 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 13, 2021 |
| Title |
Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, down-regulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive target for designing therapeutic strategies. However, whether SALL4 binds DNA directly to regulate gene expression is unclear and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) experiments, we identified and validated the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA-seq analyses after SALL4 knockdown, we discovered hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of Histone 3 Lysine 9-specific Demethylases (KDMs). Taken together, these results elucidated the mechanism of SALL4 DNA binding and revealed novel pathways and molecules to target in SALL4-dependent tumors.
|
| |
|
| Overall design |
Cut&Run on SNU398 cells, 3 replicates for both SALL4 and IgG. RNA-Seq on SNU398 cells post SALL4 knockdown.
|
| |
|
| Contributor(s) |
Kong NR, Bassal MA, Tan HK, Kurland JV, Yong K, Young JJ, Yang Y, Li F, Lee J, Liu Y, Wu C, Stein A, Luo H, Silberstein LE, Bulyk ML, Chai L, Tenen DG |
| Citation(s) |
33406418, 34458869 |
| |
| Submission date |
Aug 26, 2019 |
| Last update date |
Aug 31, 2021 |
| Contact name |
Mahmoud Adel Bassal |
| E-mail(s) |
[email protected]
|
| Organization name |
Beth Israel Deaconess Medical Center
|
| Department |
Hematology and Oncology
|
| Lab |
Tenen Lab
|
| Street address |
3 Blackfan Circle
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02131-4834 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL22790 |
Illumina MiniSeq (Homo sapiens) |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA562266 |
| SRA |
SRP219306 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE136332_CnR_SALL4_commonPeaks_3repls.txt.gz |
184.6 Kb |
(ftp)(http) |
TXT |
| GSE136332_RAW.tar |
349.8 Mb |
(http)(custom) |
TAR (of BED, BW, TXT) |
| GSE136332_rnaseq_3scr_3shSALL4_gene_exp_updated.txt.gz |
794.6 Kb |
(ftp)(http) |
TXT |
| GSE136332_rnaseq_featureCounts_exp_matrix_updated.txt.gz |
287.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...