Abstract
The binding of transcription factors (TFs) triggers activation of specific chromatin regions through the recruitment and activation of RNA polymerase. Unique nucleosome positioning (NP) occurs during gene expression and has been suggested to be involved in various other chromatin functions. However, the diversity of NP that can occur for each function has not been clarified. Here we used MNase-Seq data to evaluate NP around 258 cis-regulatory elements in the mouse genome. Principal component analysis of the 258 elements revealed that NP consisted of five major patterns. Furthermore, the five NP patterns had predictive power for the level of gene expression. We also demonstrated that selective NP patterns appeared around TF binding sites. These results suggest that the NP patterns are correlated to specific functions on chromatin.
Highlights
The binding of transcription factors (TFs) triggers activation of specific chromatin regions through the recruitment and activation of RNA polymerase
We found that TF function could be predicted by the profiles of the average nucleosome densities (PANDs) assigned to the five nucleosome positioning (NP) patterns
We identified five major NP patterns on the mouse genome that were correlated to gene expression or specific types of TF binding sites
Summary
The binding of transcription factors (TFs) triggers activation of specific chromatin regions through the recruitment and activation of RNA polymerase. Kundaje et al profiled several NP patterns at TFBSs and found that asymmetric NP is the major feature In TSSs and in TFBSs and that the asymmetric pattern was true for histone marks but not for CTCF and DNase-I hypersensitive sites[18] These data suggest that the diversity of NP patterns could depend on biological functions of TFs. To explore various types of NP pattern caused by TF binding, we first collected comprehensive profiles of the average nucleosome densities (PANDs) in 258 cis-regulatory elements (computationally predicted potential TF binding sites) using fixed MNase-Seq data from mouse C2C12 myoblast cells.
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