NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE226670 Query DataSets for GSE226670
Status Public on Nov 12, 2023
Title The alternative Nucleosome Remodeling Factor complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions (ATAC-seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Efficient treatment of Acute Myeloid Leukemia (AML) patients remains a challenge despite recent advances. Here using a CRISPRi screen targeting chromatin factors, we identified BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader modules of BPTF are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.
 
Overall design 2 ATAC-sequencing experiments; the negative controls for each set are clearly specified in the title. Experiment 1: assessing the effect of BPTF KO on chromatin accessibility. Experiment 2: assessing the effect of SMARCA5 KO on chromatin accessibility. 2 biological replicates per sample were used. Experiment 3: ATAC-sequencing experiment assessing the effect of rapid SMARCA5 degradation on chromatin accessibility. 2 biological replicates per sample were used. The cells were treated with DMSO or dTAG-V1, as indicated in the sample name.
 
Contributor(s) Radzisheuskaya A, Helin K
Citation(s) 37987160
Submission date Mar 06, 2023
Last update date Feb 10, 2024
Contact name Aliaksandra Radzisheuskaya
E-mail(s) ar570a@gmail.com
Organization name The Institute of Cancer Research
Department Cancer Biology
Street address 237 Fulham road
City London
ZIP/Postal code SW36JB
Country United Kingdom
 
Platforms (2)
GPL21697 NextSeq 550 (Homo sapiens)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (14)
GSM7081316 ATAC_exp1_sgNegCtrl_rep1
GSM7081317 ATAC_exp1_sgNegCtrl_rep2
GSM7081318 ATAC_exp1_sgBPTF-1_rep1
This SubSeries is part of SuperSeries:
GSE226688 The alternative Nucleosome Remodeling Factor complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions
Relations
BioProject PRJNA941211

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE226670_NURF_ATAC-seq.xlsx 28.1 Mb (ftp)(http) XLSX
GSE226670_RAW.tar 767.2 Mb (http)(custom) TAR (of BW)
GSE226670_S5KI_4hr_vs_S5KI_DMSO.txt.gz 11.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap