title: Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells.
abstract: BACKGROUND
  Signal transducer and activator of transcription 3 (STAT3) is constitutively activated in many human tumors, including gliomas, and regulates the expression of genes implicated in proliferation, survival, apoptosis, angiogenesis and immune regulation. Only a small fraction of those genes has been proven to be direct STAT3 targets. In gliomas, STAT3 can play tumor suppressive or oncogenic roles depending on the tumor genetic background with target genes being largely unknown.
  
  
  RESULTS
  We used chromatin immunoprecipitation, promoter microarrays and deep sequencing to assess the genome-wide occupancy of phospho (p)-Stat3 and epigenetic modifications of H3K4me3 and H3ac in C6 glioma cells. This combined assessment identified a list of 1200 genes whose promoters have both Stat3 binding sites and epigenetic marks characteristic for actively transcribed genes. The Stat3 and histone markings data were also intersected with a set of microarray data from C6 glioma cells after inhibition of Jak2/Stat3 signaling. Subsequently, we found 284 genes characterized by p-Stat3 occupancy, activating histone marks and transcriptional changes. Novel genes were screened for their potential involvement in oncogenesis, and the most interesting hits were verified by ChIP-PCR and STAT3 knockdown in human glioma cells.
  
  
  CONCLUSIONS
  Non-random association between silent genes, histone marks and p-Stat3 binding near transcription start sites was observed, consistent with its repressive role in transcriptional regulation of target genes in glioma cells with specific genetic background.
authors.affiliation: Postgraduate School of Molecular Medicine, Warsaw Medical University, Warsaw, Poland; Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden; Institute of Computer Science, Polish Academy of Sciences, Warszawa, Poland. Electronic address: kruczyk@gmail.com.
authors.forename: Marcin
authors.initials: M
authors.lastname: Kruczyk
authors.affiliation: Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Poland. Electronic address: p.przanowski@nencki.gov.pl.
authors.forename: Piotr
authors.initials: P
authors.lastname: Przanowski
authors.affiliation: Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Poland. Electronic address: m.dabrowski@nencki.gov.pl.
authors.forename: Michal
authors.initials: M
authors.lastname: Dabrowski
authors.affiliation: Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Poland. Electronic address: kswiatek@nencki.gov.pl.
authors.forename: Karolina
authors.initials: K
authors.lastname: Swiatek-Machado
authors.affiliation: Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Poland. Electronic address: j.mieczkowski@nencki.gov.pl.
authors.forename: Jakub
authors.initials: J
authors.lastname: Mieczkowski
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. Electronic address: ola.wallerman@imbim.uu.se.
authors.forename: Ola
authors.initials: O
authors.lastname: Wallerman
authors.affiliation: Faculty of Pharmacy, Medical University of Gdansk, Poland. Electronic address: 7743@gumed.edu.pl.
authors.forename: Anna
authors.initials: A
authors.lastname: Ronowicz
authors.affiliation: Faculty of Pharmacy, Medical University of Gdansk, Poland. Electronic address: arpiotr@gumed.edu.pl.
authors.forename: Arkadiusz
authors.initials: A
authors.lastname: Piotrowski
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. Electronic address: claes.wadelius@igp.uu.se.
authors.forename: Claes
authors.initials: C
authors.lastname: Wadelius
authors.affiliation: Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Poland. Electronic address: B.Kaminska@nencki.gov.pl.
authors.forename: Bozena
authors.initials: B
authors.lastname: Kaminska
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden; Institute of Computer Science, Polish Academy of Sciences, Warszawa, Poland. Electronic address: jan.komorowski@lcb.uu.se.
authors.forename: Jan
authors.initials: J
authors.lastname: Komorowski
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D044127:Epigenesis, Genetic; D015972:Gene Expression Regulation, Neoplastic; D005910:Glioma / Q000235:genetics* / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D010766:Phosphorylation; D011485:Protein Binding; D051381:Rats; D050796:STAT3 Transcription Factor / Q000378:metabolism* / Q000502:physiology; D024363:Transcription Initiation Site; D059467:Transcriptome; D014407:Tumor Cells, Cultured
chemical_list: D050796:STAT3 Transcription Factor; C494088:Stat3 protein, rat
keywords: Epigenetic modification; Glioma; Stat3; Stat3 gene regulatory network; Transcriptome–epigenome interaction; Whole genome Stat3 occupancy