOTAIR interactome

Louis Delhaye,Sven Eyckerman,Pieter Mestdagh,Daria Fijalkowska,Pieter-Jan Volders,Delphine De Sutter,Lennart Martens,Sven Degroeve,Edith De Bruycker

doi:10.1038/s41598-022-05405-6

Abstract

Accumulating evidence highlights the role of long non-coding RNAs (lncRNAs) in cellular homeostasis, and their dysregulation in disease settings. Most lncRNAs function by interacting with proteins or protein complexes. While several orthogonal methods have been developed to identify these proteins, each method has its inherent strengths and limitations. Here, we combine two RNA-centric methods ChIRP-MS and RNA-BioID to obtain a comprehensive list of proteins that interact with the well-known lncRNA HOTAIR. Overexpression of HOTAIR has been associated with a metastasis-promoting phenotype in various cancers. Although HOTAIR is known to bind with PRC2 and LSD1 protein complexes, only very limited unbiased comprehensive approaches to map its interactome have been performed. Both ChIRP-MS and RNA-BioID data sets show an association of HOTAIR with mitoribosomes, suggesting that HOTAIR has functions independent of its (post-)transcriptional mode-of-action.

Highlights

Accumulating evidence highlights the role of long non-coding RNAs in cellular homeostasis, and their dysregulation in disease settings
We set out to screen for potential interaction partners of the long non-coding RNAs (lncRNAs) HOTAIR and identified multiple MRPLs to be associated with HOTAIR
CoREST to be significantly enriched in the RNA-BioID setup, which was performed on overexpressed HOTAIR in HEK293 cells

Summary

Introduction

Accumulating evidence highlights the role of long non-coding RNAs (lncRNAs) in cellular homeostasis, and their dysregulation in disease settings. We combine two RNA-centric methods ChIRP-MS and RNA-BioID to obtain a comprehensive list of proteins that interact with the well-known lncRNA HOTAIR. HOTAIR is known to bind with PRC2 and LSD1 protein complexes, only very limited unbiased comprehensive approaches to map its interactome have been performed Both ChIRP-MS and RNA-BioID data sets show an association of HOTAIR with mitoribosomes, suggesting that HOTAIR has functions independent of its (post-)transcriptional mode-of-action. Methodological differences in iDRIP-MS, ChIRP-MS, and RAP-MS technologies have shown remarkable differences in size and content of the identified interactome of the lncRNA Xist, a crucial player in X-chromosome inactivation All these studies have revealed Xist interacting proteins using different methods, all highlighting key interactors such as SPEN/SHARP and hnRNPU/SAF-A that are required for X-chromosome inactivation. Portoso et al.[24] have shown that PRC2 is dispensable for HOTAIR-mediated gene silencing, putting forth the question whether HOTAIR recruits PRC2 or whether PRC2 is recruited to target genes as a consequence of HOTAIR-mediated gene silencing

Methods

Results

Conclusion