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Series GSE88699 Query DataSets for GSE88699
Status Public on Mar 13, 2017
Title High activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary The genomic repertoire of enhancers and promoters that control the transcriptional output of terminally differentiated cells includes cell type-specific and housekeeping elements. Whether the constitutive activity of these two groups of cis-regulatory elements relies on entirely distinct or instead shared regulators is unknown. By dissecting the cis-regulatory repertoire of macrophages, we found that the ELF subfamily of ETS proteins selectively bound within 60 bp from the transcription start sites of highly active housekeeping genes. ELFs also bound constitutively active, but not poised macrophage-specific enhancers and promoters. The role of ELFs in promoting constitutive transcription is suggested by multiple evidences: ELF sites enabled transcriptional activation by endogenous and minimal synthetic promoters; ELF recruitment was stabilized by the transcriptional machinery, and ELF proteins mediated recruitment of transcriptional and chromatin regulators to core promoters. These data indicate that a distinct subfamily of ETS proteins imparts high transcriptional activity to a broad range of housekeeping and tissue-specific cis-regulatory elements, which is consistent with the role of an ETS family ancestor in core promoter regulation in a lower eukaryote.
Overall design Chromatin immuno-precipitations of transcription factors Fli1, Elf1, Elf4, GABP-α, H3 lysine 4 trimethylated, H3 lysine 4 monomethylated, PU.1, H3 lysine 27 and RNA polymerase II followed by multiparallel sequencing, performed in bone marrow-derived macrophages from wild type (WT) mice. Cells were treated with alpha amanitin for 5 hours or left unstimulated.

This study includes re-analysis of the following samples from GSE38377: GSM940891, GSM940902, GSM940904, GSM940913, and GSM940924. The .bed files with called peaks for these samples are available on the series record.

The input sample used for all samples for which peak calling was performed, including the re-analyzed samples, is GSM2344452. No peak calling was done for RNAPolII ChIP samples. BigWig files with genome-wide IP signal are available for the RNAPolII ChIP samples.
Contributor(s) Curina A, Ghisletti S, Termanini A, Prosperini E, Natoli G
Citation(s) 28275002
Submission date Oct 13, 2016
Last update date May 15, 2019
Contact name Alberto Termanini
Organization name Istituto Clinico Humanitas
Lab Bioinformatic Unit
Street address Via Manzoni, 113
City Rozzano
State/province MI
ZIP/Postal code 20089
Country Italy
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (15)
GSM2344446 FLI1_WT_UT
GSM2344447 ELF1_WT_UT
This SubSeries is part of SuperSeries:
GSE88702 High activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins
Reanalysis of GSM940891
Reanalysis of GSM940902
Reanalysis of GSM940904
Reanalysis of GSM940913
Reanalysis of GSM940924
BioProject PRJNA348392
SRA SRP091572

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
GSE88699_MacroTFs_111_vs_MacroTFs_139-peaks-filt.bed.gz 197.6 Kb (ftp)(http) BED
GSE88699_MacroTFs_113_vs_MacroTFs_139-peaks-filt.bed.gz 85.9 Kb (ftp)(http) BED
GSE88699_MacroTFs_115_vs_MacroTFs_139-peaks-filt.bed.gz 935.1 Kb (ftp)(http) BED
GSE88699_MacroTFs_133_vs_MacroTFs_139-peaks-filt.bed.gz 180.8 Kb (ftp)(http) BED
GSE88699_MacroTFs_134_vs_MacroTFs_139-peaks-filt.bed.gz 177.0 Kb (ftp)(http) BED
GSE88699_RAW.tar 522.5 Mb (http)(custom) TAR (of BED, BIGWIG)
GSE88699_metadata_for_re-analyzed_samples.txt.gz 1.6 Kb (ftp)(http) TXT
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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