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Series GSE71831 Query DataSets for GSE71831
Status Public on Jul 19, 2016
Title Deletion of DXZ4 on the human inactive X chromosome eliminates superdomains and impairs gene silencing
Organisms Macaca mulatta; Homo sapiens; Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary During interphase, the inactive X chromosome (Xi) adopts an unusual 3D configuration known as the Barr body and is largely transcriptionally silent. Despite the importance of X inactivation, little is known about the 3D configuration of Xi and its relationship to gene silencing. We recently showed that in humans, Xi exhibits two distinctive structural features. First, Xi is partitioned into two huge intervals, called superdomains, such that pairs of loci in each superdomain show an enhanced contact frequency with one another. The boundary between the two superdomains lies near DXZ4, a macrosatellite repeat spanning ~300kb, whose Xi allele extensively binds the protein CTCF. Second, Xi exhibits extremely large loops, up to 77Mb long, called superloops. DXZ4 lies at the anchor of several superloops. Here, we use 3D mapping to study the structure of Xi, focusing on the role of DXZ4. We show that superloops and superdomains are conserved across mammals. We develop a novel variant of our in situ Hi-C protocol, dubbed COLA (COncatemer Ligation Assay) to probe the higher order structures formed by the superloops. In COLA, in situ proximity ligation of multiple extremely short fragments produced by the enzyme CviJI is used to efficiently map simultaneous proximity among three or more loci. Using data from Hi-C and COLA, we demonstrate that DXZ4 and other superloop anchors tend to co-locate simultaneously within the same cells, a result that is confirmed by 3D-FISH. Finally, we examine the effects of deleting DXZ4 from Xi in human cells. Using in situ Hi-C, microscopy, and RNA-FISH, we show that superdomains and superloops disappear; that Xi frequently dissociates into multiple separate structures; and that transcriptional silencing on Xi is compromised. Deletion of DXZ4 from the active X chromosome (Xa) has no such effect. Thus, DXZ4 is essential for proper folding and silencing of Xi.
 
Overall design Hi-C protocol was used on wildtype and DXZ4-deleted cells to examine the structure of Xi. A novel variant of our in situ Hi-C protocol, dubbed COLA (COncatemer Ligation Assay), was developed to probe the higher order structures formed by the superloops.

This series also includes RNA-seq data on Retinal Pigmented Epithelial Cells (hTERT-RPE1).

The samples starting with the prefix 'RaoHuntley-2014' were generated as part of the study described in GSE63525 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525).
 
Contributor(s) Darrow EM, Huntley MH, Lieberman Aiden E
Citation(s) 27432957
Submission date Aug 07, 2015
Last update date Mar 11, 2019
Contact name Miriam Huntley
E-mail mhuntley@fas.harvard.edu
Organization name Harvard University
Street address 29 Oxford Street
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platforms (5)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (101)
GSM1847520 DarrowHuntley-2015-HIC001
GSM1847521 DarrowHuntley-2015-HIC002
GSM1847522 DarrowHuntley-2015-HIC003
Relations
BioProject PRJNA292502
SRA SRP062870

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
GSE71831_COLA.hic.gz 2.8 Gb (ftp)(http) HIC
GSE71831_COLA_30.hic.gz 2.0 Gb (ftp)(http) HIC
GSE71831_COLA_Interchromosomal.tar.gz 1.8 Gb (ftp)(http) TAR
GSE71831_COLA_Intrachromosomal.tar.gz 516.8 Mb (ftp)(http) TAR
GSE71831_Patski.hic.gz 6.0 Gb (ftp)(http) HIC
GSE71831_Patski_30.hic.gz 4.9 Gb (ftp)(http) HIC
GSE71831_Patski_Arrowhead_domainlist_10kb_resolution.txt.gz 178.8 Kb (ftp)(http) TXT
GSE71831_Patski_HiCCUPS_looplist.txt.gz 550.4 Kb (ftp)(http) TXT
GSE71831_Patski_Interchromosomal.tar.gz 4.0 Gb (ftp)(http) TAR
GSE71831_Patski_Intrachromosomal.tar.gz 3.2 Gb (ftp)(http) TAR
GSE71831_Patski_maternal.hic.gz 319.0 Mb (ftp)(http) HIC
GSE71831_Patski_paternal.hic.gz 221.0 Mb (ftp)(http) HIC
GSE71831_RAW.tar 474.8 Gb (http)(custom) TAR (of TSV, TXT)
GSE71831_README.pdf 135.6 Kb (ftp)(http) PDF
GSE71831_README_processed_files.txt.gz 907 b (ftp)(http) TXT
GSE71831_RPE1-WT-chrX_diploid.hic.gz 17.7 Mb (ftp)(http) HIC
GSE71831_RPE1-WT.hic.gz 11.9 Gb (ftp)(http) HIC
GSE71831_RPE1-WT_30.hic.gz 11.1 Gb (ftp)(http) HIC
GSE71831_RPE1-WT_Arrowhead_domainlist_5kb_resolution.txt.gz 261.8 Kb (ftp)(http) TXT
GSE71831_RPE1-WT_HiCCUPS_looplist.txt.gz 237.0 Kb (ftp)(http) TXT
GSE71831_RPE1-WT_Interchromosomal.tar.gz 7.0 Gb (ftp)(http) TAR
GSE71831_RPE1-WT_Intrachromosomal.tar.gz 4.3 Gb (ftp)(http) TAR
GSE71831_RPE1-del-Xa_Interchromosomal.tar.gz 4.8 Gb (ftp)(http) TAR
GSE71831_RPE1-del-Xi_Interchromosomal.tar.gz 7.1 Gb (ftp)(http) TAR
GSE71831_RPE1-deltaDXZ4a-chrX_diploid.hic.gz 11.7 Mb (ftp)(http) HIC
GSE71831_RPE1-deltaDXZ4a.hic.gz 7.7 Gb (ftp)(http) HIC
GSE71831_RPE1-deltaDXZ4a_30.hic.gz 7.2 Gb (ftp)(http) HIC
GSE71831_RPE1-deltaDXZ4a_Arrowhead_domainlist_10kb_resolution.txt.gz 197.9 Kb (ftp)(http) TXT
GSE71831_RPE1-deltaDXZ4a_HiCCUPS_looplist.txt.gz 146.9 Kb (ftp)(http) TXT
GSE71831_RPE1-deltaDXZ4a_Intrachromosomal.tar.gz 2.8 Gb (ftp)(http) TAR
GSE71831_RPE1-deltaDXZ4i-chrX_diploid.hic.gz 17.8 Mb (ftp)(http) HIC
GSE71831_RPE1-deltaDXZ4i.hic.gz 12.1 Gb (ftp)(http) HIC
GSE71831_RPE1-deltaDXZ4i_30.hic.gz 11.2 Gb (ftp)(http) HIC
GSE71831_RPE1-deltaDXZ4i_Arrowhead_domainlist_5kb_resolution.txt.gz 308.9 Kb (ftp)(http) TXT
GSE71831_RPE1-deltaDXZ4i_HiCCUPS_looplist.txt.gz 269.1 Kb (ftp)(http) TXT
GSE71831_RPE1-deltaDXZ4i_Intrachromosomal.tar.gz 4.2 Gb (ftp)(http) TAR
GSE71831_Rhesus-Macaque.hic.gz 6.1 Gb (ftp)(http) HIC
GSE71831_Rhesus-Macaque_30.hic.gz 5.7 Gb (ftp)(http) HIC
GSE71831_Rhesus-Macaque_Arrowhead_domainlist_10kb_resolution.txt.gz 218.3 Kb (ftp)(http) TXT
GSE71831_Rhesus-Macaque_HiCCUPS_looplist.txt.gz 410.5 Kb (ftp)(http) TXT
GSE71831_Rhesus-Macaque_Interchromosomal.tar.gz 3.8 Gb (ftp)(http) TAR
GSE71831_Rhesus-Macaque_Intrachromosomal.tar.gz 2.3 Gb (ftp)(http) TAR
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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