|
| 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 |
| E-mail(s) |
cbenner@ucsd.edu
|
| 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)
|
|
| Relations |
| BioProject |
PRJNA347821 |
| SRA |
SRP091382 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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