Fig. 3

Mov10 knockdown affects the production of miRNA. a Read length profile for small RNAs showing that the percentage of small RNA reads were downregulated after Mov10 shRNA treatment. b Scatter plot of miRNA expression data from small RNA-seq represented as log2 values of Mov10 knockdown versus control samples. c qPCR validation of selected miRNAs with well-known function in SPCs. d Schematic representation of a general step-wise miRNA processing from pri- to mature forms (left) and the corresponding read pick-up from RNA-seq library and small RNA library (right). See the rationale in the Methods. e Scatter plot showing change of the transcript of each downregulated miRNA represented as Mov10 knockdown versus control samples. Results are mean values from three biological replicate RNA-seq libraries. f Distribution of downregulated miRNAs according to genomic origin of their mature form. g Analysis of intron-derived miRNAs using the same method as in panel E. h UCSC visualization of the genomic window of ± 200 nt flanking the hairpin of miR21a and miR20a shows lower RNA-seq read density in Mov10 knockdown SPC versus vector control (left) and qPCR confirmed significant reduction of miR21a and miR20a primary transcripts (right). PCR primer sets are marked by arrows relative to the position to the pre-miRNA shown in green. i The long isoform Vmp1-201 (ENSMUST00000018315.9) bearing the long 3′-UTR contains pre-miR21a (green line) and can be processed to produce the short isoform Vmp1-202 (ENSMUST00000123590.7) and miR21a precursor for downstream miRNA processing (left). Exons (black box), the alternative part of 3′-UTR (white box) as well as the common part (gray box) of 3′-UTR are shown. Two different primer sets (arrows) were designed. The relative ratio of the long isoform over both (long+short) was quantified by Image J software (right)