BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs with important roles in 
regulating gene expression. Recent studies indicate that transcription and 
cleavage of miRNA are coupled, and that chromatin structure may influence miRNA 
transcription. However, little is known about the relationship between the 
chromatin structure and cleavage of pre-miRNA from pri-miRNA.
RESULTS: By analysis of genome-wide nucleosome positioning data sets from human 
and Caenorhabditis elegans (C. elegans), we found an enrichment of positioned 
nucleosome on pre-miRNA genomic sequences, which is highly correlated with GC 
content within pre-miRNA. In addition, obvious enrichments of three histone 
modifications (H2BK5me1, H3K36me3 and H4K20me1) as well as RNA Polymerase II 
(RNAPII) were observed on pre-miRNA genomic sequences corresponding to the 
active-promoter miRNAs and expressed miRNAs.
CONCLUSION: Our results revealed the chromatin structure characteristics of 
pre-miRNA genomic sequences, and implied potential mechanisms that can recognize 
these characteristics, thus improving pre-miRNA cleavage.