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| Status |
Public on Jan 13, 2016 |
| Title |
Regulation of gene expression in SK-N-SH cell line |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The closely linked human protocadherin (Pcdh) α, β, and γ gene clusters encode 53 distinct protein isoforms, which are expressed in a combinatorial manner to generate enormous diversity on the surface of individual neurons. This diversity is a consequence of stochastic promoter choice and alternative pre-mRNA processing. Here, we show that Pcdhα promoter choice is achieved by DNA looping between two downstream transcriptional enhancers and individual promoters driving the expression of alternate Pcdhα isoforms. In addition, we show that this DNA looping requires specific binding of the CTCF/cohesin complex to two symmetrically aligned binding sites in both the transcriptionally active promoters and in one of the enhancers. These findings have important implications regarding enhancer/promoter interactions in the generation of complex Pcdh cell surface codes for the establishment of neuronal identity and self-avoidance in individual neurons.
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| Overall design |
Examination of CTCF, Rad21, RNAPII and 2 different histone modifications in SK-N-SH
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| Contributor(s) |
Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, Ren B, Krainer AR, Maniatis T, Wu Q |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jan 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Quan Xu |
| E-mail(s) |
qxuchn@gmail.com
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| Phone |
+8615921766307
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| Organization name |
Shanghai Jiao Tong University
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| Department |
Shanghai Center for Systems Biomedicine
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| Lab |
Wu Qiang
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| Street address |
No.800, Dong Chuan Rd.
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| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA308721 |
| SRA |
SRP068411 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE76815_RAW.tar |
969.3 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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