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Series GSE123371 Query DataSets for GSE123371
Status Public on Nov 26, 2019
Title Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (ChIP-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy 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 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 Dec 05, 2018
Last update date Feb 15, 2024
Contact name Harrison Wren Gabel
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 (62)
GSM3502265 WTKO_Input_WT1
GSM3502266 WTKO_Input_KO1
GSM3502267 WTKO_H3K27ac_WT1
This SubSeries is part of SuperSeries:
GSE123373 Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression
BioProject PRJNA508527
SRA SRP172562

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Supplementary file Size Download File type/resource
GSE123371_Enhancer_ChIP_seq_Table.tsv.gz 5.0 Mb (ftp)(http) TSV
GSE123371_peak_data_table_113018_geo.tsv.gz 12.3 Mb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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