Investigating the role of Dicer-dependent transfer RNA-derived small RNAs in gene expression regulation

We used sequencing analyses to identify small RNAs that are generated in a Dicer-dependent manner and the genes that are dysregulated upon Dicer knockdown at the mRNA level, and upon Drosha, Dicer and Ago2 knockdown at the chromatin level in HEK293 cells. We found that levels of tRNA-derived sRNAs decreased alongside microRNAs upon Dicer knockdown. Many genes are dysregulated at the chromatin levels when Dicer and Ago2 levels are reduced, indicating that Dicer and Ago2 can regulate genes directly or indirectly at the transcriptional level. Drosha knockdown, on the other hand, has a marginal effect on RNA levels at the chromatin. sRNA and mRNA profiles of HEK293 wt and Dicer knockdown cells were generated by deep sequencing, in triplicates; chromatin-associated RNA profiles of HEK293 wt, Drosha, Dicer and Ago2 knockdown cells were generated by deep sequencing, in duplicates.