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Comment
. 2022 Jun 29;13(1):3725.
doi: 10.1038/s41467-022-30351-2.

Reply to: Pitfalls in using phenanthroline to study the causal relationship between promoter nucleosome acetylation and transcription

Benjamin J E Martin  1 , LeAnn J Howe  2
Affiliations
Comment

Reply to: Pitfalls in using phenanthroline to study the causal relationship between promoter nucleosome acetylation and transcription

Benjamin J E Martin et al. Nat Commun. .
No abstract available

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Transcription inhibition by 1,10-phenanthroline (1,10-pt) does not impact Epl1 occupancy at most promoters.
Scatter plots comparing the effect of 1,10-pt on fragment midpoint counts from Epl1 (a, d), H4K8ac (b, e), or H4K12ac (c, f) ChIP-seq, over promoters (a and d) or associated +1 nucleosomes (b, c, e, and f) of all (5542) genes (a, b, c) or of 562 genes with NDR Epl1 peaks identified in MNase ChIP-seq in control cells (d, e, f). Promoters with >1.5 fold-change in Epl1 using an adjusted p-value < 0.1 (DESeq2’s binomial test) are shown in red (increased) or blue (decreased). In b, c, e, and f, the line is: y = x + 0.
Fig. 2
Fig. 2. Transcription inhibition with 1,10-phenanthroline (1,10-pt) does not mirror the effect of heat shock on RNAPII occupancy at most genes.
a Scatter plot comparing the log2 fold change (FC) in RNAPII occupancy following treatment with 1,10-pt with RNAPII serine 5 phosphorylation (s5p) following heat shock in gene 5′ regions (TSS to +400 bp) for all (5542) genes. b PCA plot showing the first two principal components calculated across TSS to +400 bp for all (5542) genes. c NET-seq 3′ read counts from TSS to +400 nt (sense), TSS to −400 nt (antisense), or in NDRs (antisense) depicted by violin plots for all (5542) genes.
See this image and copyright information in PMC

Comment on

References

    1. Martin BJE, et al. Transcription shapes genome-wide histone acetylation patterns. Nat. Commun. 2021;12:210. doi: 10.1038/s41467-020-20543-z. - DOI - PMC - PubMed
    1. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi: 10.1186/s13059-014-0550-8. - DOI - PMC - PubMed
    1. Poramba-Liyanage DW, et al. Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes. Genome Res. 2020 doi: 10.1101/gr.256255.119. - DOI - PMC - PubMed
    1. Vinayachandran V, et al. Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock. Genome Res. 2018 doi: 10.1101/gr.226761.117. - DOI - PMC - PubMed
    1. Albert, B. et al. A ribosome assembly stress response regulates transcription to maintain proteome homeostasis. Elife8, 10.7554/eLife.45002 (2019). - PMC - PubMed

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