Topoisomerase activity is linked to altered nucleosome positioning and transcriptional regulation in the fission yeast fbp1 gene.

Ryuta Asada,Satoshi Senmatsu,Ben Montpetit,Kouji Hirota

doi:10.1371/journal.pone.0242348

Ryuta Asada, Satoshi Senmatsu + Show 2 more

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https://doi.org/10.1371/journal.pone.0242348

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Abstract

Chromatin structure, including nucleosome positioning, has a fundamental role in transcriptional regulation through influencing protein-DNA interactions. DNA topology is known to influence chromatin structure, and in doing so, can also alter transcription. However, detailed mechanism(s) linking transcriptional regulation events to chromatin structure that is regulated by changes in DNA topology remain to be well defined. Here we demonstrate that nucleosome positioning and transcriptional output from the fission yeast fbp1 and prp3 genes are altered by excess topoisomerase activity. Given that lncRNAs (long noncoding RNAs) are transcribed from the fbp1 upstream region and are important for fbp1 gene expression, we hypothesized that local changes in DNA topological state caused by topoisomerase activity could alter lncRNA and fbp1 transcription. In support of this, we found that topoisomerase overexpression caused destabilization of positioned nucleosomes within the fbp1 promoter region, which was accompanied by aberrant fbp1 transcription. Similarly, the direct recruitment of topoisomerase, but not a catalytically inactive form, to the promoter region of fbp1 caused local changes in nucleosome positioning that was also accompanied by altered fbp1 transcription. These data indicate that changes in DNA topological state induced by topoisomerase activity could lead to altered fbp1 transcription through modulating nucleosome positioning.

Highlights

DNA topology, defined by the degree of interwinding of two complementary strands, is an important factor to consider in various DNA-related biological processes, such as DNA repair, replication, and transcription [1]
Top1 and Top2 resolve both positive and negative supercoils and have overlapping roles in fission yeast [36]. To overexpress these proteins in a controlled manner, Top1 and Top2 were expressed from plasmids using the nmt1 promoter, which can be conditionally induced by the depletion of thiamine from the medium [34]
Using qPCR, we found that cells carrying these plasmids have higher expression levels of both top1 (~4 fold) or top2 (~6 fold) mRNA as compared to control cells in the presence of thiamine, which increased in levels to ~100 fold upon thiamine removal (S2 Fig)

Summary

Introduction

DNA topology, defined by the degree of interwinding of two complementary strands, is an important factor to consider in various DNA-related biological processes, such as DNA repair, replication, and transcription [1]. Positive or negative DNA supercoiling refers to the over- or under- winding of DNA strands. These alterations in DNA topological state are induced by processes that cause DNA strand separation, including transcription [2]. Positively supercoiled DNA is generated ahead of, and negatively supercoiled DNA behind, RNA polymerase II [3]. To relieve topological perturbations caused by DNA-.

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