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These binding sites may reflect several additional functions for HLH-1, including its interactions with one or more co-factors to activate (or repress) gene expression or a role in chromatin organization distinct from direct transcriptional regulation of target genes.
The apparent lack of an enriched RBM47-binding motif within robust CLIP-derived binding sites may reflect the broad binding patterns observed, as exemplified by the predominantly 3′UTR binding in DKK1 and IL8.
It can be conjectured that the presence of genes, which have lost (or not still acquired) the binding sites, may reflect a relatively recent evolutionary divergence, such as is expected among strains of the same species and confirmed in the case of nolR, whose inactivation in the laboratory strain Rm1021 probably happened recently, since even its DNA-binding sites are conserved.
The reduced conservation of nucleotide sequence at the −23 and −11 positions for the potential intragenic σ binding sites may reflect varied functionality of these intragenic sites, or a level of inaccuracy inherent to in silico prediction of the binding sites associated with enriched ORFs in the ChIP-chip assays.
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Our inability to detect a lower-affinity binding site may reflect the technical difficulties involved upon examination of binding at the high radioligand concentrations needed to define the low-affinity binding site.
The increase in H3K27me3 at select sites may reflect block of PRC2 binding by REST due to close proximity of their binding sites.
The number of predicted STAT6 binding sites, however, was much larger than the experimentally observed binding sites, which may reflect the typically observed high false positive rate of computational binding predictions and the cell type specific state of chromatin as well as other competing factors affecting binding in vitro.
For RBM47 this occurred due to loss of the majority of reproducible, yet relatively small intronic binding sites, which may reflect the relative abundance of pre- and mature RNA message.
Therefore, true binding sites may have SNPs less frequently than the non-binding sites.
These data suggest that additional binding sites may exist.
Not all binding sites may evolve under the same constraints.
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