Bofill-De Ros, X. | bioRxiv Science

bioRxiv2021

Flexible pri-miRNA structures enable tunable production of 5' isomiRs

Drosha cleavage of a pri-miRNA defines mature microRNA sequence. Drosha cleavage at alternative positions generates 5 isoforms (isomiRs) which have distinctive functions. To understand how pri-miRNA structures influence Drosha cleavage, we performed a systematic analysis of the maturation of endogenous pri-miRNAs and their variants both in vitro and in vivo. We show that, in addition to previously known features, the overall structural flexibility of pri-miRNA impacts Drosha cleavage fidelity. Internal loops and nearby G{middle dot}U wobble pairs on the pri-miRNA stem induce the use of non-canonical cleavage sites by Drosha, resulting in 5 isomiR production. By analyzing patient data deposited in The Cancer Genome Atlas, we provide evidence that alternative Drosha cleavage of pri-miRNAs is a tunable process that responds to the level of pri-miRNA-associated RNA-binding proteins. Together, our findings reveal that Drosha cleavage fidelity can be modulated by altering pri-miRNA structure, a potential mechanism underlying 5 isomiR biogenesis in tumors. HIGHLIGHTSO_LIFlexible pri-miRNA structures lead to 5 isomiR production C_LIO_LIInternal loops and G{middle dot}U pairs of pri-miRNA contribute to alternative Drosha cleavages C_LIO_LIAlternative Drosha cleavage results in 5 isomiRs from both strands of pre-miRNAs C_LIO_LI5 isomiR production is upregulated by pri-miRNA-associated RBPs in cancers C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/456839v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@cab9aorg.highwire.dtl.DTLVardef@1d613b1org.highwire.dtl.DTLVardef@1a6e200org.highwire.dtl.DTLVardef@13f7607_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Tumor IsomiR Encyclopedia (TIE): a pan-cancer database of miRNA isoforms

MicroRNAs (miRNAs) function as master regulators of gene expression in many physiological and pathological conditions including cancer. Sequence variants or isoforms (isomiRs) can account for between 40 to 60% of total miRNA counts, yet despite this overwhelming abundance, their function continues to be debated. Recent studies demonstrate that certain isomiRs can regulate unique sets of target mRNAs by altering their seed sequence or stabilizing 3 pairing, while others are decay intermediates indicating an active miRNA turnover. Given their short sequence length and high heterogeneity, mapping isomiRs can be challenging; without adequate depth and data aggregation, low frequency events are often disregarded. To address these challenges, we present the Tumor IsomiR Encyclopedia (TIE): a dynamic database of isomiRs from over 10,000 adult and pediatric tumor samples in The Cancer Genome Atlas (TCGA) and The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects. A key novelty of TIE is its ability to annotate heterogeneous isomiR sequences and aggregate the variants obtained across all samples and datasets. The database provides annotation of templated and non-templated nucleotides as well as other advanced analysis. All data can be browsed online or downloaded as simple spreadsheets. Here we show analysis of isomiRs of miR-21 and miR-30a to demonstrate the utility of TIE. TIE search engine and data are hosted at https://isomir.ccr.cancer.gov/.

genomics↗