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| Status |
Public on Nov 01, 2010 |
| Title |
Wide-ranging fucntions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The transcription factor E2F4 is a member of the E2F family of regulators which has critical roles in cell cycle control and differentiation. We investigated the genome-wide binding profile of E2F4 using a newly developed peak calling program based on a kernel density estimation and identified approximately 16 thousands E2F4 binding sites at a 1% FDR threshold, which potentially modulate 7,346 downstream target genes. Gene Ontology (GO) functional analysis of E2F4 target genes revealed several novel functions of E2F4 including I-kappaB kinase/NF-kappaB cascade, protein transport and targeting, protein folding, and sterol biosynthetic process. In addition to mRNA target genes, E2F4 also binds and regulates some miRNA targets such as let-7a, mir-17 and mir-22. Interestingly, we found that about 20% of E2F4 sites are in intergenic regions, which suggests that E2F4 may function at enhancer sites. De novo motif discovery revealed 5 novel, significantly enriched motifs within E2F4 sites. Only 5% of binding sites contain a canonical motif, indicating that E2F4 can use diverse motifs to bind DNA and regulate transcription. Overexpression of E2F4 and its cofactors such as RBL2 and DP-1, followed by microarray analysis, revealed that E2F4 functions as an activator and a repressor. Taken together, our genome-wide E2F4 ChIP sequencing data provided evidences of versatile physiological roles of E2F4 and insights into its functions.
This SuperSeries is composed of the SubSeries listed below.
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| Overall design |
Refer to individual Series
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| Citation(s) |
21247883 |
| Submission date |
Apr 23, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Vishy Iyer |
| E-mail(s) |
iyerlab@gmail.com
|
| Phone |
5122327833
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2500 Speedway Dr. MBB 3.212
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL5621 |
SFGF HEEBO Human Set v1.00 |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
|
| Samples (12)
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| This SuperSeries is composed of the following SubSeries: |
| GSE21439 |
E2F4 and its cofactor transfection vs empty vector transfection |
| GSE21488 |
Genome-wide target discovery of transcripton factor E2F4 by ChIP-seq |
|
| Relations |
| BioProject |
PRJNA126027 |
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