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Series GSE138613 Query DataSets for GSE138613
Status Public on Nov 26, 2019
Title Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (Bisulfite-Seq)
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary The genomes of mammalian neurons contain uniquely high levels of non-CG DNA methylation that can be bound by the Rett syndrome protein, MeCP2, to regulate gene expression. How patterns of non-CG methylation at genes are established and the mechanism by which this methylation works with MeCP2 to control gene expression is unclear. Here we find that genes repressed by MeCP2 are found within regions of high non-CG methylation that are defined by domains of chromatin folding. Rather than working directly at transcriptional start sites to regulate these genes, MeCP2 represses enhancer elements that are enriched for methylated cytosines occurring in the CA or CG context. Enhancers repressed by MeCP2 are found within genes that are upregulated upon loss of the protein, providing a regulatory logic for how disruption of MeCP2 can lead to wide-spread changes in gene expression. Hence, we have found that DNA topology can shape non-CG DNA methylation across the genome to dictate MeCP2-mediated enhancer regulation in the brain.
 
Overall design Total RNA-seq and ChIP-seq from the brains of MeCP2 KO, OE, and WT mice
 
Contributor(s) Clemens AW, Wu DY, Zhao G, Gabel HW
Citation(s) 31784360, 33238114, 37952155
Submission date Oct 08, 2019
Last update date Feb 15, 2024
Contact name Harrison Wren Gabel
E-mail(s) gabelh@pcg.wustl.edu
Organization name Harvard Medical School
Department Neurbiology
Lab Michael Greenberg
Street address 220 longwood avenue
City brookline
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (12)
GSM4114259 Dnmt3a_WT_6_bs
GSM4114260 Dnmt3a_WT_7_bs
GSM4114261 Dnmt3a_WT_9_bs
This SubSeries is part of SuperSeries:
GSE123373 Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression
Relations
BioProject PRJNA576509
SRA SRP224867

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Supplementary file Size Download File type/resource
GSE138613_RAW.tar 329.4 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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