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Series GSE140614 Query DataSets for GSE140614
Status Public on Feb 10, 2020
Title Ruler elements in chromatin remodelers set nucleosome array spacing and phasing
Organisms Escherichia coli; Schizosaccharomyces pombe; Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Arrays of regularly spaced nucleosomes dominate chromatin and are often phased, i.e., aligned at reference sites like active promoters. How distances between nucleosomes and distances between phasing sites and nucleosomes are determined remained unclear, specifically, the role of ATP dependent chromatin remodelers in it. Here, we used a genome-wide reconstitution system to probe how yeast remodelers generate phased nucleosome arrays. We find that remodelers bear a structural element named the ‘ruler’ that sets nucleosome spacing, in the order Chd1 < ISW1a < ISW2 < INO80. Structure-based mutagenesis confirmed the functional significance of the ruler element in INO80. Differences in the ruler elements of different remodelers explain the observed nucleosome array features. More generally, we propose that remodelers use their rulers to regulate the direction of nucleosome sliding in response to nucleosome density and environment, leading to nucleosome positioning relative to other nucleosomes, DNA bound factors or DNA sequence elements.
Overall design We used our genome-wide in vitro reconstitution system (Krietenstein et al. 2016, Cell) to investigate the effect of varying nucleosome densities, different barriers (Reb1 and DNA double strand breaks) and underlying DNA sequences from different genomes (S. cerevisiae, S. pombe and E. coli) on all S. cerevisiae remodelers with spacing activity (INO80, ISW2, ISW1a and Chd1). Additionally, we used structural-guided INO80 mutans to find insights into INO80s' spacing mechanism.
Contributor(s) Oberbeckmann E, Niebauer V, Watanabe S, Farnung L, Moldt M, Schmid A, Cramer P, Peterson CL, Eustermann S, Hopfner K, Korber P
Citation(s) 34050140, 34050142
Submission date Nov 18, 2019
Last update date Jun 15, 2021
Contact name Elisa Oberbeckmann
Phone +49 551 2012809
Organization name Max-Planck Institute for Multidisciplinary Sciences
Department Molecular Biology
Lab Cramer
Street address Am Faßberg 11
City Göttingen
ZIP/Postal code 37077
Country Germany
Platforms (3)
GPL18085 Illumina HiSeq 1500 (Saccharomyces cerevisiae)
GPL20045 Illumina HiSeq 1500 (Escherichia coli)
GPL22681 Illumina HiSeq 1500 (Schizosaccharomyces pombe)
Samples (450)
GSM4175391 Rep1_ec_none_INO80_40
GSM4175392 Rep1_ec_none_none_40
GSM4175393 Rep1_ec_Reb1_INO80_40
BioProject PRJNA590247
SRA SRP230452

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Supplementary file Size Download File type/resource 250.8 Kb (ftp)(http) TAB
GSE140614_BamHI_cuts_in_EF2.txt.gz 6.4 Kb (ftp)(http) TXT
GSE140614_BamHI_cuts_in_Rel606.txt.gz 2.4 Kb (ftp)(http) TXT
GSE140614_BamHI_cuts_in_Saccer3.txt.gz 6.9 Kb (ftp)(http) TXT
GSE140614_RAW.tar 5.8 Gb (http)(custom) TAR (of BW)
GSE140614_SLIM-ChIP-Reb1-hits_Gutin2018_.bed.gz 14.5 Kb (ftp)(http) BED
GSE140614_reb1_hits_SacCer3.csv.gz 8.4 Kb (ftp)(http) CSV
GSE140614_reb1_hits_pombe.rds.gz 6.7 Kb (ftp)(http) RDS
GSE140614_reb1_rel606.csv.gz 7.1 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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