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Series GSE113399 Query DataSets for GSE113399
Status Public on Nov 14, 2018
Title SETDB1 compacts the inactive X chromosome in part through silencing an enhancer in the IL1RAPL1 gene
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The product of dosage compensation in human females is the compacted inactive X chromosome (Xi). Here we show that loss of SET domain bifurcated 1 (SETDB1) results in decompaction of the Xi territory coupled with reactivation on the Xi of a powerful enhancer within the 1.4 Mb interleukin-1 receptor accessory protein like 1 (IL1RAPL1) gene at Xp21.2. The enhancer is centrally located in a 0.5 Mb region corresponding to the 3’ third of the IL1RAPL1 locus that transitions from a heterochromatic territory to a euchromatic configuration on the Xi in the absence of SETDB1. This same region showing chromatin instability is part of a common chromosome fragile site that is frequently deleted or rearranged in patients afflicted with intellectual disability and other neurological ailments. Immediately adjacent to the enhancer is an ERVL-MaLR element that drives bi-directional transcription of novel long sense and antisense transcripts. Deletion of the enhancer from the Xa (but not Xi), resulted in detection of bi-directional expression from the Xi coupled with decompaction of the chromosome territory, supporting a critical role for SETDB1 in maintaining this interval in a silent state to facilitate Xi compaction.
Overall design Examination of three different histone modifications in parental and knock out cells, as well as rRNA-depleted total-RNA-Seq in the parental cells and two independent knock-out clones.
Contributor(s) Sun Z, Chadwick BP
Citation(s) 30103804
Submission date Apr 19, 2018
Last update date Mar 21, 2019
Contact name Brian P Chadwick
Phone 850-645-9279
Organization name Florida State University
Department Biological Science
Street address 319 Stadium Drive, King 3076
City Tallahassee
State/province FL
ZIP/Postal code 32306
Country USA
Platforms (2)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (16)
GSM3105085 RPE1_H3K4me2_ChIPSeq
GSM3105086 RPE1_H3K9me3_ChIPSeq
GSM3105087 RPE1_H3K27Ac_ChIPSeq
BioProject PRJNA451021
SRA SRP141213

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Supplementary file Size Download File type/resource
GSE113399_RAW.tar 4.3 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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