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| Status |
Public on Nov 29, 2022 |
| Title |
Chromatin occupancy and chromatin status of K562 cells with a mutation causing exclusive expression of N-terminally truncated GATA1 (GATA1s). |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
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| Summary |
Children with Down syndrome (DS) are at high risk of transient abnormal myelopoiesis (TAM) and acute megakaryoblastic leukemia (DS-AMKL). GATA1 gene mutations are detected in almost all TAM and DS-AMKL samples, leading to exclusive expression of short GATA1 protein (GATA1s) lacking of N-terminal domain (NTD). However, it remains to be clarified how GATA1s is involved with both disorders. To investigate how the loss of GATA1 NTD is involved in the molecular mechanisms of leukemogenesis in DS, we established the K562 GATA1s (K562-G1s) clones expressing only GATA1s by CRISPR/Cas9 genome editing. The K562-G1s clones expressed KIT at higher levels compared to the wild type K562 (K562-WT). With Chromatin-Immunoprecipitation (ChIP) studies, we found that both GATA1 and GATA1s were bound upstream of the KIT gene. To understand the status of the KIT gene in K562-WT and one of K562-G1 subclone, C1 #26, we also performed ChIP-seq of histone modifications. Although the ChIP-seq signals of C1 #26 tended to be slightly lower than those of K562-WT, the activation status of the KIT gene demonstrated by the histone modifications was not significantly different between K562-WT and C1#26. Chromosome conformation capture (3C)-modified proximity assays revealed the difference in the conformation of the KIT gene between the K562-WT and C1 #26. We found that the lack of the NTD of GATA1 altered the genomic structure of the KIT gene, resulting in dysregulation of KIT expression. These results suggest that the NTD of GATA1 is essential for proper genomic conformation and gene expression regulation of the KIT gene and that perturbation of this mechanism might be involved in the pathogenesis of TAM and DS-AMKL.
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| Overall design |
Chromatin and RNA samples from K562-WT and K562-G1 subclones were analyzed.
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| Contributor(s) |
Kanezaki R, Toki T, Ito E |
| Citation(s) |
36447001 |
| |
| Submission date |
Oct 06, 2020 |
| Last update date |
Dec 04, 2022 |
| Contact name |
Rika Kanezaki |
| E-mail(s) |
r_kanez@hirosaki-u.ac.jp
|
| Organization name |
Hirosaki University Graduate School of Medicine
|
| Street address |
5 Zaifucho
|
| City |
Hirosaki |
| ZIP/Postal code |
036-8562 |
| Country |
Japan |
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| Platforms (2) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA667612 |
| SRA |
SRP286495 |
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