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| Status |
Public on Sep 15, 2011 |
| Title |
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
DNA methylation has been implicated as an epigenetic component of mechanisms that stabilize cell fate decisions. Here, we have characterized the methylomes of human female hematopoietic stem/progenitor cells (HSPCs) and mature cells from the myeloid and lymphoid lineages. Hypomethylated regions (HMRs) associated with lineage-specific genes were often methylated in the opposing lineage. In HSPCs, these sites tended to show intermediate, complex patterns that resolve to uniformity upon differentiation, by increased or decreased methylation. Promoter HMRs shared across diverse cell-types typically display a constitutive core that expands and contracts in a lineage-specific manner to fine-tune the expression of associated genes. Many newly identified intergenic HMRs, both constitutive and lineage-specific, were enriched for factor binding sites with an implied role in genome organization and regulation of gene expression, respectively. Overall, our studies represent an important reference dataset and provide insights into directional changes in DNA methylation as cells adopt terminal fates.
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| Overall design |
Genomic DNA from purified human peripheral blood cells was isolated, bisulfite converted and sequenced using the Illumina GA2 paltform
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| Contributor(s) |
Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren P, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ |
| Citation(s) |
21924933 |
| Submission date |
Sep 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew D Smith |
| E-mail(s) |
andrewds@usc.edu
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| Organization name |
University of Southern California
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| Department |
Molecular and Computational Biology
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| Lab |
Smith Lab
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| Street address |
1050 Childs Way
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (4)
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| Relations |
| SRA |
SRP008144 |
| BioProject |
PRJNA144977 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE31971_RAW.tar |
1.4 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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