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| Status |
Public on Mar 01, 2019 |
| Title |
Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X |
| Organism |
Mus musculus |
| Experiment type |
Other
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
During X-inactivation, Xist RNA spreads along an entire chromosome to establish silencing. However, the mechanism and functional RNA elements involved in spreading remain undefined. By performing a comprehensive endogenous Xist deletion screen, we identify Repeat B as crucial for spreading Xist and maintaining Polycomb repressive complexes 1 and 2 (PRC1/PRC2) along the inactive X (Xi). Unexpectedly, spreading of these three factors is inextricably linked. Deleting Repeat B or its direct binding partner, HNRNPK, compromises recruitment of PRC1 and PRC2. In turn, ablating PRC1 or PRC2 impairs Xist spreading. Therefore, Xist and Polycomb complexes require each other to propagate along the Xi, suggesting a positive feedback mechanism between RNA initiator and protein effectors. Perturbing Xist/Polycomb spreading causes failure of de novo Xi silencing, with partial compensatory downregulation of the active X, and also disrupts topological Xi reconfiguration. Thus, Repeat B is a multifunctional element that integrates interdependent Xist/ Polycomb spreading, silencing, and changes in chromosome architecture.
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| Overall design |
Xist CHART-seq, H3K27me3 ChIP-seq, H2AK119ub ChIP-seq in WT, Xist RepB, EED KO, RING1A/B KO MEF cells.
RNA-seq in WT MEF, Xist RepB mutant MEF, WT ES and two RepB mutant ES cells.
in situ HiC in WT MEF, Xist RepB mutant MEF, WT ES, and RepB mutant ES cells
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| Contributor(s) |
Colognori D, Sunwoo H, Kriz AJ, Wang C, Lee JT |
| Citation(s) |
30827740 |
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| Submission date |
Nov 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hongjae Sunwoo |
| E-mail(s) |
sunwoo@molbio.mgh.harvard.edu
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| Organization name |
Massachusetts General Hospital, Harvard Medical School, HHMI
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| Department |
Molecular Biology
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| Lab |
Jeannie Lee lab
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| Street address |
185 Cambridge St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (50)
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| GSM2862876 |
Repeat B MEF_CHART, input DNA, rep1 |
| GSM2862877 |
Repeat B MEF_Xist CHART, rep1 |
| GSM2862878 |
Repeat B MEF_Tsix CHART, rep1 |
| GSM2862879 |
WT MEF_CHART, input DNA, rep2 |
| GSM2862880 |
WT MEF_Xist CHART, rep2 |
| GSM2862881 |
WT MEF_Tsix CHART, rep2 |
| GSM2862882 |
Repeat B MEF_CHART, input DNA, rep2 |
| GSM2862883 |
Repeat B MEF_Xist CHART, rep2 |
| GSM2862884 |
Repeat B MEF_Tsix CHART, rep2 |
| GSM2862885 |
WT MEF_H3K27me3, input DNA, rep1 |
| GSM2862886 |
WT MEF_H3K27me3, ChIP DNA, rep1 |
| GSM2862887 |
Repeat B MEF_H3K27me3, input DNA, rep1 |
| GSM2862888 |
Repeat B MEF_H3K27me3, ChIP DNA, rep1 |
| GSM2862889 |
WT MEF_H3K27me3, input DNA, rep2 |
| GSM2862890 |
WT MEF_H3K27me3, ChIP DNA, rep2 |
| GSM2862891 |
Repeat B MEF_H3K27me3, input DNA, rep2 |
| GSM2862892 |
Repeat B MEF_H3K27me3, ChIP DNA, rep2 |
| GSM2862893 |
WT MEF_H2AK119ub, input DNA, rep1 |
| GSM2862894 |
WT MEF_H2AK119ub, ChIP DNA, rep1 |
| GSM2862895 |
Repeat B MEF_H2AK119ub, input DNA, rep1 |
| GSM2862896 |
Repeat B MEF_H2AK119ub, ChIP DNA, rep1 |
| GSM2862897 |
WT MEF_RNAseq, rep1 |
| GSM2862898 |
Repeat B MEF_RNAseq, rep1 |
| GSM2862899 |
WT ES cell_RNAseq, rep1 |
| GSM2862900 |
Repeat B +/- ES cell_RNAseq, rep1 |
| GSM2862901 |
Repeat B -/- ES cell_RNAseq, rep1 |
| GSM2862902 |
WT ES cell_RNAseq, rep2 |
| GSM2862903 |
Repeat B +/- ES cell_RNAseq, rep2 |
| GSM2862904 |
Repeat B -/- ES cell_RNAseq, rep2 |
| GSM3517940 |
WT, MEF_in situ HiC |
| GSM3517944 |
Repeat B MEF_in situ HiC |
| GSM3517946 |
WT ES cell_in situ HiC |
| GSM3517947 |
Repeat B -/- ES cell_in situ HiC |
| GSM3517948 |
EED KO MEF_CHART, input DNA |
| GSM3517949 |
EED KO MEF_Xist CHART, rep1 |
| GSM3517950 |
EED KO MEF_Tsix CHART, rep1 |
| GSM3517951 |
EED KO MEF_Xist CHART, rep2 |
| GSM3517952 |
RING1A/B KO MEF_CHART, input DNA |
| GSM3517953 |
RING1A/B KO MEF_Xist CHART, rep1 |
| GSM3517954 |
RING1A/B KO MEF_Tsix CHART, rep1 |
| GSM3517955 |
RING1A/B KO MEF_Xist CHART, rep2 |
| GSM3517956 |
RING1A/B KO MEF_H3K27me3, input DNA, rep1 |
| GSM3517957 |
RING1A/B KO MEF_H3K27me3, ChIP DNA, rep1 |
| GSM3517958 |
RING1A/B KO MEF_H3K27me3, ChIP DNA, rep2 |
| GSM3517959 |
EED KO MEF_H2AK119ub, input DNA, rep1 |
| GSM3517960 |
EED KO MEF_H2AK119ub, ChIP DNA, rep1 |
| GSM3517961 |
EED KO MEF_H2AK119ub, ChIP DNA, rep2 |
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| Relations |
| BioProject |
PRJNA419343 |
| SRA |
SRP125395 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE107217_CHART_log2ratio_RepBoverWT_Rep1.bw |
3.3 Mb |
(ftp)(http) |
BW |
| GSE107217_CHART_log2ratio_RepBoverWT_Rep2.bw |
3.3 Mb |
(ftp)(http) |
BW |
| GSE107217_RAW.tar |
8.4 Gb |
(http)(custom) |
TAR (of BW, HIC) |
| GSE107217_RNA_ES_count_rep1.txt.gz |
635.1 Kb |
(ftp)(http) |
TXT |
| GSE107217_RNA_ES_count_rep2.txt.gz |
612.3 Kb |
(ftp)(http) |
TXT |
| GSE107217_RNA_MEF_count_rep1.txt.gz |
533.4 Kb |
(ftp)(http) |
TXT |
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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