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Series GSE39241 Query DataSets for GSE39241
Status Public on Mar 31, 2013
Title FoxA1 binding in asynchronous and mitotic HUH7 cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary During mitosis, RNA polymerase and most transcription factors are excluded from the chromosomes and transcription ceases. The transcriptional re-activation of the genome, following mitosis, requires the re-setting of cell-type specific programs that were initially established during development. However, only about one-fifth of transcription factors are retained on chromosomes throughout mitosis and a subset of these have been shown to facilitate target gene reactivation during mitotic exit. How such “bookmarking” factors bind to chromatin in mitosis and re-activate transcription is central to the stability of transcriptional programs across multiple cell cycles. We compared a diverse set of transcription factors involved in liver differentiation and found different modes of mitotic chromosome binding. The pioneer transcription factor FoxA1, which is among the first to bind liver genes in development, exhibits virtually complete mitotic chromosome binding, whereas other liver factors bind with a range of efficiencies. Yet genome-wide analysis shows that only about 15% of the FoxA1 interphase target sites are bound in mitosis; the latter include sites at genes for maintaining cell differentiation. FoxA1 mutants that perturb specific and nonspecific DNA binding reveal a significant contribution of nonspecific binding events in mitotic chromatin. Such nonspecific binding appears to spread from interphase FoxA1 targets and may serve as storage sites. The hierarchy of specific binding, nonspecific binding, partial chromatin binding, and failure to bind mitotic chromosomes reflects the temporal sequence of the factors’ developmental roles in gene activation.
Overall design Three replicate chIP-seq data sets each are included for mitotic and asynchronously cycling cells; a single input lane from each condition is also included.
Contributor(s) Caravaca JM, Donahue G, Becker JS, Zaret KS
Citation(s) 23355396
Submission date Jul 10, 2012
Last update date May 15, 2019
Contact name Kenneth S. Zaret
Phone 2155735813
Organization name University of Pennsylvania School of Medicine
Department Cell and Developmental Biology
Lab Zaret lab
Street address 9-132, SCTR, 3400 Civic Center Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104-5157
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (8)
GSM958752 FoxA1 ChIP-seq in Asynchronous Cells 1
GSM958753 FoxA1 ChIP-seq in Asynchronous Cells 2
GSM958754 FoxA1 ChIP-seq in Asynchronous Cells 3
This SubSeries is part of SuperSeries:
GSE39243 Expression and FoxA1 binding in asynchronous and mitotic HUH7 cells
BioProject PRJNA170314
SRA SRP014187

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Supplementary file Size Download File type/resource
GSE39241_Asynchronous_Peaks.bed.gz 31.8 Kb (ftp)(http) BED
GSE39241_Mitotic_Peaks.bed.gz 5.2 Kb (ftp)(http) BED
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