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Genome-wide analysis of phased nucleosomal arrays reveals the functional characteristic of the nucleosome remodeler ACF

Dhawal S. Jain, Sandro Baldi, Angelika Zabel, Tobias Straub, Peter B. Becker
doi: https://doi.org/10.1101/093666
Dhawal S. Jain
1Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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Sandro Baldi
1Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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Angelika Zabel
1Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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Tobias Straub
2Bioinformatics Units, Biomedical Center and Center for Integrated Protein Science Munich Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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  • For correspondence: pbecker@med.uni-muenchen.de tstraub@med.uni-muenchen.de
Peter B. Becker
1Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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  • For correspondence: pbecker@med.uni-muenchen.de tstraub@med.uni-muenchen.de
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Abstract

The nature of chromatin as regular succession of nucleosomes has gained iconic status. The average nucleosome repeat length (NRL) determined by classical means serves as index for bulk chromatin of a given specimen. However, this value is dominated by regular heterochromatin since nucleosomal arrays are often not regular at individual single copy sequences.

To obtain a measure for nucleosome regularity in euchromatin we subjected nucleosome profiles of D. melanogaster embryos to autocorrelation and spectral density estimation. These revealed variation in nucleosome regularity and NRL at different types of euchromatin and yielded a comprehensive catalog of regular phased nucleosome arrays (PNA). The absence of the nucleosome sliding factor ACF1 correlated with global loss of regularity and increased NRL in euchromatin and specifically compromised phasing at a novel class of PNA. Our approach is generally applicable to characterize the functional diversification of nucleosome remodelers in euchromatin organization.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 13, 2016.
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Genome-wide analysis of phased nucleosomal arrays reveals the functional characteristic of the nucleosome remodeler ACF
Dhawal S. Jain, Sandro Baldi, Angelika Zabel, Tobias Straub, Peter B. Becker
bioRxiv 093666; doi: https://doi.org/10.1101/093666
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Genome-wide analysis of phased nucleosomal arrays reveals the functional characteristic of the nucleosome remodeler ACF
Dhawal S. Jain, Sandro Baldi, Angelika Zabel, Tobias Straub, Peter B. Becker
bioRxiv 093666; doi: https://doi.org/10.1101/093666

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