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Series GSE104676 Query DataSets for GSE104676
Status Public on Mar 30, 2018
Title Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Fetal hemoglobin (HbF) level is genetically controlled and modifies severity of adult hemoglobin (HbA) disorders. Common genetic variation affects expression of BCL11A, a critical regulator of HbF silencing. Current models suggest that BCL11A acts at a distance from the gamma-globin genes via long-distance chromosomal interactions. Here we use a functional cellular assay and protein-binding microarray to establish a requirement for a zinc-finger cluster of BCL11A for globin repression, and identify a preferred DNA recognition sequence (TGACCA). The motif is present in embryonic and fetal-expressed globin promoters, and duplicated in gamma-globin promoters, yet only the distal motif is mutated in alleles of individuals with hereditary persistence of hemoglobin. Using CUT&RUN to map protein binding sites, we detected BCL11A occupancy preferentially at the distal motif, and validated its absence in HbF-expressing, promoter-edited erythroid cells. Taken together, our findings reveal that direct gamma-globin gene promoter repression by BCL11A underlies hemoglobin switching.
 
Overall design To assess DNA binding of BCL11A, CUT&RUN experiments with BCL11A as antibody were performed on HUDEP-2 and CD34+ differentiated cells at various differentiation days. Various pA-MNase digestion times, and controls (IgG, knockout) were included. CUT&RUN was also assessed on CRISPR promoter edited cells where the gamma-globin promoter was modified.

ATAC-seq experiments were performed in HUDEP-2 cells, single clone edited cells, bulk edited cells to assess their chromatin accessibility. ChIP-seq experiments were also performed in HUDEP-2 cells.
 
Contributor(s) Zhu Q, Liu N, Hargreaves V, Orkin S
Citation(s) 29606353
Submission date Oct 06, 2017
Last update date May 15, 2019
Contact name Stuart Orkin
E-mail(s) Stuart_Orkin@dfci.harvard.edu
Phone 6173557910
Organization name Boston Children's Hospital
Department Hematology and Oncology
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (36)
GSM2805352 BCL11A_CD34_Day3_30min
GSM2805353 BCL11A_CD34_Day3_60min
GSM2805354 BCL11A_CD34_Day3_90min
Relations
BioProject PRJNA413473
SRA SRP119506

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
GSE104676_BCL11A_CD34_30min_combined.TGACCA.log.odds.binding.bed.gz 99.9 Kb (ftp)(http) BED
GSE104676_BCL11A_CD34_60min_combined.TGACCA.log.odds.binding.bed.gz 124.6 Kb (ftp)(http) BED
GSE104676_BCL11A_CD34_90min_combined.TGACCA.log.odds.binding.bed.gz 142.4 Kb (ftp)(http) BED
GSE104676_BCL11A_HUDEP_115edit_60min_combined.TGACCA.log.odds.binding.bed.gz 78.1 Kb (ftp)(http) BED
GSE104676_BCL11A_HUDEP_WT_60min_combined.TGACCA.log.odds.binding.bed.gz 55.1 Kb (ftp)(http) BED
GSE104676_RAW.tar 9.2 Gb (http)(custom) TAR (of BROADPEAK, BW, GAPPEDPEAK, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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