Mime-seq: sequencing microRNAs in complex animal tissues at single-cell resolution
MicroRNAs play a pivotal role in shaping cell phenotype. However, until recently, there were no effective methods to observe miRNA expression within an individual cell, within complex animal tissues, without introducing technical and/or biological artefacts. Now, such obstacles have been overcome with the development of mime-seq (microRNome by methylation-dependent sequencing), a high-throughput methylation and cloning technique, developed by two teams at the Vienna BioCenter [1,2]. The hero of Mime-seq is the plant RNA methyltransferase, HEN1, from Arabidopsis thaliana (Ath-HEN1), which methylates small, mature RNAs in plants, and has no counterpart in most animal cells. Ath-HEN1 methylates both strands of mature duplex miRNA at the 2’ position of the 3’-terminal ribose with 2-nt 3’ overhangs, and a length of 21-24 nt. These methylated products are resistant to periodate-induced oxidation, and therefore retain an adapter-ligatable 3’OH group for cDNA library preparation . Tested in nematodes and fruit flies, mime-seq is sufficiently powerful to enable resolution of miRNA expression within a single cell. Furthermore, mime-seq increases the miRNA “signal- to-noise” ratio within a specific cell type, even when those cells may only be present in complex tissues in vanishingly small numbers. Mime-seq not only resolves mature miRNAs in diverse animal tissues of any genetic background, but it can also chart their post-transcriptional regulation and decay . Mime-seq therefore, appears to paint a more comprehensive portrait of the life cycle of miRNA in a given animal cell, regardless of its context.
1. VIENNA BIOCENTER. “Mime-seq – single-cell sequencing of microRNAs”. RNA-Seq March 9, 2018. https://www.rna-seqblog.com/?s=mime-seq
2. ALBERTI, C, MANZENREITHER, RA, SOWEMIMO, I, et al. “Cell-type specific sequencing of microRNAs from complex animal tissues”. Nat Methods 2018; 15(4): 283-289.