|
| Status |
Public on Aug 01, 2020 |
| Title |
Genome-wide maps of ZCWPW1 in HEK293T cells with or without PRDM9, plus DMC1 ChIP-seq in ZCWPW1 KO mouse |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
During meiosis, homologous chromosomes pair (synapse) and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, recombination initiates with double-strand breaks (DSBs) within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have yet been identified. We identified Zcwpw1, which possesses H3K4me3 and H3K36me3 recognition domains, as highly co-expressed with Prdm9. In this study we used ChIP-sequencing in human HEK293T cells (co)-transfected with HA tagged ZCWPW1 (and human or chimp PRDM9). This enabled us to determine that PRDM9 causes the recruitment of ZCWPW1 to its binding sites, and to determine the general binding properties of ZCWPW1 including a preference for CpG sites. We also performed SSDS ChIP-sequencing of mice testis that are homozygous KO for ZCWPW1, revealing that double strand breaks occour at completely normal positions in the ZCWPW1 KO, but with persistant DMC1 at many hotspots, particularly those more strongly bound by PRDM9.
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| |
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| Overall design |
ChIP-sequencing of HA-tagged ZCWPW1 in HEK293T cells (either alone or with co-transfection of either human or chimp PRDM9). Additionally SSDS DMC1 ChIP-sequencing in ZCWPW1 KO mice testis
***Please note that the series includes re-analysis of GSE99407 (Mapping PRDM9 binding and its effects in transfected HEK293T cells).
The 'GSE99407_re-processed_readme.xls' includes the source of the sequence data accession numbers (GSMnnnn/SRRnnnn) and the re-analysis data processing details/output.
The re-processed 'SingleBasePeaks.NA15* and ForceCalledPeaks_NA15* bed.gz' files are linked as Series supplementary files.
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| |
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| Contributor(s) |
Wells D, Bitoun E, Moralli D, Zhang G, Hinch AG, Donnelly P, Green C, Myers SR |
| Citation(s) |
32744506 |
| |
| Submission date |
Dec 05, 2019 |
| Last update date |
Sep 28, 2020 |
| Contact name |
Simon Myers |
| E-mail(s) |
myers@stats.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Wellcome Center for Human Genetics
|
| Lab |
Myers Group
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
| Samples (6)
|
| GSM4205419 |
HEK293T transfected with ZCWPW1-HA |
| GSM4205420 |
HEK293T transfected with ZCWPW1-HA [input] |
| GSM4205421 |
HEK293T transfected with ZCWPW1-HA and humanPRDM9-V5 |
| GSM4205422 |
HEK293T transfected with ZCWPW1-HA and humanPRDM9-V5 [input] |
| GSM4205423 |
HEK293T transfected with ZCWPW1-HA and chimpPRDM9-V5 |
| GSM4205424 |
ZCWPW1 Homozygous KO |
|
| Relations |
| Reanalysis of |
GSM2643616 |
| Reanalysis of |
GSM2643619 |
| Reanalysis of |
GSM2643617 |
| Reanalysis of |
GSM2643618 |
| Reanalysis of |
GSM2643620 |
| Reanalysis of |
GSM2643622 |
| Reanalysis of |
GSM2643625 |
| Reanalysis of |
GSM2643626 |
| Reanalysis of |
GSM2643615 |
| Reanalysis of |
GSM2643623 |
| Reanalysis of |
GSM2643624 |
| Reanalysis of |
GSM2643621 |
| BioProject |
PRJNA593768 |
| SRA |
SRP234875 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE141516_ForceCalledPeaks_ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_ChIPHA_ZCWPW1-HA_AT_100bpWindows.bed.gz |
287.3 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz |
472.1 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_ChIPHA_ZCWPW1-HA_AT_100bpWindows.bed.gz |
350.7 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_ChIPHA_ZCWPW1-HA_AT_NA15-ChIPHA_humanPRDM9-HA_AND_NA15-ChIPV5_humanPRDM9-V5_vs_NA15-Input_humanPRDM9-HA.bed.gz |
5.2 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz |
462.6 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz |
486.2 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_NA15-ChIH3K36me3_Untransfected_vs_NA15-Input_Untransfected_AT_100bpWindows.bed.gz |
415.9 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_NA15-ChIPH3K36me3_humanPRDM9-HA_vs_NA15-Input_humanPRDM9-HA_AT_100bpWindows.bed.gz |
461.0 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_NA15-ChIPH3K4me3_Untransfected_Rep1_vs_NA15-Input_Untransfected_AT_100bpWindows.bed.gz |
324.8 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_NA15-ChIPH3K4me3_humanPRDM9-HA_Rep1_AND_NA15-ChIPH3K4me3_humanPRDM9-HA_Rep2_vs_NA15-Input_humanPRDM9-HA_AT_100bpWindows.bed.gz |
486.4 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_NA15-ChIPHA_humanPRDM9-HA_AND_NA15-ChIPV5_humanPRDM9-V5_vs_NA15-Input_humanPRDM9-HA_AT_100bpWindows.bed.gz |
465.1 Mb |
(ftp)(http) |
BED |
| GSE141516_ForceCalledPeaks_NA15-ChIPV5_chimpPRDM9-V5_AND_NA15-ChIPHA_chimpPRDM9-HA_vs_NA15-Input_humanPRDM9-HA_AT_100bpWindows.bed.gz |
535.2 Mb |
(ftp)(http) |
BED |
| GSE141516_GSE99407_re-processed_readme.xls |
175.0 Kb |
(ftp)(http) |
XLS |
| GSE141516_RAW.tar |
2.7 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, BIGWIG) |
| GSE141516_SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_ChIPHA_ZCWPW1-HA.p0.000001.sep250.ALL.bed.gz |
51.3 Kb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz |
37.0 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz |
43.5 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_ChIPHA_ZCWPW1-HA.p0.000001.sep250.ALL.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz |
36.4 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz |
41.3 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA.p0.000001.sep250.ALL.bed.gz |
48.1 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz |
49.7 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIH3K36me3_Untransfected_vs_NA15-Input_Untransfected.p0.000001.sep250.ALL.bed.gz |
7.8 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPH3K36me3_humanPRDM9-HA_vs_NA15-ChIH3K36me3_Untransfected.p0.000001.sep250.ALL.bed.gz |
43.6 Kb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPH3K36me3_humanPRDM9-HA_vs_NA15-Input_humanPRDM9-HA.p0.000001.sep250.ALL.bed.gz |
394.8 Kb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPH3K4me3_Untransfected_Rep1_AND_NA15-ChIPH3K4me3_Untransfected_Rep2_vs_NA15-Input_Untransfected.p0.000001.sep250.ALL.bed.gz |
1.5 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPH3K4me3_Untransfected_Rep1_vs_NA15-Input_Untransfected.p0.000001.sep250.ALL.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPH3K4me3_humanPRDM9-HA_Rep1_AND_NA15-ChIPH3K4me3_humanPRDM9-HA_Rep2_vs_NA15-ChIPH3K4me3_Untransfected_Rep1_AND_NA15-ChIPH3K4me3_Untransfected_Rep2.p0.000001.sep250.ALL.bed.gz |
5.4 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPH3K4me3_humanPRDM9-HA_Rep1_AND_NA15-ChIPH3K4me3_humanPRDM9-HA_Rep2_vs_NA15-Input_humanPRDM9-HA.p0.000001.sep250.ALL.bed.gz |
7.0 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPHA_chimpPRDM9-HA_vs_NA15-Input_humanPRDM9-HA.p0.000001.sep250.ALL.bed.gz |
1.5 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPHA_humanPRDM9-HA_AND_NA15-ChIPV5_humanPRDM9-V5_vs_NA15-Input_humanPRDM9-HA.p0.000001.sep250.ALL.bed.gz |
6.9 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPHA_humanPRDM9-HA_AND_NA15-ChIPV5_humanPRDM9-V5_vs_NA15-Input_humanPRDM9-HA.p0.000001.sep250.ALL_MotifCenteredStranded.bed.gz |
689.0 Kb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPHA_humanPRDM9-HA_vs_NA15-Input_humanPRDM9-HA.p0.000001.sep250.ALL.bed.gz |
2.9 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPV5_chimpPRDM9-V5_AND_NA15-ChIPHA_chimpPRDM9-HA_vs_NA15-Input_humanPRDM9-HA.p0.000001.sep250.ALL.bed.gz |
3.5 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPV5_chimpPRDM9-V5_vs_NA15-Input_humanPRDM9-HA.p0.000001.sep250.ALL.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE141516_SingleBasePeaks.NA15-ChIPV5_humanPRDM9-V5_vs_NA15-Input_humanPRDM9-HA.p0.000001.sep250.ALL.bed.gz |
6.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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