Abstract

The microRNAs in the miR-34 family, consisting of miR-34a, miR-34b and miR-34c, are tumour suppressors. The annotated human miR-34b-5p has one additional base at the 5’ end of the common miR-34 family seed sequence, compared to miR-34a-5p and miR-34c-5p. This extra base results in a shift of the seed sequence, which would affect the target gene repertoire and have functional consequences. During our studies of miR-34 functions, we investigated the precise sequence of mature miR-34b-5p in human cells by deep sequencing. We found that a miR-34b-5p without the extra base was the predominant form in both non-malignant and malignant cells derived from several human tissues, indicating that the miR-34b annotation is misleading. We evaluated the functional implications of the seed shift, by comparing the effect of mimics representing the alternative miR-34b-5p sequences in MDA-MB-231 cells. In contrast to the annotated miR-34b, the endogenously expressed miR-34b displayed tumour suppressive characteristics in vitro similarly to miR-34c. These data demonstrate the importance of determining the precise sequence of a mature microRNA before exploring miRNA functions.

Highlights

  • MicroRNAs are small, non-coding RNAs that affect many fundamental biological processes, such as development, cell differentiation and cell growth, by functioning as regulators of gene expression

  • We separately introduced synthetic mimics representing human annotated versions of the miR-34b-5p and miR-34c-5p into the breast cancer cell line MDA-MB-231

  • The analysis revealed that the levels of 777 and 1001 transcripts significantly changed upon introduction of miR-34b and miR-34c, respectively (Supplementary data S1). 305 transcripts were regulated in the same manner by both mimics

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Summary

Introduction

MicroRNAs (miRNAs) are small, non-coding RNAs that affect many fundamental biological processes, such as development, cell differentiation and cell growth, by functioning as regulators of gene expression. The consensus is that members of the same miRNA family target a related set of genes, and are to some extent biologically redundant, but may allow multiple regulatory mechanisms and expression profiles in different cells or conditions. In humans miR-34b-5p has an additional base at the 5′ end, shifting its seed sequence by one base, relative to the other miR-34 family members as annotated in databases like miRBase and miRNAMap 2.0 and found in scientific reviews[13,14,15]. Functional analyses demonstrated that the miR-34b expressed in the MDA-MB-231 cells had tumour suppressive capacity resembling that of miR-34c, while the annotated miR-34b did not

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