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| Status |
Public on Oct 31, 2018 |
| Title |
Megadomains and superloops form dynamically during X-chromosome inactivation but are dispensable for silencing and escape |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
The mammalian inactive X-chromosome (Xi) is structurally distinct from all other chromosomes and serves as a model for higher order chromosome organization. The Xi lacks strong topologically associated domains and is instead organized into megadomains and superloops mediated in part by the noncoding loci, Dxz4 and Firre. Their functional significance is presently unclear, though one study suggests that they permit Xi genes to escape silencing. Here, we find that megadomains do not form before silencing spreads along the Xi. Deletional analysis shows that Dxz4, but not Firre, is required for megadomains. Surprisingly, however, deleting neither Dxz4 nor Firre impacts Xi silencing or gene escape. Nor does it affect Xi nuclear localization, stability, or H3K27 methylation. Furthermore, ectopic integration of Dxz4 and Xist is not sufficient to form megadomains on autosomes, thereby uncoupling megadomain formation from chromosomal silencing. We conclude that Dxz4 and megadomains are dispensable for Xi silencing and escape.
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| Overall design |
Hi-C, Hi-C^2, 4C, ATAC-seq, ChIP-seq, RNA-seq
Please note that, to make data access easier, the 'GEO_readme.xls' lists Sample names with expriments and their associated files.
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| Contributor(s) |
Froberg JE |
| Citation(s) |
30479398 |
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| Submission date |
Jul 05, 2018 |
| Last update date |
May 10, 2019 |
| Contact name |
John Edward Froberg |
| E-mail(s) |
jfroberg@fas.harvard.edu
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| Phone |
8479770174
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| Organization name |
Harvard University
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| Department |
Stem Cell & Regenerative Biology
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| Lab |
Macklis Lab
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| Street address |
7 Divinity Avenue
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platforms (3) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (65)
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| Relations |
| BioProject |
PRJNA479812 |
| SRA |
SRP152219 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE116649_Dxz4-HiC2_probes.bed.gz |
55.3 Kb |
(ftp)(http) |
BED |
| GSE116649_GEO_readme.xls |
55.0 Kb |
(ftp)(http) |
XLS |
| GSE116649_Mecp2-HiC2_probes.bed.gz |
103.1 Kb |
(ftp)(http) |
BED |
| GSE116649_RAW.tar |
13.6 Gb |
(http)(custom) |
TAR (of BEDGRAPH, BW, HIC) |
| GSE116649_TSTvsDFH12wPureLines.genetable.xlsx |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE116649_TimecourseWPureLines.genetable_renamed.xlsx |
4.3 Mb |
(ftp)(http) |
XLSX |
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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