Gene expression is regulated at different levels. RNA interference is the mechanism through which double-stranded short RNAs silence cognate genes. Recent research work demonstrates that double short RNAs can not only repress the gene expression at post-transcriptional level, but also have a close relationship with chromatin silencing by directed H3 Lys9 methylation, DNA methylation and combining with other heterochromatin proteins. The mechanism existed in RNA interference, short RNAs, chromatin modification and chromatin silencing has been disclosed.