miR-222 isoforms are differentially regulated by type-I interferon

Abstract

Endogenous microRNAs (miRNAs) often exist as multiple isoforms (known as "isomiRs") with predominant variation around their 3'-end. Increasing evidence suggests that different isomiRs of the same family can have diverse functional roles, as recently demonstrated with the example of miR-222-3p 3'-end variants. While isomiR levels from a same miRNA family can vary between tissues and cell types, change of templated isomiR stoichiometry to stimulation has not been reported to date. Relying on small RNA-sequencing analyses, we demonstrate here that miR-222-3p 3'-end variants >23 nt are specifically decreased upon interferon (IFN) β stimulation of human fibroblasts, while shorter isoforms are spared. This length-dependent dynamic regulation of long miR-222-3p 3'-isoforms and >40 other miRNA families was confirmed in human monocyte-derived dendritic cells following infection with Typhimurium, underlining the breadth of 3'-length regulation by infection, beyond the example of miR-222-3p. We further show that stem-loop miRNA Taqman RT-qPCR exhibits selectivity between 3'-isoforms, according to their length, and that this can lead to misinterpretation of results when these isoforms are differentially regulated. Collectively, and to our knowledge, this work constitutes the first demonstration that the stoichiometry of highly abundant templated 3'-isoforms of a same miRNA family can be dynamically regulated by a stimulus. Given that such 3'-isomiRs can have different functions, our study underlines the need to consider isomiRs when investigating miRNA-based regulation.

Milk MicroRNAs in Health and Disease

“…Moreover, microRNA isomiRs might not target the same proteins and, thus, depending on the sequence of the microRNAs found in milk, such approaches could mislead investigators on the real targets of milk microRNAs (Cloonan et al., ; Neilsen, Goodall, & Bracken, ; Nejad et al., ; Ple et al., ; Tan et al., ; Yu et al., ).…”

qPCR-Based Methods for Expression Analysis of miRNAs

“…Recently, it has been shown that the use of assays designed for the analysis of canonical miRNAs can lead to problems due to the finding that isomiRs are quite common and their levels are affected in biological models and diseases [42,45]. In this context, the polyadenylation-based methods are less affected by changes in isomiRs [45,46].…”

Characterising the genetic basis of immune response variation to identify causal mechanisms underlying disease susceptibility

“…46,50 Furthermore, extensive changes in isomiRs have been observed upon stimulation, including for key immune miRNAs. 51 For instance, upon stimulation by interferon, mir-222 expresses shorter isoforms, which are associated to lower apoptosis, 52,53 highlighting how changes of miRNA isoform can contribute to regulate the response to immune stimuli.…”