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Series GSE88734 Query DataSets for GSE88734
Status Public on May 02, 2018
Title Cooptation of tandem DNA repeats for the control of epithelial-to-mesenchymal transition [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary During normal or pathological epithelial-to-mesenchymal transition, epithelium-specific gene expression is shut down, with the DNA-binding factor ZEB1 acting as a master suppressor of epithelial identity. Here, we show that ZEB1 occupies primate-specific tandem repeats (TRs) harboring dozens of copies of its DNA-binding motif and located within genomic loci relevant for epithelial identity. Deletion of one such repeat in a quasi-mesenchymal human cancer cell line induced the reacquisition of epithelial features and phenocopied the effects of ZEB1 gene deletion. Since ZEB1 binds clustered motifs in a non-cooperative manner, changes in its nuclear concentration enable graded adjustments of TR occupancy, thus fine-tuning repression level. In addition, high motif density in TRs allows ZEB1 binding (and shutdown of epithelial programs) despite differences in chromatin organization and accessibility among epithelial cell types.
 
Overall design Chromatin from human pancreatic ductal adenocarcinoma cell line and human colon carcinoma cell line was immunoprecipitated with anti- ZEB1 or anti-CTCF antibodies and subjected to multiparallel sequencing. Experiments were carried out in unmodified cells (MiaPaCa2 and RKO) and genome edited clonal MiaPaCa2 cells (MiaPaCa2.delta-Repeats and the respective control MiaPaCa2.WT).
 
Contributor(s) Balestrieri C, Natoli G
Citation(s) 29706544
Submission date Oct 14, 2016
Last update date May 15, 2019
Contact name Chiara Balestrieri
E-mail(s) balestrieri.c@gmail.com
Organization name Humanitas University
Lab Transcription and Chromatin Lab
Street address Via Rita Montalcini
City Pieve Emanuele (MI)
ZIP/Postal code 20090
Country Italy
 
Platforms (2)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (9)
GSM2344911 MiaPaCa2.ZEB1
GSM2344912 MiaPaCa2.Input.rep2
GSM2344913 RKO.ZEB1
This SubSeries is part of SuperSeries:
GSE88738 Cooptation of tandem DNA repeats for the control of epithelial-to-mesenchymal transition.
Relations
BioProject PRJNA348428
SRA SRP091543

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE88734_RAW.tar 1.1 Mb (http)(custom) TAR (of NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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