Identification of miRNA transcription start sites from nascent transcriptome

miRNAs are key post-transcriptional regulators of gene expression. However, it is still poorly understood how miRNAs themselves are regulated, mainly due to the sparse annotation of miRNA transcription start sites (TSSs). Here, we developed a novel method for identifying active miRNA TSSs from nascent transcriptomes generated by nuclear run-on sequencing. With the least data requirement, our method demonstrated better performance than existing methods. Moreover, it provided ways not only to recognize miRNA TSSs but also to quantify primary miRNA expression in one experiment, which is very useful for revealing miRNAs directly regulated by the regulator(s) of interest. Overall design: PRO-seq was performed for five human cell lines including Kasumi-1, Daudi, Ly-1, MV4-11 and U936. Biological replicates were included for each cell line.