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  DNA sequence encodes the position of DNA supercoils

Kim, S. H., Ganji, M., Kim, E., van der Torre, J., Abbondanzieri, E., & Dekker, C. (2018). DNA sequence encodes the position of DNA supercoils. eLife, 7: e36557. doi:10.7554/eLife.36557.

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 Creators:
Kim, Sung Hyun1, Author
Ganji, Mahipal2, Author              
Kim, Eugene1, Author
van der Torre, Jaco1, Author
Abbondanzieri, Elio1, Author
Dekker, Cees1, Author
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1external, ou_persistent22              
2Jungmann, Ralf / Molecular Imaging and Bionanotechnology, Max Planck Institute of Biochemistry, Max Planck Society, ou_2149679              

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Free keywords: ESCHERICHIA-COLI; GENE-REGULATION; CURVED DNA; IN-VITRO; TRANSCRIPTION; ORGANIZATION; CURVATURE; TOPOLOGY; DYNAMICS; RNALife Sciences & Biomedicine - Other Topics;
 Abstract: The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes (extended intertwined DNA structures formed upon supercoiling) on individual DNA molecules. Remarkably, our experiments show that the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences. We develop a physical model that predicts that sequence-dependent intrinsic curvature is the key determinant of pinning strength and demonstrate this simple model provides very good agreement with the data. Analysis of several prokaryotic genomes indicates that plectonemes localize directly upstream of promoters, which we experimentally confirm for selected promotor sequences. Our findings reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA.

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Language(s): eng - English
 Dates: 2018
 Publication Status: Published online
 Pages: 23
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: 000453820000001
DOI: 10.7554/eLife.36557
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Title: eLife
Source Genre: Journal
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Publ. Info: Cambridge : eLife Sciences Publications
Pages: - Volume / Issue: 7 Sequence Number: e36557 Start / End Page: - Identifier: ISSN: 2050-084X
CoNE: https://pure.mpg.de/cone/journals/resource/2050-084X