Fig. 1

RNA sequencing of DROSHA knockout cells to identify the transcription start sites of human miRNAs. a Experimental scheme: In wild-type cells in which DROSHA protein is intact, RNA fragments made by DROSHA-mediated cleavage of pri-miRNAs, except for pre-miRNAs, are rapidly degraded (left panel). In DROSHA knockout cells, pri-miRNAs with the sequence of intact 5′ ends are accumulated (right panel). By analyzing the RNA sequences in these cells and verifying the 5′ end sequences through 5′ RACE, the transcription start sites can be identified precisely. b Total read numbers analyzed in this study, and the read numbers mapped near pre-miRNAs were shown. The enrichment of reads near pre-miRNAs in comparison to total reads were calculated by Fisher’s exact test. See Additional file 2 for details. c Pri-let-7a-1 ~ let-7f-1 ~ let-7d cluster as an example. Note that in comparison to the graph showing RNA signals from wild-type cells, the one representing DROSHA knockout cells delineates the 5′ end of pri-miRNAs more clearly. By utilizing the ChIP-seq data at the promoter region of pri-miRNAs, transcription factors that may affect the expression of pri-miRNAs can be analyzed. The ChIP-seq data was obtained from the ENCODE project [21], and vertebrate conservation data were downloaded from The USCS Genome Browser [30]