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E-GEOD-58206 - Pontin functions as an essential coactivator for Oct4 target genes and lincRNAs in embryonic stem cells

Status
Released on 8 April 2015, last updated on 19 August 2015
Organism
Mus musculus
Samples (10)
Protocols (2)
Description
The actions of transcription factors, chromatin modifiers, and noncoding RNAs are crucial for the programming of cellular states. Although chromatin remodeling factors regulate the functional status of cells including pluripotency and differentiation, how they cross-talk with embryonic stem (ES) cell-specific transcription factors and noncoding RNAs to coordinate networks controlling of ES cell identity remain unknown. Here, we find that Pontin chromatin remodeling factor plays an essential role as a coactivator for Oct4 target genes and large intergenic noncoding RNAs (lincRNAs) in ES cells. mRNA- and ChIP-sequencing analyses reveal that Pontin and Oct4 share a substantial set of target genes involved in maintenance of ES cells. Intriguingly, Oct4-dependent coactivator function of Pontin extends to transcription of lincRNAs that are mainly involved in repression of differentiation in ES cells. Together, our findings demonstrate newly identified Oct4-Pontin-lincRNA module plays critical roles in the ES cell circuitry to orchestrate cell fate determination program. For mRNA-sequencing, we obtained mRNAs from 1) Pontinf/f; CreER ES cells at 0, 3, or 4 days post-treatment with 4-hydroxy tamoxifen (OHT) for Pontin-depleted ES cells without biological replicates (n=1), 2) ZHBTc4 ES cells at 2 days post-treatment with tetracycline (Tc) for Oct4-depleted ES cells (n=1), and 3) ZHBTc4 ES cells infected by pLKO control or pLKO-shlinc1253 lentivirus at 4 days post infection for knockdown of linc1253 (n=2). For ChIP-sequencing, chromatin extracts containing DNA fragments with an average size of 400bp were immmunoprecipitated by using antibodies against GFP (control) or Pontin. Eluted ChIP DNA (n=1).
Experiment types
ChIP-seq, RNA-seq of coding RNA 
Contacts
Bhin Jin-hyuk <bynjh007@postech.ac.kr>, Daehee Hwang, Ho Lee, Jinhyuk Bhin, Kyungjin Boo, Sung H Baek
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-58206.idf.txt
Sample and data relationshipE-GEOD-58206.sdrf.txt
Processed data (2)E-GEOD-58206.processed.1.zip, E-GEOD-58206.processed.2.zip
Additional data (1)E-GEOD-58206.additional.1.zip
Links