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Especially, genes identified from transgenic rice may provide more information about the affect of drought response mechanisms on gene functions, cis-acting elements and downstream genes in cascades.
In addition, two auxiliary sequence elements (upstream U-rich elements and downstream G-rich elements) have also been identified.
Furthermore, a genomic organization of IS elements and downstream genes similar to the loci analyzed in this study was found in 44 other regions on the A. asiaticus genome (data not shown), suggesting that contiguous transcripts between IS elements and downstream genes are even more widespread and represent a more general feature of A. asiaticus.
As previous reports have shown that IS elements can influence the transcription of neighboring genes [ 17- 21], we investigated whether contiguous transcripts between A. asiaticus IS elements and downstream genes occur.
Thus, while our analysis supports the view that this specific integrative epigenetic-transcriptomic landscape is fairly homogeneous in ER+ breast cancer, this does not by any means exclude the possibility that ER+ breast cancer is highly heterogeneous in relation to the correlative patterns of DNA methylation at distal regulatory elements and downstream gene expression.
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Extract a list with all elements in the network (name, type and upstream element and downstream element, if a pipe or connector) and separate them in edges and nodes.
Canonical core promoter motifs include TATA, the initiator (INR), TFIIB recognition element (BRE) and downstream promoter element (DPE) motifs.
bglGFB encodes cryptic genes for ß-glucoside catabolism and is ordinarily silenced by H-NS filaments that emanate from high-affinity sites flanking the promoter (upstream regulatory element, URE, and downstream regulatory element, DRE, respectively; Figure 1A).
b, Transposable elements up- and downstream of genes.
Expression in the midbrain of murine embryos has been suggested to rely on specific positive and negative regulatory elements upstream and downstream of the Col2a1 promoter [ 3].
Evidence is emerging that not only proximal promoters, but also distant elements upstream and downstream from TSS can regulate transcription [ 90, 91].
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