Tiwari2011 Data: NF-Y recruits JNK to Chromatin during Stem Cell Differentiation (RNA-Seq)

By (Secondary Ownership. The experiment uses only third-party data.)

Description from GEO:

Signaling mediates cellular responses to extracellular stimuli. The c-Jun NH2-terminal kinase (JNK) pathway exemplifies one sub-group of Mitogen-activated protein (MAP) kinases, which besides established functions in stress response, also contributes to developmental processes by an unknown mechanism 1-4. Here we show by genome-wide location analysis that JNK binds directly to a large set of active promoters during differentiation of stem cells to neurons. Bound promoters are not enriched for the canonical AP?1 target sites yet for binding motifs for the transcription factor NF?Y. NF-Y indeed occupies these predicted sites genome-wide in vivo and overexpression of a dominant-negative form of NF?YA reduces JNK presence on chromatin. Histone H3 is a substrate for JNK kinase activity in vitro and JNK bound promoters are preferentially enriched for Histone H3 phosphorylated at Serine 10. Inhibition of JNK signaling in postmitotic neurons reduces this chromatin phosphorylation as well as expression of target genes. Together this establishes MAP kinase binding and function on chromatin at a novel class of target genes during stem cell differentiation.
brain / neural histone modifications RNA-seq stem cells polymerase ChIP-seq gene expression / transcription transcription factors
Show history? PUBLIC
Illumina Genome Analyzer II

Some things you might want to do with these data..

Input Data

Sample Groups and Experimental Factors

Main Experimental Results

This is a selection of main results from the data analysis in this experiment. All intermediate results and more data are available from the workflow designer.

Other data generated in this experiment:

Typical analysis workflows my generate dozens or even hundreds of outputs. To condense the amount of information into more easily digestible portions, GeneProf will, by default, only display the experiments input data (here: input data) and a selection of the most important outputs (here: main results). You can drill down into the details of the analysis via the workflow designer or you can display other intermediate outputs here.

Analysis Workflow

This is a schematic representation of the analysis workflow used in this experiment. For more details (parameters, etc.) use the fully-featured workflow designer.
Colours represent types of data (sequences, genomic regions, features, references and files.
Get a simple, static workflow diagram as PNG | JPEG | PDF | SVG | EPS, or get the complete, detailed version as PNG | JPEG | PDF | SVG | EPS.