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Series GSE234564 Query DataSets for GSE234564
Status Public on Apr 21, 2024
Title Swd2/Cps35 determines H3K4 tri-methylation via interactions with Set1 and Rad6_Chromatin occupancy of Set1 in several strains
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Histone H3K4 tri-methylation (H3K4me3) catalyzed by Set1/COMPASS, is a prominent epigenetic mark found in promoter-proximal regions of actively transcribed genes. H3K4me3 relies on prior monoubiquitination at the histone H2B (H2Bub) by Rad6 and Bre1. Swd2/Cps35, a Set1/COMPASS component, has been proposed as a key player in facilitating H2Bub-dependent H3K4me3. However, a more comprehensive investigation regarding the relationship among Rad6, Swd2 and Set1 is required to further understand the mechanisms and functions of the H3K4 methylation. We investigated the genome-wide occupancy patterns of Rad6, Swd2 and Set1 under various genetic conditions, aiming to clarify the roles of Set1 and Rad6 for occupancy of Swd2. Swd2 peaks appear on both 5’region and 3’region of genes, which are overlapped with its tightly bound two complexes, Set1 and CPF (Cleavage and Polyadenylation Factor), respectively. In the absence of Rad6/H2Bub, Set1 predominantly localized to the 5ʹ region of genes, while Swd2 lost all the chromatin binding. However, in the absence of Set1, Swd2 occupancy near the 5’region was impared and rather increased in the 3’ region. This study highlights that catalytic activity of Rad6 is essential for all the ways of Swd2’s binding to the transcribed genes and Set1 redistributes the Swd2 to 5’region for accomplishments of H3K4me3 in the genome-wide level.
 
Overall design Sample number (1) ~ (16): We performed a-Set1 ChIPseq with WT(1~2), Δset1(3~4), Δrad6(5~6), Δbre1(7~8), Sen1overexpressed WT(9~10), Sen1overexpressed Δswd2(11~12), 551WT(13~14), and 551Δbre1(15~16) strains. Experiments were performed in duplicates, and a-Set1 ChIPseq with Δset1 strain(3~4) was performed to reveal the background signal of the experiment.
Please note that each processed data file was generated from both replicates and is linked to the corresponding rep1 sample records.
 
Contributor(s) Lee J, Oh J, Park S, Kim J, Lee E, Cho Y
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Submission date Jun 09, 2023
Last update date Apr 22, 2024
Contact name Junsoo Oh
E-mail(s) ohjunsu1007@naver.com
Organization name Kangwon National University
Street address Kangwondaehakgil-1
City Chuncheon
ZIP/Postal code 24341
Country South Korea
 
Platforms (1)
GPL17342 Illumina HiSeq 2500 (Saccharomyces cerevisiae)
Samples (16)
GSM7471017 1_a-Set1_WT_strain_rep1
GSM7471018 2_a-Set1_WT_strain_rep2
GSM7471019 3_a-Set1_Δset1_strain_rep1
Relations
BioProject PRJNA982058

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE234564_RAW.tar 47.4 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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