Background:MicroRNAs (miRNAs) regulate target gene expression at post-transcriptional level.Intense research has been conducted for miRNA identification and the target finding.However,much less is known about the transcriptional regulation of miRNA genes themselves.Recently,a special group of pre-miRNAs that are produced directly by transcription without Drosha processing were validated in mouse,indicating the complexity of miRNA biogenesis.Methods:In this work,we detect clusters of aligned Cap-seq reads to find the transcription start sites (TSSs) for intergenic miRNAs and study their transcriptional regulation in Caenorhabditis elegans and mouse.Results:In both species,we have identified a class of special pre-miRNAs whose 5’ends are capped,and are most probably generated directly by transcription.Furthermore,we distinguished another class of special pre-miRNAs that are 5’-capped but are also part of longer primary miRNAs,suggesting they may have more than one transcription mechanism.We detected multiple cap reads peaks within miRNA clusters in C.elegans.We surmised that the miRNAs in a cluster may either be transcribed independently or be re-capped during the microprocessor cleavage process.We also observed that H3K4me3 and Pol Ⅱ are enriched at those identified miRNA TSSs.Conclusions:The Cap-seq datasets enabled us to annotate the primary TSSs for miRNA genes with high resolution.Special class of 5’-capped pre-miRNAs have been identified in both C.elegans and mouse.The capping patter of miRNAs in a cluster indicate that clustered miRNA transcripts probably undergo a re-capping procedure during the microprocessor cleavage process.