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The main difference between a single TF and multiple TFs regulating a gene is that combinatorial regulation requires all TFs to have at least one binding site for (at least) one of their motif models.
RPT5 appears to have a binding site for at least two diverse substrates, but the ultimate fate of each substrate differs.
FruA, FruB and FruC sites are found in overlapping sets of genes and the presence of a motif for one significantly increases the likelihood of finding a binding site for at least one of the other.
Transcription factor binding site analysis revealed that, out of the changed genes that did not contain a PPRE, 27% contained a binding site for at least one of the other five selected transcription factors These genes appear not to be regulated by PPARα directly, but indirectly, via these other transcription factors, a mechanism which has been suggested before [ 27, 28].
Notably, this mutation occurs before the WD-40 repeats, which are common protein-protein interacting motifs, and therefore, even if the Q775X generates a stable protein, the binding site for at least some of the PALB2 partners will have been lost.
One of them above all, the C/G polymorphism at position +3142, putative binding site for at least three miRNAs, hsa-mir-148a, hsa-mir-148b, and hsa-mir152, has been subsequently confirmed to be the binding site for mir152, and this binding reduces HLA-G expression [ 58].
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Our data suggest that this 3' flank includes binding sites for at least two activators.
In total, 176 of 602 down-regulated genes (29%) contained predicted binding sites for at least 1 out of the 6 microRNAs.
Of the transcripts downregulated in this analysis, 83 contained predicted binding sites for at least 2 of the 6 microRNAs upregulated after 4 hours (confirmed by at least 3 different algorithms, see Materials and Methods).
Those downregulated genes with binding sites for at least 2 out of the 6 selected microRNAs were then subjected to pathway analysis at http://david.abcc.ncifcrf.gov/tools.jsp [35].
The proximal promoters of Ppargc1a and Ppargc1b showed no similarities not also shared by that of Pprc, but the 3'UTRs of the two genes showed binding sites for at least three of the same miRNAs, none of which were found in the 3'UTR of Pprc.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com