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Status |
Public on Dec 18, 2011 |
Title |
A chromatin-modifying function of JNK during stem cell differentiation |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing
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Summary |
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.
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Overall design |
Our Dataset comprises 5 ChIP-seq samples using chromatin from ES, NP and TN cells which was immunoprecipitated, using antibodies against H3K27me3, H3K4me2, RNA Pol II, JNK1/3 and NF-YA. From the same cells we generated biological replicates of RNA-seq data.
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Contributor(s) |
Tiwari V, Stadler MB, Wirbelauer C, Paro R, Schübeler D, Beisel C |
Citation(s) |
22179133, 22474351 |
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Submission date |
Nov 22, 2010 |
Last update date |
May 15, 2019 |
Contact name |
Dirk Schuebeler |
Organization name |
Friedrich Miescher Institute for Biomedical Research
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Street address |
Maulbeerstrasse 66
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City |
Basel |
ZIP/Postal code |
4058 |
Country |
Switzerland |
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Platforms (1) |
GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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Samples (33)
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GSM632032 |
ES_H3K27me3_technical_replicate_a1 [ChIP-Seq] |
GSM632033 |
ES_H3K27me3_technical _replicate_a2 [ChIP-Seq] |
GSM632034 |
ES_H3K27me3_biological_replicate_b1 [ChIP-Seq] |
GSM632035 |
ES_H3K4me2 [ChIP-Seq] |
GSM632036 |
ES_JNK13_biological_replicate_a [ChIP-Seq] |
GSM632037 |
ES_JNK13_biological_replicate_b [ChIP-Seq] |
GSM632038 |
ES_NFYA_biological_replicate_a [ChIP-Seq] |
GSM632039 |
ES_NFYA_biological_replicate_b [ChIP-Seq] |
GSM632040 |
ES_PolII [ChIP-Seq] |
GSM632041 |
Input [ChIP-Seq] |
GSM632042 |
NP_H3K27me3_technical_replicate_a1 [ChIP-Seq] |
GSM632043 |
NP_H3K27me3_technical _replicate_a2 [ChIP-Seq] |
GSM632044 |
NP_H3K27me3_biological_replicate_b1 [ChIP-Seq] |
GSM632045 |
NP_H3K4me2 [ChIP-Seq] |
GSM632046 |
NP_JNK13_biological_replicate_a [ChIP-Seq] |
GSM632047 |
NP_JNK13_biological_replicate_b [ChIP-Seq] |
GSM632048 |
NP_NFYA_biological_replicate_a [ChIP-Seq] |
GSM632049 |
NP_NFYA_biological_replicate_b [ChIP-Seq] |
GSM632050 |
NP_PolII [ChIP-Seq] |
GSM632051 |
TN_H3K27me3_technical_replicate_a1 [ChIP-Seq] |
GSM632052 |
TN_H3K27me3_technical _replicate_a2 [ChIP-Seq] |
GSM632053 |
TN_H3K27me3_biological_replicate_b1 [ChIP-Seq] |
GSM632054 |
TN_H3K4me2 [ChIP-Seq] |
GSM632055 |
TN_JNK13_biological_replicate_a [ChIP-Seq] |
GSM632056 |
TN_JNK13_biological_replicate_b [ChIP-Seq] |
GSM632057 |
TN_NFYA_biological_replicate_a [ChIP-Seq] |
GSM632058 |
TN_NFYA_biological_replicate_b [ChIP-Seq] |
GSM632059 |
TN_PolII [ChIP-Seq] |
GSM768537 |
TN_DMSO_JNK13 [ChIP-Seq] |
GSM768538 |
TN_JNKi_JNK1/3 [ChIP-Seq] |
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This SubSeries is part of SuperSeries: |
GSE25533 |
A chromatin-modifying function of JNK during embryonic stem cell differentiation |
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Relations |
BioProject |
PRJNA142433 |
SRA |
SRP004709 |