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These extended gene loci may harbor binding sites for nervous tissue-specific transcription factors.
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Interestingly, our co-factor TFBSs analysis revealed enrichment for the presence of associated binding sites not just for SOX9, but also three additional Sox family members (Sox17, Sox5, and SRY) within the vicinity of predicted NR2E1 binding sites for genes of the "nervous system development" GO term category (Table 2).
3'UTRs of transcripts rarely encountered in the nervous tissue were enriched with binding sites for neuron-specific miRNAs (Figure 8), which likely facilitate targeted degradation of these transcripts in the nervous tissues through the RNAi mechanism.
A customized bioinformatics analysis, based on the oPOSSUM combination site analysis feature, was performed to identify TFBS patterns that were significantly enriched in the vicinity of predicted NR2E1 binding sites for the 64 candidate genes found in the "nervous system development" GO term category.
Transcripts rarely encountered in the nervous tissue were enriched 2 3 fold with binding sites for neuron-specific miRNAs, which likely facilitated targeted degradation of these transcripts in the nervous tissue through the RNA inhibition mechanism.
To discover novel candidate co-interactors of Nr2e1, we designed a computational experiment to identify TFBS within the vicinity of the predicted NR2E1 binding sites for each differentially-regulated gene found in the GO term category "nervous system development".
Each of the R2B genes also had multiple transcription factor binding sites for engrailed-1, which is active in specific cell types of the developing central nervous system [ 27].
As seen from the Table, binding sites for POU, Pit, Pbx, Pax, Olf, Meis and other neuron-specific transcription factors that perform specific functions in the central nervous system were highly overrepresented in evolutionarily conserved in regions of PK genes predominantly expressed in the nervous tissue.
Furthermore two binding sites for bHLH factors were retrieved.
By phosphorylation of Bad, binding sites for 14-3-3-protein 14-3-3-protein 14-3-3-protein 14-3-3-protein
Among these cis-acting elements are often multiple GR binding sites as well as binding sites for other transcriptional regulators.
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