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Series GSE78803 Query DataSets for GSE78803
Status Public on Jun 02, 2016
Title Dissection of a super-enhancer in vivo (Capture-C)
Organism Mus musculus
Experiment type Other
Summary Many genes determining cell identity are regulated by a set of enhancer elements collectively referred to as super-enhancers. It has been suggested that super-enhancers represent a new class of cis-element, in which the assembly of enhancers confers an emergent property from the extended regulatory domain. To investigate this, we used published criteria to define one of the strongest super-enhancers in mouse erythroid cells – a 24kb region regulating α-globin expression, which comprises five enhancer-like components. Using homologous recombination, we deleted each component of this super-enhancer, singly and in informative combinations, and examined hematologic phenotype, gene expression, chromatin structure and chromosome conformation. Each component behaves independently, in an additive rather than synergistic manner. We conclude that the sub-classification of enhancers is unjustified beyond a description of their strength, which is defined by the number of lineage-specific transcription factors they bind. These findings ask afresh why enhancer-like elements cluster at key genes.
Overall design NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments, in this case the promoters of genes were exclusively used. The method was applied to Wlidtype erythroid cells and to in vivo models where the globin R1 and R2 regulatory elements and the R2 and R3 regulatory elements were deleted in combination.
Contributor(s) Davies JO, Hughes JR, Hay D, Higgs D, Oudelaar AM
Citation(s) 27376235
Submission date Mar 01, 2016
Last update date May 15, 2019
Contact name Jim Hughes
Phone 1865222113
Organization name University of Oxford
Department MHU
Lab Genome Biology Group
Street address Weatherall Institute Of Molecular Me
City oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (15)
GSM2077391 Fetal liver Knockout of alpha globin regulatory elements R1 and R2, biological replicate 1 [Capture C]
GSM2077392 Fetal liver Knockout of alpha globin regulatory elements R1 and R2, biological replicate 2 [Capture C]
GSM2077393 Fetal liver Knockout of alpha globin regulatory elements R1 and R2, biological replicate 3 [Capture C]
This SubSeries is part of SuperSeries:
GSE78835 Genetic dissection of the α-globin super-enhancer
BioProject PRJNA314073
SRA SRP071068

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
GSE78803_HbaCombined_Enhancer_KO_30gH_Combined_PF_BF.txt.gz 4.0 Mb (ftp)(http) TXT
GSE78803_HbaCombined_KO_PF_BF.txt.gz 4.7 Mb (ftp)(http) TXT
GSE78803_HbbCombined_Enhancer_KO_30gH_Combined_PF_BF.txt.gz 3.6 Mb (ftp)(http) TXT
GSE78803_HbbCombined_KO_PF_BF.txt.gz 3.5 Mb (ftp)(http) TXT
GSE78803_Slc25A37_Enhancer_KO_30gH_Combined_PF_BF.txt.gz 2.0 Mb (ftp)(http) TXT
GSE78803_Slc25A37_KO_PF_BF.txt.gz 2.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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