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These DHSs could be regulatory elements of nearby coding genes, but do also raise the possibility that some assumed pseudogenes are active as non-coding genes.
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To test whether these peaks could be regulatory elements, we cloned each of them upstream of a minimal SV40 promoter driving the expression of the luciferase gene.
Enhancers are regulatory elements activating the transcription of target genes.
The TATA-box and TATA-variants are regulatory elements involved in the formation of a transcription initiation complex.
The other four regions have not yet been described, and are likely to be new regulatory elements of importance for the regulation of COL2A1 expression.
A number of conserved noncoding sequences of 60 to hundreds of nucleotides have been identified in the intergenic regions of Hox clusters by comparative genomic studies, and they were considered to be putative regulatory elements of Hox genes [ 41].
In particular, both the AP-1 and NF- κB-binding sites have been shown to be important regulatory elements of the MMP9 promoter (Ricca et al, 2000; Troussard et al, 2000).
Most recently, a New RNA World has been recognized in current organisms, in which the RNA is an integral component of chromosomes and the different types of RNA are key regulatory elements of gene expression (e.g. [16]).
Even if not widely identified, the targets of these mechanisms characterised so far are mainly regulatory elements of the stress response pathways.
Thus, there are some regulatory elements of Tbp not accessible by the other two genes.
Other studies exclude RNA transcripts located in the 5′ or 3′ UTRs of annotated genes, assuming that these RNAs were cis regulatory elements of the flanking gene.
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