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. 2021 Feb 11;217(4):iyab021. doi: 10.1093/genetics/iyab021

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© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Nucleosomes in transcribed coding sequences are more susceptible to MNase digestion.

(A) Schematic showing potential generation of MNase-protected DNA fragments (MPDFs) from nucleosomes. MNase digestion of DNA wrapped around histone octamer would likely generate MPDFs ∼130–160 bp, whereas a remodeled nucleosomes might be more accessible, leading to shorter MPDFs (<130 bp).

(B) MPDF profiles for fragment lengths ranging from 130-160 bp, <120–110 bp, <110–100 bp, <100–90 bp, and <90 bp are plotted for 5746 genes. MPDFs are plotted ±1000 bp around the transcription start site (TSS.)

(C) Metagene profile showing the average occupancies of MPDFs for the top (Pol II-T10) and bottom 10% (Pol II-B10) Pol II-occupied genes. MPDFs sizes <130 bp and >130 bp are plotted ±1000 bp around the TSS.

(D) Metagene profiles showing the average occupancies of MPDFs for the Gcn4-activated genes (n = 70 (Rawal et al.2018)) induced in the presence of SM (sulfometuron methyl; +SM) or in the absence of SM (–SM). MPDFs sizes <130 bp and >130 bp are plotted ±1 kb around the TSS. The values are plotted on the left-hand Y-axis, and <130 bp/> 130bp ratios for +SM (dashed-orange traces) and –SM (orange traces) are plotted on the right-hand Y-axis.

(E) Metagene profiles showing MPDFs sizes (<130 bp and >130 bp) for the TBP anchor-away strain treated without Rapa (–Rapa) or with (+Rapa) at the Pol II-T10 genes. The values are plotted on the left-hand Y-axis, and <130 bp/> 130bp ratio for the –Rapa (orange trace) and +Rapa (orange dashed trace) are plotted on the right-hand Y-axis. The TBP anchor-away data was taken from a previous study (Kubik et al.2018). MPDFs sizes <130 bp and >130 bp are plotted ±1000 bp around the TSS.