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Series GSE71156 Query DataSets for GSE71156
Status Public on Jun 30, 2016
Title Allele-specific ATAC-seq
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary One of the two X chromosomes in female somatic cells is transcriptionally silenced across cell generations, a classic paradigm of epigenetic regulation.  Although most genes are stably silenced, certain X-linked genes escape X-chromosome inactivation (XCI), providing a fundamental dosage difference between females and males.  A role for chromosome conformation has been proposed in XCI as the process is  accompanied by a massive structural reorganisation. However a detailed molecular understanding of the three-dimensional architecture of the Xi has been lacking.  Here we reveal an unusual three-dimensional configuration of the Xi, that provides novel insights into the relationship between gene expression and TAD organisation.  Using allele-specific Hi-C, RNA-Seq and ATAC-seq, as well as DNA FISH, we show that the Xi is spatially segregated into two ‘mega-domains’ separated by a 200kb boundary including the DXZ4 macrosatellite, and is globally devoid of typical autosomal structural features such as active/inactive compartments and topologically associating domains (TADs). However, we find that a few regions along the Xi display TAD signatures corresponding to regions containing escape genes, and display DNA accessibility at promoter-proximal TF binding sites.  Strikingly, when the DXZ4-containing boundary region is deleted prior to XCI, most facultative escapees are no longer expressed from the Xi, and the escape associated  chromatin domains are no longer observed. Deletion of the DXZ4-containing boundary region from the Xi also results in fusion of the two mega-domains.   We show that Xist A-repeat containing (gene silencing competent) RNA is sufficient to induce this spatial segregation of the X chromosome. Combined, our results point to a critical role for the DXZ4-boundary region, together with Xist RNA, in shaping the higher order structure of the Xi and in allowing facultative escape from XCI during differentiation. They also point to direct and uncover a close relationships between transcription and TAD formation organisation in the context of the Xi.
Overall design ATAC-seq was performed in mESCs and mNPCs as well as deltaFT NPCs. Libraries(2 replicates per line) were sequenced on an Illumina NextSeq (2x75bp) and data was analyzed allele-specifically. ATAC-seq was also performed inmale mESCs containing a doxycycline-inducible Xist construct at the endogenous locus with or without the functional RepA region. Samples with Xist induction (+dox) and without (-dox) are included.
Contributor(s) Carter AC, Xu J, Chang HY
Citation(s) 27437574
Submission date Jul 21, 2015
Last update date May 15, 2019
Contact name Howard Chang
Phone 650-725-7022
Organization name Stanford University
Department Dermatology
Lab Howard Y. Chang
Street address CCSR 2130, 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (7)
GSM1828645 WT mESCs
GSM1828646 WT NPCs
GSM1828647 deltaFT NPCs
BioProject PRJNA290471
SRA SRP061369

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Supplementary file Size Download File type/resource
GSE71156_RAW.tar 2.0 Gb (http)(custom) TAR (of BW, NARROWPEAK, TXT)
GSE71156_RepA_minusdox_merge.bed_peaks.narrowPeak.gz 2.6 Mb (ftp)(http) NARROWPEAK
GSE71156_Wt_minusdox_merge.bed_peaks.narrowPeak.gz 2.9 Mb (ftp)(http) NARROWPEAK
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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