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Series GSE211232 Query DataSets for GSE211232
Status Public on Aug 18, 2022
Title Multipartite super-enhancers function in an orientation-dependent manner [ATAC-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcriptional enhancers regulate gene expression in a developmental-stage and cell-specific manner. They were originally defined as individual regulatory elements that activate expression regardless of distance and orientation to their cognate genes. Genome-wide studies have shown that the mammalian enhancer landscape is much more complex, with different classes of individual enhancers and clusters of enhancer-like elements combining in additive, synergistic and redundant manners, possibly acting as single, integrated regulatory elements. These so-called super-enhancers are largely defined as clusters of enhancer-like elements which recruit particularly high levels of Mediator and often drive high levels of expression of key lineage-specific genes. Here, we analysed 78 erythroid-specific super-enhancers and showed that, as units, they preferentially interact in a directional manner, to drive expression of their cognate genes. Using the well characterised a-globin super-enhancer, we show that inverting this entire structure severely downregulates a-globin expression and activates flanking genes 5’ of the super-enhancer. Our detailed genetic dissection of the a-globin locus clearly attributes the cluster’s functional directionality to its sequence orientation, demonstrating that, unlike regular enhancers, super-enhancers act in an orientation-dependent manner. Together, these findings identify a novel emergent property of super-enhancers and revise current models by which enhancers are thought to contact and activate their cognate genes.
Overall design An inversion spanning the alpha globin superenhancer and including both the Nprl3 and Mpg genes was genetically engineered in mouse ESCs and a mouse model was created by blastocyst injection of these mESCs. Primary erythroid cells derived from APH-treated spleens of these mice (INVEN) as well as WT mice were subjected to various analyses (ATAC-Seq, ChIP-Seq, RNA-Seq, Capture C) to examine the effect this inversion has on the expression of the erythroid -specific alpha globin genes. Embryonic blood (E10.5) was also analysed to differentiate the effect of the inversion on primitive (embryonic) versus dfinitive (adult) erythropoiesis. Moues ESCs were also generated; these harbour additional mutations that allow the effect of the inversion to be untangled from other confoudning factors (such as the boundary elements HS3839 or the repoistioned Mpg gene). These mESCs were subjected to an in vitro erythroid differentiation protocol (doi: 10.1371/journal.pone.0261950) and purified CD71+ erythroid cells derived from differentiated Wildtype (WT) or mutant mouse Embryonic Stem (mES) cells were analysed similarly to the primary spleen erythroid cells.
Contributor(s) Kassouf M, Gosden M, Francis H
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Submission date Aug 15, 2022
Last update date Aug 21, 2022
Contact name Mira Tony Kassouf
Organization name University of Oxford
Department Weatherall Institute of Molecular Medicine
Lab Doug Higgs
Street address John Radcliffe Hospital, Headly way
City Oxford
State/province England
ZIP/Postal code OX3 9DS
Country United Kingdom
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (25)
GSM6456399 EB_CD71_WT_ATAC_1
GSM6456400 EB_CD71_WT_ATAC_2
GSM6456401 EB_CD71_WT_ATAC_3
This SubSeries is part of SuperSeries:
GSE211238 Multipartite super-enhancers function in an orientation-dependent manner
BioProject PRJNA869661

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Supplementary file Size Download File type/resource
GSE211232_RAW.tar 3.8 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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