factor binding sites that were annotated across the human genome. a search algorithm is applied to the data set to identify possible combinations of transcription factors, which have binding sites that are close to the promoter of the gene set of interest. the possible cis-regulatory modules are then statistically analyzed and the significant combinations are graphically represented active cis-regulatory modules in a genomic sequence have been difficult to identify. problems in identification arise because often scientists find themselves with a small set of known transcription factors, so it makes it harder to identify statistically significant clusters of transcription factor binding sites. additionally, high costs limit the use of large whole genome tiling arrays. binding sites of gene regulatory factors. transcription factors binding dna, rna-binding proteins and micrornas binding rna examples an example of a cis-acting regulatory sequence is the operator in the lac operon. this dna sequence is bound by the lac repressor, which, in turn, prevents transcription of the adjacent genes on the same dna molecule. the lac operator is, thus, considered to "act in cis" on the regulation of the nearby genes. the operator itself does not code for any protein or rna. in contrast, trans-regulatory elements are diffusible factors, usually proteins, that may modify the expression of genes distant from the gene that was originally transcribed to create them. for example, a transcription factor that regulates a gene on chromosome 6 might itself have been transcribed from a gene on chromosome 11. the term trans-regulatory is constructed from the latin root trans, which means "across from". there are cis-regulatory and trans-regulatory elements. cis-regulatory elements are often binding sites for one or more trans-acting factors. to summarize, cis-regulatory elements are present on the same molecule of dna as the gene they regulate whereas trans-regulatory elements can regulate genes distant from the gene from which they were transcribed. examples in rna rna elements typeabbr.functiondistributionref. frameshift elementregulates alternative frame use with messenger rnasarchaea, bacteria, eukaryota, rna viruses internal ribosome entry siteiresinitiates translation in the middle of a messenger rnarna virus, eukaryota iron response elementireregulates the expression of iron associated geneseukaryota leader peptideregulates transcription of associated genes and/or operonsbacteria riboswitchgene regulationbacteria, eukaryota rna thermometergene regulationbacteria selenocysteine insertion sequencesecisdirects the cell to translate uga stop-codons as selenocysteinesmetazoa