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| 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.
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| 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
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| 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
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| Organization name |
Biomedical Center, Ludwig Maximilians University Munich
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| Department |
Molecular Biology
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| Lab |
Becker lab
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| Street address |
57 Nusselstrasse, 57
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| City |
Munich |
| State/province |
Munich (city) |
| ZIP/Postal code |
81245 |
| Country |
Germany |
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| Platforms (2) |
| GPL19951 |
Illumina HiSeq 1500 (Drosophila melanogaster) |
| GPL33093 |
NextSeq 1000 (Drosophila melanogaster) |
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| 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 |
| GSM8019699 |
CUT&RUN, IgG, WT S2 cells, Replicate 2 |
| GSM8019700 |
MNase-ChIP, Input, Control 7-day RNAi, Batch 0 |
| GSM8019701 |
MNase-ChIP, Input, Control_2 7-day RNAi, Batch 0 |
| GSM8019702 |
MNase-ChIP, Input, Control RNAi, Batch 1 |
| GSM8019703 |
MNase-ChIP, Input, Control RNAi, Batch 2 |
| GSM8019704 |
MNase-ChIP, Input, Control RNAi, Batch 3 |
| GSM8019705 |
MNase-ChIP, Input, Control RNAi, Batch 4 |
| GSM8019706 |
MNase-ChIP, Input, Control RNAi, Batch 5 |
| GSM8019707 |
MNase-ChIP, Input, Control_2 RNAi, Batch 6 |
| GSM8019708 |
MNase-ChIP, Input, Control_2 RNAi, Batch 7 |
| GSM8019709 |
MNase-ChIP, Input, Set2 (KK) 7-day RNAi, Batch 0 |
| GSM8019710 |
MNase-ChIP, Input, Set2 (1) 7-day RNAi, Batch 0 |
| GSM8019711 |
MNase-ChIP, Input, Set2 RNAi, Batch 1 |
| GSM8019712 |
MNase-ChIP, Input, Set2 RNAi, Batch 2 |
| GSM8019713 |
MNase-ChIP, Input, Set2 RNAi, Batch 5 |
| GSM8019714 |
MNase-ChIP, Input, Set2 RNAi, Batch 7 |
| GSM8019715 |
MNase-ChIP, Input, NSD RNAi, Batch 1 |
| GSM8019716 |
MNase-ChIP, Input, NSD RNAi, Batch 2 |
| GSM8019717 |
MNase-ChIP, Input, NSD RNAi, Batch 5 |
| GSM8019718 |
MNase-ChIP, Input, NSD RNAi, Batch 7 |
| GSM8019719 |
MNase-ChIP, Input, DKD (Set2+NSD) RNAi, Batch 1 |
| GSM8019720 |
MNase-ChIP, Input, DKD (Set2+NSD) RNAi, Batch 2 |
| GSM8019721 |
MNase-ChIP, Input, DKD (Set2+NSD) RNAi, Batch 5 |
| GSM8019722 |
MNase-ChIP, Input, Ash1 RNAi, Batch 6 |
| GSM8019723 |
MNase-ChIP, Input, Ash1 RNAi, Batch 7 |
| GSM8019724 |
MNase-ChIP, IgG ChIP, Control RNAi, Batch 5 |
| GSM8019725 |
MNase-ChIP, S2Ph-PolII (ePol) ChIP, Control RNAi S2 cells, Batch 3, Replicate 1 |
| GSM8019726 |
MNase-ChIP, S2Ph-PolII (ePol) ChIP, Control RNAi S2 cells, Batch 4, Replicate 2 |
| GSM8019727 |
MNase-ChIP, S2Ph-PolII (ePol) ChIP, Control RNAi S2 cells, Batch 7, Replicate 3 |
| GSM8019728 |
MNase-ChIP, dMes4(NSD) ChIP, Control RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019729 |
MNase-ChIP, dMes4(NSD) ChIP, Control RNAi S2 cells, Batch 4, Replicate 2 |
| GSM8019730 |
MNase-ChIP, dMes4(NSD) ChIP, Control RNAi S2 cells, Batch 7, Replicate 3 |
| GSM8019731 |
MNase-ChIP, K36me3 ChIP, Control 7-day RNAi, Batch 0, Replicate 1 |
| GSM8019732 |
MNase-ChIP, K36me3 ChIP, Control_2 7-day RNAi, Batch 0, Replicate 2 |
| GSM8019733 |
MNase-ChIP, K36me3 ChIP, Control RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019734 |
MNase-ChIP, K36me3 ChIP, Control RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019735 |
MNase-ChIP, K36me3 ChIP, Control RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019736 |
MNase-ChIP, K36me3 ChIP, Set2 (KK) 7-day RNAi, Batch 0, Replicate 1 |
| GSM8019737 |
MNase-ChIP, K36me3 ChIP, Set2 (1) 7-day RNAi, Batch 0, Replicate 2 |
| GSM8019738 |
MNase-ChIP, K36me3 ChIP, Set2 RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019739 |
MNase-ChIP, K36me3 ChIP, Set2 RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019740 |
MNase-ChIP, K36me3 ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019741 |
MNase-ChIP, K36me3 ChIP, NSD RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019742 |
MNase-ChIP, K36me3 ChIP, NSD RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019743 |
MNase-ChIP, K36me3 ChIP, NSD RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019744 |
MNase-ChIP, K36me3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019745 |
MNase-ChIP, K36me3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019746 |
MNase-ChIP, K36me3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019747 |
MNase-ChIP, K36me2 ChIP, Control 7-day RNAi, Batch 0, Replicate 1 |
| GSM8019748 |
MNase-ChIP, K36me2 ChIP, Control_2 7-day RNAi, Batch 0, Replicate 2 |
| GSM8019749 |
MNase-ChIP, K36me2 ChIP, Control RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019750 |
MNase-ChIP, K36me2 ChIP, Control RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019751 |
MNase-ChIP, K36me2 ChIP, Control RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019752 |
MNase-ChIP, K36me2 ChIP, Set2 (KK) 7-day RNAi, Batch 0, Replicate 1 |
| GSM8019753 |
MNase-ChIP, K36me2 ChIP, Set2 (1) 7-day RNAi, Batch 0, Replicate 2 |
| GSM8019754 |
MNase-ChIP, K36me2 ChIP, Set2 RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019755 |
MNase-ChIP, K36me2 ChIP, Set2 RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019756 |
MNase-ChIP, K36me2 ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019757 |
MNase-ChIP, K36me2 ChIP, NSD RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019758 |
MNase-ChIP, K36me2 ChIP, NSD RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019759 |
MNase-ChIP, K36me2 ChIP, NSD RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019760 |
MNase-ChIP, K36me2 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019761 |
MNase-ChIP, K36me2 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019762 |
MNase-ChIP, K36me2 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019763 |
MNase-ChIP, K36me1 ChIP, Control RNAi S2 cells, Batch 5, Replicate 1 |
| GSM8019764 |
MNase-ChIP, K36me1 ChIP, Control RNAi S2 cells, Batch 6, Replicate 1 |
| GSM8019765 |
MNase-ChIP, K36me1 ChIP, Control RNAi S2 cells, Batch 7, Replicate 2 |
| GSM8019766 |
MNase-ChIP, K36me1 ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 1 |
| GSM8019767 |
MNase-ChIP, K36me1 ChIP, Set2 RNAi S2 cells, Batch 7, Replicate 2 |
| GSM8019768 |
MNase-ChIP, K36me1 ChIP, NSD RNAi S2 cells, Batch 5, Replicate 1 |
| GSM8019769 |
MNase-ChIP, K36me1 ChIP, NSD RNAi S2 cells, Batch 7, Replicate 2 |
| GSM8019770 |
MNase-ChIP, K36me1 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 1 |
| GSM8019771 |
MNase-ChIP, K36me1 ChIP, Ash1 RNAi S2 cells, Batch 6, Replicate 1 |
| GSM8019772 |
MNase-ChIP, K36me1 ChIP, Ash1 RNAi S2 cells, Batch 7, Replicate 2 |
| GSM8019773 |
MNase-ChIP, Msl3 ChIP, Control RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019774 |
MNase-ChIP, Msl3 ChIP, Control RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019775 |
MNase-ChIP, Msl3 ChIP, Control RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019776 |
MNase-ChIP, Msl3 ChIP, Set2 RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019777 |
MNase-ChIP, Msl3 ChIP, Set2 RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019778 |
MNase-ChIP, Msl3 ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019779 |
MNase-ChIP, Msl3 ChIP, NSD RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019780 |
MNase-ChIP, Msl3 ChIP, NSD RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019781 |
MNase-ChIP, Msl3 ChIP, NSD RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019782 |
MNase-ChIP, Msl3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 1, Replicate 1 |
| GSM8019783 |
MNase-ChIP, Msl3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019784 |
MNase-ChIP, Msl3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019785 |
MNase-ChIP, JASPer ChIP, Control 7-day RNAi, Batch 0, Replicate 1 |
| GSM8019786 |
MNase-ChIP, JASPer ChIP, Control_2 7-day RNAi, Batch 0, Replicate 2 |
| GSM8019787 |
MNase-ChIP, JASPer ChIP, Control RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019788 |
MNase-ChIP, JASPer ChIP, Control RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019789 |
MNase-ChIP, JASPer ChIP, Set2 (KK) 7-day RNAi, Batch 0, Replicate 1 |
| GSM8019790 |
MNase-ChIP, JASPer ChIP, Set2 (1) 7-day RNAi, Batch 0, Replicate 2 |
| GSM8019791 |
MNase-ChIP, JASPer ChIP, Set2 RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019792 |
MNase-ChIP, JASPer ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019793 |
MNase-ChIP, JASPer ChIP, NSD RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019794 |
MNase-ChIP, JASPer ChIP, NSD RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8019795 |
MNase-ChIP, JASPer ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 2, Replicate 2 |
| GSM8019796 |
MNase-ChIP, JASPer ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 3 |
| GSM8172279 |
MNase-ChIP, K27me3 ChIP, GST RNAi S2 cells, Batch 7, Replicate 1 |
| GSM8172280 |
MNase-ChIP, K27me3 ChIP, Ash1 RNAi S2 cells, Batch 7, Replicate 1 |
| GSM8172281 |
MNase-ChIP, K27me3 ChIP, Set2 RNAi S2 cells, Batch 7, Replicate 1 |
| GSM8172282 |
MNase-ChIP, K27me3 ChIP, NSD RNAi S2 cells, Batch 7, Replicate 1 |
| GSM8172283 |
MNase-ChIP, K9me2 ChIP, GST RNAi S2 cells, Batch 6, Replicate 1 |
| GSM8172284 |
MNase-ChIP, K9me2 ChIP, NSD RNAi S2 cells, Batch 6, Replicate 1 |
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| Relations |
| BioProject |
PRJNA1065448 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
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