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Series GSE253391 Query DataSets for GSE253391
Status Public on May 07, 2024
Title Genomic context-dependent histone H3K36 methylation by Drosophila methyltransferases
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary How different histone methyltransferases (HMT) cooperate to progressively catalyze different methylation states of the same residue as well the functional consequences of the different methylation states are not well known. Here, we address in the context of Drosophila H3K36 methylation by using single and combinatorial RNAi of HMTs along with genome-wide MNase-ChIPseq analyses. Our study reveals that K36me1/2/3 each mark distinct chromatin compartments. Each HMT predominantly contributes to only one modification state, however our approach also identifies context-dependent cooperative and compensative patterns. Further, correlating changes in K36me1/2/3 to reader binding reveals that K36me2/3 can redundantly contribute to faithful reader binding ensuring robustness.
 
Overall design MNase Chromatin Immunoprecipitation DNA Sequencing (ChIP-seq) for K36me1/2/3, K27me3, K9me2, HMTs(ePol, Mes4) and readers (JASPer/PW, Msl3) in RNAi treated (10/7 days; RNAi targets - GST/GFP=Control, Set2, NSD,Ash1, Comb=Set2+NSD) S2 cells
 
Contributor(s) Jayakrishnan M, Krause S, Shetty R
Citation(s) 38813825
Submission date Jan 16, 2024
Last update date Aug 07, 2024
Contact name Muhunden Nallappa Jayakrishnan
E-mail(s) j_muhunden@hotmail.com, M.Jayakrishnan@bmc.med.lmu.de
Organization name Biomedical Center, Ludwig Maximilians University Munich
Department Molecular Biology
Lab Becker lab
Street address 57 Nusselstrasse, 57
City Munich
State/province Munich (city)
ZIP/Postal code 81245
Country Germany
 
Platforms (2)
GPL19951 Illumina HiSeq 1500 (Drosophila melanogaster)
GPL33093 NextSeq 1000 (Drosophila melanogaster)
Samples (107)
GSM8019696 CUT&RUN, H3K36me3, WT S2 cells, Replicate 1
GSM8019697 CUT&RUN, IgG, WT S2 cells, Replicate 1
GSM8019698 CUT&RUN, H3K36me3, WT S2 cells, Replicate 2
Relations
BioProject PRJNA1065448

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
GSE253391_Ash1_Input_batch7.dvirNorm.dir.bw 104.7 Mb (ftp)(http) BW
GSE253391_Comb_Input_batch5.dvirNorm.dir.bw 171.7 Mb (ftp)(http) BW
GSE253391_Ctl_K36me1_peaks.bed.gz 37.0 Kb (ftp)(http) BED
GSE253391_Ctl_K36me2_peaks.bed.gz 104.3 Kb (ftp)(http) BED
GSE253391_Ctl_K36me3_peaks.bed.gz 85.6 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me1_Ash1_KD.bed.gz 129.0 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me1_DKD.bed.gz 60.8 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me1_NSD_KD.bed.gz 4.7 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me1_Set2_KD.bed.gz 35.3 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me2_DKD.bed.gz 187.4 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me2_NSD_KD.bed.gz 117.0 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me2_Set2_KD.bed.gz 120.5 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me3_DKD.bed.gz 225.3 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me3_NSD_KD.bed.gz 59.6 Kb (ftp)(http) BED
GSE253391_DiffRegions_3kb_tol100_K36Me3_Set2_KD.bed.gz 107.4 Kb (ftp)(http) BED
GSE253391_GST_Input_batch7.dvirNorm.dir.bw 169.0 Mb (ftp)(http) BW
GSE253391_GeneBodyFeatures.txt.gz 1.7 Mb (ftp)(http) TXT
GSE253391_GeneBodyFeatures_Jayakrishnan2024.txt.gz 4.4 Mb (ftp)(http) TXT
GSE253391_K27me_Regions.bed.gz 40.7 Kb (ftp)(http) BED
GSE253391_K9me_Regions.bed.gz 13.2 Kb (ftp)(http) BED
GSE253391_NSD_Input_batch7.dvirNorm.dir.bw 159.3 Mb (ftp)(http) BW
GSE253391_RAW.tar 19.8 Gb (http)(custom) TAR (of BW)
GSE253391_README.txt 2.6 Kb (ftp)(http) TXT
GSE253391_README_2024.txt 3.7 Kb (ftp)(http) TXT
GSE253391_Set2_Input_batch7.dvirNorm.dir.bw 165.1 Mb (ftp)(http) BW
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