Genome information processing by the INO80 chromatin remodeler positions nucleosomes
| Autor: | Kevin Schall, Vanessa Niebauer, Manuela Moldt, Nils Krietenstein, Elisa Oberbeckmann, Sebastian Eustermann, Karl-Peter Hopfner, Tobias Straub, Yingfei Wang, Philipp Korber, Remo Rohs |
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| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Saccharomyces cerevisiae Proteins Science General Physics and Astronomy Chromatin remodelling Saccharomyces cerevisiae Computational biology Biology Genome General Biochemistry Genetics and Molecular Biology Article DNA sequencing Histones 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Allosteric Regulation Animals Drosophila Proteins Humans Nucleosome DNA Fungal Promoter Regions Genetic 030304 developmental biology 0303 health sciences Multidisciplinary Fungal genetics General Chemistry Chromatin Assembly and Disassembly Linker DNA Recombinant Proteins Nucleosomes Chromatin 030104 developmental biology Drosophila melanogaster Histone Gene Expression Regulation chemistry Larva Enzyme mechanisms biology.protein Nucleic Acid Conformation Genome Fungal Sequence motif 030217 neurology & neurosurgery DNA |
| Zdroj: | Nature Communications, Vol 12, Iss 1, Pp 1-19 (2021) bioRxiv Nature Communications |
| Popis: | The fundamental molecular determinants by which ATP-dependent chromatin remodelers organize nucleosomes across eukaryotic genomes remain largely elusive. Here, chromatin reconstitutions on physiological, whole-genome templates reveal how remodelers read and translate genomic information into nucleosome positions. Using the yeast genome and the multi-subunit INO80 remodeler as a paradigm, we identify DNA shape/mechanics encoded signature motifs as sufficient for nucleosome positioning and distinct from known DNA sequence preferences of histones. INO80 processes such information through an allosteric interplay between its core- and Arp8-modules that probes mechanical properties of nucleosomal and linker DNA. At promoters, INO80 integrates this readout of DNA shape/mechanics with a readout of co-evolved sequence motifs via interaction with general regulatory factors bound to these motifs. Our findings establish a molecular mechanism for robust and yet adjustable +1 nucleosome positioning and, more generally, remodelers as information processing hubs that enable active organization and allosteric regulation of the first level of chromatin. DNA sequence preferences or statistical positioning of histones has not explained genomic patterns of nucleosome organisation in vivo. Here, the authors establish DNA shape/mechanics as key elements that have evolved together with binding sites of DNA sequence-specific barriers so that such information directs nucleosome positioning by chromatin remodelers. |
| Databáze: | OpenAIRE |
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