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Series GSE94467 Query DataSets for GSE94467
Status Public on Apr 12, 2017
Title GRHL3 binding and the enhancer landscape are reorganized during transitions between different functional states of epidermal keratinocytes [siREST-migration]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The genomic mechanisms underlying progressive, irreversible cell lineage commitments and differentiation, which include large scale chromatin re-organization, transcription factor binding, and chromatin modifications, have been well defined. However, we know little about the chromatin changes during transitions between transient cell states such as cell migration. Here we demonstrate the formation of unique complements of typical enhancers and super-enhancers as human progenitor keratinocytes either differentiate or migrate. Unique super-enhancers for each cellular state are linked to gene expression that confer functions associated with each cell state, and sequence variants associated with skin diseases are enriched within super-enhancers. GRHL3, a factor that promotes both differentiation and migration, exhibits prominent super-enhancer interactions in differentiating keratinocytes, while during migration, it preferentially binds to promoters along with REST, repressing the expression of migration inhibitors. Key epidermal differentiation transcription factor genes, including GRHL3, are located within super-enhancers, and many of these transcription factors in turn bind to and regulate super-enhancers. Of note, GRHL3 also represses the formation of a number of progenitor and non-keratinocyte super-enhancers in differentiating keratinocytes. Thus, coordinated GRHL3 binding and enhancer rearrangements regulate the functional states of keratinocytes.
 
Overall design pooled siRNA was used to knockdown REST in duplicate, with 2 scramble siRNA control replicates. Cells were induced to migrate and collected 12 hours later. RNA was extracted and submitted for microarray.
 
Contributor(s) Herndon Klein R, Andersen B
Citation(s) 28445475
Submission date Feb 03, 2017
Last update date Jul 26, 2018
Contact name Bogi Andersen
Organization name University of California, Irvine
Department Medicine
Lab Andersen
Street address 839 Health Sciences Dr.
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platforms (1)
GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
Samples (4)
GSM2476173 scramble control replicate 1 NHEK [siREST-migration]
GSM2476174 scramble control replicate 2 NHEK [siREST-migration]
GSM2476175 siREST replicate 1 NHEK [siREST-migration]
This SubSeries is part of SuperSeries:
GSE94471 GRHL3 binding and the enhancer landscape are reorganized during transitions between different functional states of epidermal keratinocytes
Relations
BioProject PRJNA369793

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Supplementary file Size Download File type/resource
GSE94467_RAW.tar 15.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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