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The most conserved binding feature is the central hydrophobic core that is contributed by residues L1276, L1277, I1280 in the case of ATRX and residues L31, Y34, F35 in the case of Rassf1c (Fig. 2H).
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This group is significantly enriched with cell adhesion of synaptic contact (p-value 5.272E-6), and the H3K4me2 binding feature is quite uniform as shown to form a tight cluster in Figure 5B.
Importantly, the AG-rich binding feature was not disrupted in the deletion mutants, suggesting that Htz1 intrinsically favours AG-rich DNA sequences.
And to investigate whether HM features and TF binding features are redundant, we next predicted the "openness" of chromatin using all features.
Based on analysis of molecular dynamics simulation data of peptide C3 complexes, novel binding features were designed by introducing intermolecular salt bridge-forming arginines at the N-terminus and at position −1 of N-terminal dipeptide extensions.
However, for the relatively variation-poor lineage α1-VI such unique peptide binding features are not predicted, and analysis of MHCI evolution in mammals has shown that quite different peptide binding pockets can occur in a set of relatively similar sequences [ 61, 62].
The previous analyses suggest that both histone modification features and transcription factor binding features are predictive for chromatin accessibility with high accuracy in DNase I hypersensitive sites.
Our results indicate that both histone modification features and transcription factor binding features are predictive for chromatin accessibility with high accuracy and these chromatin features are highly redundant.
These TF binding features are used as predictors in our model to classify cell cycle gene versus non-cell cycle ones.
Another example is that the SlbZIP proteins with predicated ABRE-binding feature are also clustered together with rice TRAB1 and Arabidopsis ABF1/3/4, ABI5 and DPBF2/4 [ 35, 36].
For the prediction power of particular TF binding feature, there is a difference with that of histone modifications; that is, most transcription factors exhibit important effects to chromatin accessibility).
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CEO of Professional Science Editing for Scientists @ prosciediting.com