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Pontin functions as an essential coactivator for Oct4 target genes and lincRNAs in embryonic stem cells.

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE58206 | GEO | 2015/04/08

SECONDARY ACCESSION(S): PRJNA251568

REPOSITORIES: GEO

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Pontin functions as an essential coactivator for Oct4 target genes and lincRNAs in embryonic stem cells.

Project 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).

2015-04-08 | E-GEOD-58206 | biostudies-arrayexpress

mRNA profiling of Pontin depleted ES cells and Oct4 depleted ES cells

Project description:In order to investigate the cooperative roles of Pontin and Oct4 for self-renewal and pluripotency in mouse ES cells, we performed mRNA-sequencing analysis from mRNAs isolated from Pontin- and Oct4-depleted ES cells. This analysis provides insight into molecular mechanisms for maintaining ES cell identity. mRNA expression profiles of Pontinf/f; CreER ES cells at 0, 3, or 4 days post-treatment with OHT (wild type and Pontin-depleted ES cells) and ZHBTc4 ES cells at 2 days post-treatment with tetracycline (Oct4-depleted ESE cells) were examined by Illumina Hiseq2000.

2015-10-16 | E-MTAB-1953 | biostudies-arrayexpress

mRNA profiling of Pontin depleted ES cells and Oct4 depleted ES cells

Project description:mRNA profiling of Pontin depleted ES cells and Oct4 depleted ES cells

| PRJEB4779 | ENA

Linear and circular long noncoding RNAs regulate cellular reprogramming by sponging multiple miRNAs

Project description:Using a doxycycline inducible expression of Yamanaka factors (Oct4, Sox2, Klf4 and c-Myc) to generate induced pluripotent stem cells (iPSCs) from mouse embryonic fibroblasts (MEFs), we investigated the dynamic changes of miRNAs, long intergenic noncoding RNAs (lincRNAs) and noncoding circular RNAs (circRNAs) from cells collected at early reprogramming stage. We found that the pools of miRNAs highly expressed in MEFs remain unchanged from day 0 to day 6 after doxycycline induction; unexpectedly, many genes targeted by these miRNAs were actually up-regulated during reprogramming; meanwhile, lincRNAs and circRNAs which have complementary binding sites with the miRNAs were also highly expressed in the reprogramming MEFs (rMEFs). Intriguingly, we found that knockdown of lincRNAs and circRNAs sharing the miRNA binding sites with Oct4 mRNA resulted in down-regulation of Oct4 expression, and significantly decreased the colony formation during reprogramming. Our results suggest that the ceRNA network plays an important role in reprogramming somatic cells to pluripotent stem cells.

2019-07-03 | GSE116684 | GEO

Pontin Functions as A Transcriptional Co-activator for Retinoic Acid-induced HOX Gene Expression [GRO-seq]

Project description:Pontin is a AAA+ ATPase protein that has functions in various biological contexts including gene transcription regulation, chromatin remodeling, DNA damage sensing and repair, as well as assembly of protein and ribonucleoprotein complexes. Pontin is known to regulate the transcription of several important signaling pathways, including Wnt signaling. However, its role in early embryonic signaling regulation remains unclear. Retinoic acid (RA) signaling plays a central role in vertebrate development. Using an in vivo biotin tagging technology, we mapped the genome-wide binding pattern of Pontin before and after RA-induced differentiation in the pluripotent embryo carcinoma cell line NTEAR-2. Biotin ChIP-seq revealed significant changes in genome-wide Pontin binding sites upon RA stimulation. We also identified a substantial amount of overlapping binding peaks between Pontin and RARα, especially on all of the HOX gene loci (A-D clusters). Pontin knockdown experiments showed that its chromatin binding at the HOX gene clusters is required for RA-induced HOX gene expression. Furthermore, we performed Global Run-On sequencing (GRO-seq) to map de novo transcripts genome-wide and found that Pontin knockdown significantly diminished nascent HOX gene transcripts, indicating that Pontin regulates HOX gene expression at the transcriptional level. Finally, proteomic analysis demonstrated that Pontin associates with chromatin organization/remodeling complexes and various other functional complexes. Altogether, we have demonstrated that Pontin is a critical transcriptional co-activator for RA-induced HOX gene activation.

2021-06-16 | GSE162371 | GEO

Pontin Functions as A Transcriptional Co-activator for Retinoic Acid-induced HOX Gene Expression [ChIP-seq]

2021-06-16 | GSE162360 | GEO

Mus musculus

Project description:Pontin functions as an essential coactivator for Oct4 target genes and lincRNAs in embryonic stem cells.

| PRJNA251568 | ENA

Genome-wide analysis of gene expression perturbed by Pontin shRNA in MCF7 subjected to normoxic and hypoxic conditions

2011-12-02 | GSE27813 | GEO

Genome-wide analysis of gene expression perturbed by Pontin shRNA in MCF7 subjected to normoxic and hypoxic conditions

Project description:In order to investigate the role of Pontin methylation on the expression of hypoxia responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shNS) or Pontin shRNA(shPontin) in normoxic and hypoxic conditions. MCF7 cells were transiently transfected with either non-specific shRNA or Pontin shRNA in replicates. Cells were grown for 24 hours before being exposed to either normoxic (21% Oxygen) or hypoxic condition (1% oxygen) for 6,9 hours. Cells were then lysed and RNA isolated.

2011-12-02 | E-GEOD-27813 | biostudies-arrayexpress

mRNA profiling of Pontin WT and RA under glucose starvation

Project description:To determine which genes are affected by methylated Pontin, we performed RNA-sequencing (RNA-seq) in Pontin WT and RA MEFs after glucose starvation.

2020-10-26 | GSE130069 | GEO

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