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Series GSE87831 Query DataSets for GSE87831
Status Public on Nov 15, 2016
Title Nucleoporin-mediated regulation of cell identity genes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that Nuclear Pore Complex (NPC) components Nup93 and Nup153 bind super-enhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.
Overall design DamID-Seq of Nup153 and Nup93 in human U2OS, DamID-Seq of Nup153 in IMR90 cells, RNA-seq of control and knocked-down populations in U2OS and IMR90 cells, ChIP-Seq of histone modifications in U2OS and IMR90 cells and DNAseI-Seq of U2OS cells.
Contributor(s) Ibarra A, Benner C, Hetzer MW
Citation(s) 27807035
Submission date Oct 11, 2016
Last update date May 15, 2019
Contact name Christopher Benner
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (33)
GSM2341623 GFP-DamID-forLBR
GSM2341624 LBR-DamID-r1
GSM2341625 LBR-DamID-r2
BioProject PRJNA347821
SRA SRP091382

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Supplementary file Size Download File type/resource
GSE87831_CTCF.peaks.bed.gz 333.3 Kb (ftp)(http) BED
GSE87831_DNase-Seq.r1.peaks.bed.gz 1.2 Mb (ftp)(http) BED
GSE87831_DNase-Seq.r2.peaks.bed.gz 982.4 Kb (ftp)(http) BED
GSE87831_H3K27ac.IMR90.SE.bed.gz 10.3 Kb (ftp)(http) BED
GSE87831_H3K27ac.U2OS.SE.bed.gz 5.3 Kb (ftp)(http) BED
GSE87831_H3K4me3-IMR90.peaks.bed.gz 226.9 Kb (ftp)(http) BED
GSE87831_H3K4me3.peaks.bed.gz 198.7 Kb (ftp)(http) BED
GSE87831_H3K9me2.peaks.bed.gz 1.5 Kb (ftp)(http) BED
GSE87831_LBR-DamID.LADs.bed.gz 14.2 Kb (ftp)(http) BED
GSE87831_Nup153-DamID-IMR90.peaks.bed.gz 337.2 Kb (ftp)(http) BED
GSE87831_Nup153-DamID-IMR90.toppeaks.bed.gz 26.3 Kb (ftp)(http) BED
GSE87831_Nup153-DamID.peaks.bed.gz 24.4 Kb (ftp)(http) BED
GSE87831_Nup93-DamID.peaks.bed.gz 14.3 Kb (ftp)(http) BED
GSE87831_fpkm.txt.gz 1.5 Mb (ftp)(http) TXT
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