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| Status |
Public on Mar 24, 2016 |
| Title |
Sequence Features Accurately Predict Genome-wide MeCP2 Binding in vivo |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
|
| Summary |
MECP2 is critical for proper brain development and expressed at near-histone levels in neurons, but the mechanism of its genomic localization remains poorly understood. Using high-resolution MeCP2 binding data, we show that genetic features alone can predict binding with 88% accuracy. Integrating MeCP2 binding and DNA methylation in a probabilistic graphical model, we demonstrate that previously reported methylation preferences may be due to MeCP2’s affinity to GC-rich chromatin, a result replicated using published data. Furthermore, MeCP2 co-localized with nucleosomes, and Mecp2 deletion led to nucleosome repositioning. Finally, MeCP2 binding downstream of promoters correlated with increased expression in Mecp2 deficient neurons.
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| Overall design |
Study of genetic and epigenetic determinants of MeCP2 binding using MeCP2 ChIP-seq, MNase-seq, Bisulfite-seq and RNA-seq. Please see individual sample record for details on experimental design.
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| |
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| Contributor(s) |
Rube HT |
| Citation(s) |
27008915 |
| |
| Submission date |
Jul 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hans Tomas Rube |
| Organization name |
University of Illinois at Urbana Champaign
|
| Department |
Physics
|
| Lab |
Jun Song
|
| Street address |
1110 West Green Street
|
| City |
Urbana |
| State/province |
Illinois |
| ZIP/Postal code |
61801 |
| Country |
USA |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA290401 |
| SRA |
SRP061339 |
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