Synthetic small duplex RNAs that are complementary to gene promoters can activate or inhibit target gene expression. duplex RNAs that target mRNA. agRNAs recruit members of the argonaute (AGO) protein family to RNA transcripts that originate from the target gene promoter in either the sense or antisense direction.6-9 Data suggests that recognition of the target RNA occurs in close proximity to the chromosome resulting in transcriptional modulation of the target gene. One remarkable feature of the synthetic agRNAs that we have examined is the potency and robustness of their activity when they are introduced into cells. This potency coupled with the presence of protein machinery that facilitates their function suggests that endogenous small RNAs may possess the ability to recognize gene promoters. If RNA could direct proteins to specific gene promoters such RNA-mediated modulation of transcription might have evolutionary advantages relative to the development of gene-specific protein transcription factors. Synthetic duplex RNAs that are complementary to mRNA (small interfering RNAs or siRNAs) are also potent and robust agents for modulating gene expression.10 siRNAs are known to have endogenous analogs that regulate gene expression called microRNAs (miRNAs).11 miRNAs are processed inside the cell from RNA precursors that contain stem-loop structures. These stem-loop structures are processed by the double-stranded nucleases Drosha and Dicer to produce mature miRNAs. As of the current release of the miRNA repository (miRBase v12.0) 866 individual miRNAs possess been annotated but this true amount continues to boost. Many miRNAs that understand sequences inside the AV-412 3′-untranslated locations (3′UTR) of mRNA transcripts have already been characterized. Many miRNAs nevertheless haven’t any known goals12 13 although some can understand multiple mRNAs13 recommending the fact that determinants of miRNA connections are complicated and poorly grasped. Two reports predicated on computational analyses possess recommended that miRNAs can modulate gene appearance through promoter reputation. Dahiya and co-workers utilized AV-412 publically available software program (RegRNA) to find potential miRNA focus on sites inside the promoter from the E-cadherin gene.14 They identified one potential binding site for miR-373 inside the E-cadherin promoter and reported that introduction of the synthetic miR-373 imitate increased expression from the gene by 6 fold at the amount of the AV-412 mRNA. Co-workers and Rossi sought out best complementarity between miRNAs and gene promoters.15 Their analysis suggested AV-412 that miR-320 targets TMEM8 the genomic location that it really is transcribed and showed that expression of miR-320 as well as the adjacent gene POLR3D are anti-correlated. The above-mentioned research either analyzed an individual gene promoter or utilized highly stringent series comparison requirements. These approaches weren’t intended to evaluate broader prospect of miRNAs to identify gene promoters warranting a far more comprehensive evaluation of the partnership between miRNAs and promoter sequences. A useful justification to get more extensive research is certainly that validating organic gene targets of miRNAs is usually a complex and difficult process. The development of systematic and efficient methods for identifying promoter sequences that may be miRNA targets is essential for prioritizing predictions and efficiently allocating experimental resources towards validating the most promising targets. Here we examine computational methods for predicting potential miRNA targets within gene promoters and demonstrate that promoters are strong candidates for miRNA regulation. Sequence Acquisition To identify putative promoter-targeting miRNAs we constructed a database comprised of miRNA and gene promoter sequences from public sequence repositories. Promoter sequences were AV-412 acquired from the UCSC genome browser (hg 18) and consisted of the 200 nucleotides immediately 5′ to the annotated transcription start site for each gene.16 17 We chose 200 base sequences (?200 to ?1) for initial evaluations but larger promoter regions can also be examined. Mature miRNA sequences were obtained from miRBase (Build 12.0) which contains sequences of experimentally determined precursor and mature miRNAs.18 19 20 Analysis of seed sequence matches.