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Series GSE287238 Query DataSets for GSE287238
Status Public on Jan 16, 2025
Title Native nucleosome-positioning elements for the investigation of nucleosome repositioning.
Organism synthetic construct
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Nucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer. Due to the artificial nature of 601, a library of native NPEs is needed to explore the role of DNA sequence in nucleosome repositioning. Here, we characterize the position distributions and nucleosome formation free energy for a set of yeast native nucleosomes (YNNs) from Saccharomyces cerevisiae. We show these native NPEs can be used in biochemical studies of nucleosome repositioning by transcription factors (TFs) and the chromatin remodeler Chd1. TFs could directly reposition a fraction of nucleosomes containing native NPEs, but not 601-containing nucleosomes. In contrast, partial unwrapping was similar for 601 and native NPE sequences. The rate of ATP-dependent remodeling by Chd1 was within the range of the fast and slow directions of the 601 nucleosomes. This set of native NPEs provides an alternative to the 601 NPE that can be used for probing the repositioning of nucleosomes that contain native DNA sequences.
 
Overall design MNase-seq to determine nucleosome positioning of YNN candidates or 601 with and without yeast transcription factors.
 
Contributor(s) Chen R, Stoeber S, Nodelman I, Chen H, Yang L, Bowman G, Bai L, Poirier M
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Submission date Jan 16, 2025
Last update date Jan 17, 2025
Contact name Shane Douglas Stoeber
E-mail(s) shanestoeber@gmail.com
Phone 9046161285
Organization name Penn State
Department BMMB
Lab Bai
Street address 406 South Frear Building
City State College
State/province Pennsylvania
ZIP/Postal code 16802
Country USA
 
Platforms (1)
GPL32628 NextSeq 2000 (synthetic construct)
Samples (25)
GSM8741950 601
GSM8741951 YNN1
GSM8741952 YNN2
Relations
BioProject PRJNA1211672

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Supplementary file Size Download File type/resource
GSE287238_RAW.tar 290.0 Kb (http)(custom) TAR (of BED)
GSE287238_fasta_files.tar.gz 1.1 Kb (ftp)(http) TAR
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Raw data are available in SRA

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