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| Status |
Public on Sep 16, 2022 |
| Title |
Human Core Nucleoporin Selectively Regulates Gene Transcription but is Dispensable for 3D Genome Organization |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
NUPs have been shown to be important in transcriptional regulation and in three-dimensional (3D) genome organization. However, evidence in support of their direct roles remains limited, and their action mechanisms are elusive.here,we take advantage of a few advanced techniques including Cut&Run, auxin-induced rapid degron, PRO-Seq, dCas9 chromatin tethering, in situ Hi-C and HiChIP to directly address these outstanding questions in human cells, and our results provide new insights into the direct but also specific roles of core NUPs in gene transcription, while revealing their dispensity for the overall organization of 3D genome architecture.
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| Overall design |
the role of core human nucleoporins in human cells
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| Contributor(s) |
Li W |
| Citation(s) |
36323253 |
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| Submission date |
Jan 25, 2021 |
| Last update date |
Nov 03, 2022 |
| Contact name |
chuangye Qi |
| E-mail(s) |
[email protected]
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| Organization name |
Baylor College of Medicine
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| Department |
Huffington Center
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| Lab |
Zheng
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| Street address |
6450 E Cullen St
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| City |
HOUSTON |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (2) |
| GPL21697 |
NextSeq 550 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (42)
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| GSM5034225 |
HCT116-NUP93-mAC, PRO-Seq,UT, biological replicate 1 |
| GSM5034226 |
HCT116-NUP93-mAC, PRO-Seq, IAA, biological replicate 1 |
| GSM5034227 |
HCT116-NUP93-mAC, PRO-Seq,UT, biological replicate 2 |
| GSM5034228 |
HCT116-NUP93-mAC, PRO-Seq, IAA, biological replicate 2 |
| GSM5034230 |
HCT116-NUP93-mAC,ChIP-Seq,H3K27ac,UT |
| GSM5034231 |
HCT116-NUP93-mAC,ChIP-Seq,H3K27ac,IAA |
| GSM5034232 |
HCT116-NUP93-mAC,ChIP-Seq,Ser2p,UT,biological replicate 1 |
| GSM5034233 |
HCT116-NUP93-mAC,ChIP-Seq,Ser2p,IAA,biological replicate 1 |
| GSM5034234 |
HCT116-NUP93-mAC,ChIP-Seq,Ser2p,UT,biological replicate 2 |
| GSM5034235 |
HCT116-NUP93-mAC,ChIP-Seq,Ser2p,IAA,biological replicate 2 |
| GSM5034238 |
HCT116,Cut&Run,NUP93, biological replicate 1 |
| GSM5034239 |
HCT116,Cut&Run,NUP93, biological replicate 2 |
| GSM5034240 |
HCT116,Cut&Run,NUP205 |
| GSM5034241 |
HCT116,Cut&Run,SEC13 |
| GSM5034242 |
HCT116,Cut&Run,NUP35 |
| GSM5034243 |
HCT116,Cut&Run,IgG |
| GSM5034244 |
HeLa,Cut&Run,NUP93 |
| GSM5034245 |
HCT116-NUP93-mAC,Cut&Run for BRD4,UT, biological replicate 1 |
| GSM5034246 |
HCT116-NUP93-mAC,Cut&Run for BRD4,IAA, biological replicate 1 |
| GSM5034247 |
HCT116-NUP93-mAC,Cut&Run for BRD4,UT, biological replicate 2 |
| GSM5034248 |
HCT116-NUP93-mAC,Cut&Run for BRD4,IAA, biological replicate 2 |
| GSM5034249 |
HCT116-NUP93-mAC,Hi-C,MboI,UT,biological replicate 1 |
| GSM5034250 |
HCT116-NUP93-mAC,Hi-C,MboI,IAA,biological replicate 1 |
| GSM5034255 |
HCT116,HiChIP, MboI, H3K27ac |
| GSM5075996 |
HCT116-NUP93-mAC,ChIP-Seq,H3K27me3,UT |
| GSM5075997 |
HCT116-NUP93-mAC,ChIP-Seq,H3K27me3,IAA |
| GSM5219235 |
HCT116-NUP93-mAC,ChIP-Seq,RPB1,UT |
| GSM5219236 |
HCT116-NUP93-mAC,ChIP-Seq,RPB1,IAA |
| GSM5239424 |
HCT116-NUP93-mAC,ChIP-Seq,RPB2,UT |
| GSM5239425 |
HCT116-NUP93-mAC,ChIP-Seq,RPB2,IAA |
| GSM5962442 |
HCT116-NUP93-mAC,ChIP-Seq for BRD4,UT, biological replicate 1 |
| GSM5962443 |
HCT116-NUP93-mAC,ChIP-Seq for BRD4,IAA, biological replicate 1 |
| GSM5962444 |
HCT116-NUP93-mAC,Hi-C,MboI,UT,biological replicate 2 |
| GSM5962445 |
HCT116-NUP93-mAC,Hi-C,MboI,IAA,biological replicate 2 |
| GSM5962446 |
HCT116-NUP93-mAC,Hi-C,MboI,UT,biological replicate 3 |
| GSM5962447 |
HCT116-NUP93-mAC,Hi-C,MboI,IAA,biological replicate 3 |
| GSM6431855 |
HCT116-NUP93-mAC,HiChIP,H3K27ac,MboI,UT,biological replicate 1 |
| GSM6431856 |
HCT116-NUP93-mAC,HiChIP,H3K27ac,MboI,UT,biological replicate 2 |
| GSM6431857 |
HCT116-NUP93-mAC,HiChIP,H3K27ac,MboI,IAA,biological replicate 1 |
| GSM6431858 |
HCT116-NUP93-mAC,HiChIP,H3K27ac,MboI,IAA,biological replicate 2 |
| GSM6431859 |
HCT116-NUP93-mAC,HiChIP,H3K4me1,MboI,UT,biological replicate 1 |
| GSM6431860 |
HCT116-NUP93-mAC,HiChIP,H3K4me1,MboI,IAA,biological replicate 1 |
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| Relations |
| BioProject |
PRJNA694667 |
| SRA |
SRP303189 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE165463_RAW.tar |
19.2 Gb |
(http)(custom) |
TAR (of BEDPE, BIGWIG, MCOOL, PAIRS) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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