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| Status |
Public on May 17, 2018 |
| Title |
CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
We analyzed RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to find that CTCF binding site located between HOXA7 and HOXA9 genes (CBS7/9) is critical for establishing and maintaining aberrant HOXA9-HOXA13 gene expression in AML. Disruption of the CBS7/9 boundary resulted in spreading of repressive H3K27me3 into the posterior active HOXA chromatin domain that subsequently impaired enhancer/promoter chromatin accessibility and disrupted ectopic long-range interactions among the posterior HOXA genes. Consistent with the role of the CBS7/9 boundary in HOXA locus chromatin organization, attenuation of the CBS7/9 boundary function reduced posterior HOTTIP lincRNA and HOXA gene expression and altered myeloid specific transcriptome profiles important for pathogenesis of myeloid malignancies.
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| |
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| Overall design |
We have submitted our RAW sequence datasets into SRA database (SRP115103 and Bioproject: PRJNA396046), including RNA-SEQ, ATAC-seq, ChIP-seq and 4C-seq for WT and CBS7/9KO MOLM13 leukemia cells
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| |
|
| Contributor(s) |
Huang S, Luo H |
| Citation(s) |
29760161 |
| Submission date |
Apr 16, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Suming Huang |
| E-mail(s) |
huanglabseq@hotmail.com
|
| Organization name |
Penn State University
|
| Department |
Pediatrics
|
| Street address |
500 University Dr.
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
|
| Samples (16)
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| Relations |
| BioProject |
PRJNA450401 |
| SRA |
SRP140526 |
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