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Series GSE240586 Query DataSets for GSE240586
Status Public on Aug 10, 2023
Title Large-scale analysis of the integration of enhancer-enhancer signals by promoters
Organism Mus musculus
Experiment type Other
Summary Genes are often regulated by multiple enhancers. It is poorly understood how the individual enhancer activities are combined to control promoter activity. Anecdotal evidence has shown that enhancers can combine sub-additively, additively, synergistically, or redundantly. However, it is not clear which of these modes are more frequent in mammalian genomes. Here, we systematically tested how pairs of enhancers activate promoters using a three-way combinatorial reporter assay in mouse cells. By assaying about 69,000 enhancer-enhancer-promoter combinations we found that enhancer pairs generally combine near-additively. This behaviour was conserved across seven developmental promoters tested. Surprisingly, these promoters scale the enhancer signals approximately following a power-law, but the exponent of this response varies between promoters. A housekeeping promoter showed an overall different response to enhancer pairs, and a smaller dynamic range. Thus, our data indicate that enhancers mostly act additively, but promoters transform their collective effect non-linearly.
 
Overall design Per EEP library 1 iPCR sample was prepared and sequenced paired end. The Klf2 library iPCR was sequenced twice, first on a MiSeq and then on a NovaSeq 6000. 1 pDNA sample was prepared per EEP library. For cDNA samples 3 Biological replicates were performed for each EEP library. All pDNA and cDNA samples were sequenced twice on a NovaSeq 6000
 
Contributor(s) Martinez-Ara M, Comoglio F, van Steensel B
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Submission date Aug 10, 2023
Last update date Aug 10, 2023
Contact name Bas van Steensel
E-mail(s) b.v.steensel@nki.nl
Organization name The Netherlands Cancer Institute (NKI)
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
 
Platforms (3)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (73)
GSM7703049 iPCR_EEP_Sox2
GSM7703050 iPCR_EEP_Klf2_run2
GSM7703051 iPCR_EEP_Otx2
Relations
BioProject PRJNA1004277

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
GSE240586_EEP_normalized_data_MMA2023030806.tsv.gz 12.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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