Mass Spectrometry-Based Proteomics Approach Characterizes the Dual Functionality of miR-328 in Monocytes.

Meike J Saul,Marc Vogel,Johan Lengqivst,Dieter Steinhilber,Elena Ossipova,Anett B Hegewald,Kim Kultima,Anne C Emmerich,Isabell Baumann,Per Johan Jakobsson

doi:10.3389/fphar.2019.00640

Abstract

MicroRNAs (miRs) are small noncoding RNAs which control the expression of target genes by either translational repression or RNA degradation, known as canonical miR functions. The recent discovery that miR-328 has a noncanonical function and can activate gene expression by antagonizing the activity of heterogeneous ribonuclear protein E2 (hnRNP E2) opens an unexplored and exciting field of gene expression regulation. The global importance of such noncanonical miR function is not yet known. In order to achieve a better understanding of the new miR activity, we performed a compartment specific tandem mass tag (TMT)-based proteomic analysis in differentiated MonoMac6 (MM6) cells, to monitor gene expression variations in response to miR-328 knockdown. We identified a broad spectrum of novel potential miR-328/hnRNP E2 and miR-328 targets involved in regulation of compartment specific cellular processes, such as inflammation or RNA splicing. This study provides first insights of the global significance of noncanonical miR function.

Highlights

MicroRNAs are a family of small noncoding RNAs of about 21–24 nucleotides that regulate a wide spectrum of cellular biological processes including inflammation and cancerogenesis (Croce, 2009; Ochs et al, 2011; Ochs et al, 2014)
This study identified a broad spectrum of novel potential miR-328/hnRNP E2 and miR-328 targets involved in important cellular processes such as inflammation, p53 signalling or messenger RNA (mRNA) splicing
To investigate changes in the proteome in response to miR-328 knockdown, a tandem mass tag (TMT)-based proteomics approach was carried out in MM6 cells treated with TGFβ and calcitriol for 4 days (Figure 1)

Summary

Introduction

MicroRNAs (miRs) are a family of small noncoding RNAs of about 21–24 nucleotides that regulate a wide spectrum of cellular biological processes including inflammation and cancerogenesis (Croce, 2009; Ochs et al, 2011; Ochs et al, 2014). MiRs are generated by enzymatic processes from precursor transcripts and assembled with the RNA interference silencing complex (RISC) They are directed to their binding sites in the 3′ untranslated region (UTR) of the target messenger RNA (mRNA) and mediate either translational repression or degradation of their target transcript (Croce, 2009; Ochs et al, 2011; Ochs et al, 2014). MiRs can bind to RNA binding proteins (RBPs) sequestering them away from their target mRNAs in a RISC independent manner (Eiring et al, 2010). Such a function was described for the first time

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