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Series GSE76815 Query DataSets for GSE76815
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
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.
Overall design Examination of CTCF, Rad21, RNAPII and 2 different histone modifications in SK-N-SH
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
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Submission date Jan 13, 2016
Last update date May 15, 2019
Contact name Quan Xu
Phone +8615921766307
Organization name Shanghai Jiao Tong University
Department Shanghai Center for Systems Biomedicine
Lab Wu Qiang
Street address No.800, Dong Chuan Rd.
City Shanghai
ZIP/Postal code 200240
Country China
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (5)
GSM2038347 CTCF_ChIPSeq
GSM2038348 Rad21_ChIPSeq
GSM2038349 H3K4me3_ChIPSeq
BioProject PRJNA308721
SRA SRP068411

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE76815_RAW.tar 969.3 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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