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Series GSE124596 Query DataSets for GSE124596
Status Public on Dec 01, 2019
Title A conserved noncoding locus modulates random monoallelic Xist expression across a TAD boundary
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Topologically associating domains (TADs) are thought to restrict the action of distal cis-regulatory elements, such as enhancers, to target gene promoters within the same TAD. Here we discover that a cis-regulatory element of Xist is located almost 200kb away from its promoter and across a TAD boundary. This element, the promoter of a noncoding RNA, Linx, opposes Xist up-regulation in cis and influences the choice of X chromosome to be inactivated. Even though Linx lies in the same TAD as Xist’s antisense Tsix locus, we show that the repressive action of Linx on Xist is independent of Tsix. Furthermore, this Xist regulatory action is independent of Linx transcript or of its transcription. Finally, we demonstrate that Linx cis-regulatory repressive element is well conserved in mammals, unlike Tsix, suggesting that it represents an ancestral mechanism for random monoallelic Xist expression. Our study uncovers a novel regulatory axis for X-chromosome inactivation and a new class of cis-regulatory effects that rely on TAD partitioning to modulate developmental decisions.
Overall design Our dataset includes 8 RNA-seq samples, 22 5C-samples, 20 Capture-C samples and 6 ATAC-seq samples. These include at least two biological replicates for each condition. Control/reference samples were included and processed in parallel: "wildtype" genotype to compare with deletions/inversions, and "day 0 (undifferentiated)" to compare with differentiated samples.
Contributor(s) Galupa R, Nora EP, Worsley-Hunt R, Picard C, Gard C, vanBemmel JG, Servant N, Zhan Y, ElMarjou F, Johanneau C, Diabangouaya P, LeSaux A, Lameiras S, Fonseca JP, Loos F, Gribnau J, Baulande S, Ohler U, Giorgetti L, Heard E
Citation(s) 31759823, 35502750
Submission date Jan 03, 2019
Last update date Jul 07, 2022
Contact name Nicolas Servant
Organization name Institut Curie
Street address 26 rue d'ulm
City Paris Cedex 05
ZIP/Postal code 75248
Country France
Platforms (4)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (56)
GSM3537377 RNA_E14_d0_rep1
GSM3537378 RNA_E14_d0_rep2
GSM3537379 RNA_E14_d1.5_rep1
BioProject PRJNA512622
SRA SRP175081

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE124596_RAW.tar 2.7 Gb (http)(custom) TAR (of BEDGRAPH, BW, TXT)
GSE124596_Xic3_MAIN_primer_pool_mm9_my5C_FOR.bed.gz 6.2 Kb (ftp)(http) BED
GSE124596_Xic3_MAIN_primer_pool_mm9_my5C_REV.bed.gz 6.4 Kb (ftp)(http) BED
GSE124596_rafael_XXd0_idrValues_withpool_thrp05.bed.gz 297.5 Kb (ftp)(http) BED
GSE124596_rafael_XXd1_idrValues_withpool_thrp05.bed.gz 306.6 Kb (ftp)(http) BED
GSE124596_rafael_XXd2_idrValues_withpool_thrp05.bed.gz 327.5 Kb (ftp)(http) BED
GSE124596_tablecounts_raw.csv.gz 678.5 Kb (ftp)(http) CSV
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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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