Expression Microdissection for the Analysis of miRNA in a Single-Cell Type

Jenike, Ana E; Bunkelman, Brady; Mandell, Kira A. Perzel; Oduor, Cliff I.; Chin, Deborah; Mair, Devin B.; Jenike, Katharine M.; Kim, Deok Ho; Bailey, Jeffrey A.; Rafailovich, Miriam; Rosenberg, Avi; Halushka, Marc K.

doi:10.1016/j.labinv.2023.100133

Cited by 1 publication

(1 citation statement)

References 27 publications

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“…Instead, profiling of miRNAs from individual cell types has mainly relied on two different approaches. First, the sorting or microdissection of the cells of interest for subsequent RNA extraction and small RNA library preparation (e.g., Jenike et al, 2023 ; Grolmusz et al, 2016 ). Second, the cell-specific expression of an epitope-tagged Argonaute protein, into which miRNAs are loaded, that can be immunoprecipitated to retrieve the associated small RNAs (Than et al, 2013 ; He et al, 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types

Mandlbauer,

Sun,

Popitsch

et al. 2024

EMBO J

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Many microRNAs (miRNAs) are expressed with high spatiotemporal specificity during organismal development, with some being limited to rare cell types, often embedded in complex tissues. Yet, most miRNA profiling efforts remain at the tissue and organ levels. To overcome challenges in accessing the microRNomes from tissue-embedded cells, we had previously developed mime-seq (miRNome by methylation-dependent sequencing), a technique in which cell-specific miRNA methylation in C. elegans and Drosophila enabled chemo-selective sequencing without the need for cell sorting or biochemical purification. Here, we present mime-seq 2.0 for profiling miRNAs from specific mouse cell types. We engineered a chimeric RNA methyltransferase that is tethered to Argonaute protein and efficiently methylates miRNAs at their 3′-terminal 2′-OH in mouse and human cell lines. We also generated a transgenic mouse for conditional expression of this methyltransferase, which can be used to direct methylation of miRNAs in a cell type of choice. We validated the use of this mouse model by profiling miRNAs from B cells and bone marrow plasma cells.

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