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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 24, 2010 |
Title |
Deciphering the cis-regulatory architecture of mammalian photoreceptors |
Organism |
Mus musculus |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
In order to define the genomic targets of Crx, we carried out Crx chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) of eight-week-old mouse retinas using the Solexa platform. Sequence reads were mapped to the genome and 'peaks' were identified. These data were subjected to extensive bioinformatic analysis. In addition, selected peaks were experimentally tested for cis-regulatory activity by electroporation as promoter-reporter fusions into living mouse retinas. Over 5,000 Crx-bound regions (CBRs) were identified throughout the mouse genome. Many of these clusters of CBRs occur specifically around photoreceptor genes. In fact, Crx directly regulates the majority of known photoreceptor transcription factors as well as most known photoreceptor disease genes. Cis-regulatory analysis revealed that individual CBRs contribute in a combinatorial fashion to the overall activity of the gene they control. In addition, multiple Crx-binding sites within CBRs cooperatively interact via precise spacing rules to generate optimal levels of transcription.
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Overall design |
Crx ChIP-Seq analysis of C57BL/6 and Nrl-/- retinas. IgG ChIP-Seq was performed as a control. 1-2 replicates each.
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Contributor(s) |
Langmann T, Corbo JC |
Citation(s) |
20693478 |
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Submission date |
Jan 22, 2010 |
Last update date |
May 15, 2019 |
Contact name |
Thomas Langmann |
E-mail(s) |
thomas.langmann@klinik.uni-regensburg.de
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Phone |
+49-941-944-5423
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Fax |
+49-941-944-5402
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Organization name |
Institute of Human Genetics
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Department |
University of Regensburg
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Street address |
Franz-Josef-Strauss-Allee 11
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City |
Regensburg |
ZIP/Postal code |
93042 |
Country |
Germany |
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Platforms (1) |
GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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Samples (7)
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Relations |
SRA |
SRP002186 |
BioProject |
PRJNA124083 |
Supplementary file |
Size |
Download |
File type/resource |
GSE20012_RAW.tar |
957.7 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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