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This percentage continues to increase for probe-sets detecting transcripts carrying more miRNA binding sites, reaching 100% for probe-sets detecting transcripts with 4 or more binding sites.
Both Stark et al. and Sood et al. reported a bias of a longer 3' UTR length and more miRNA binding sites in genes involved in neurogenesis and in genes highly expressed in neuronal tissues [15] [16].
Increased regulatory complexity in long 3'UTRs may be a result of more miRNA binding sites.
We found that miRNA binding sites had an additive effect on mRNA decay rate, for which genes with more miRNA binding sites displayed higher mRNA decay rate.
While the number of miRNA binding sites for miRNA target genes used in this study ranges from 1 to 173, with average number > 8, more than 82% of genes have 2 or more miRNA binding sites, indicating that majority of miRNA target genes are under multiple miRNA regulation.
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Genes in regulatory networks with more transcription factor binding sites have, on average, more miRNA-binding sites and a higher probability of being targeted by miRNAs [ 6].
Importantly, the genes with more transcription factor-binding sites have a higher probability of being targeted by miRNAs and have more miRNA-binding sites [ 74].
Importantly, they found that the genes with more transcription factor-binding sites have a higher probability of being targeted by miRNAs and have more miRNA-binding sites.
To summarize, we have demonstrated that older genes tend to be bound by more TFs, have more conserved upstream sequences, use more alternative TSSs, produce more alternative splicing isoforms, use more alternative polyadenylation sites, and contain more miRNA-binding sites and that they are also more likely targets of NMD and RNA editing.
It was already reported that genes having more distinct miRNA binding sites at the 3′UTR regions tend to have slower evolutionary rates [ 9].
When one considers the 6,574 probe-sets detecting transcripts carrying at least 2 target sites, the percentage improves to 54.4% (p<1.3·10−4 by a hypergeometric test), and it continues to increase for probe-sets detecting transcripts carrying more sites for miRNA binding, reaching about 70% for the 228 probe-sets detecting transcripts with more than 15 target sites.
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