title: In Vivo Chromatin Targets of the Transcription Factor Yin Yang 2 in Trophoblast Stem Cells.
abstract: Yin Yang 2 (YY2) is a zinc finger protein closely related to the well-characterized Yin Yang 1 (YY1). YY1 is a DNA-binding transcription factor, with defined functions in multiple developmental processes, such as implantation, cell differentiation, X inactivation, imprinting and organogenesis. Yy2 has been treated as a largely immaterial duplication of Yy1, as they share high homology in the Zinc Finger-region and similar if not identical in vitro binding sites. In contrast to these similarities, gene expression alterations in HeLa cells with attenuated levels of either Yy1 or Yy2 were to some extent gene-specific. Moreover, the chromatin binding sites for YY2, except for its association with transposable retroviral elements (RE) and Endogenous Retroviral Elements (ERVs), remain to be identified. As a first step towards defining potential Yy2 functions matching or complementary to Yy1, we considered in vivo DNA binding sites of YY2 in trophoblast stem (TS) cells.
  
  
  
  We report the presence of YY2 protein in mouse-derived embryonic stem (ES) and TS cell lines. Following up on our previous report on ERV binding by YY2 in TS cells, we investigated the tissue-specificity of REX1 and YY2 binding and confirm binding to RE/ERV targets in both ES cells and TS cells. Because of the higher levels of expression, we chose TS cells to understand the role of Yy2 in gene and chromatin regulation. We used in vivo YY2 association as a measure to identify potential target genes. Sequencing of chromatin obtained in chromatin-immunoprecipitation (ChIP) assays carried out with αYY2 serum allowed us to identify a limited number of chromatin targets for YY2. Some putative binding sites were validated in regular ChIP assays and gene expression of genes nearby was altered in the absence of Yy2.
  
  
  
  YY2 binding to ERVs is not confined to TS cells. In vivo binding sites share the presence of a consensus binding motif. Selected sites were uniquely bound by YY2 as opposed to YY1, suggesting that YY2 exerts unique contributions to gene regulation. YY2 binding was not generally associated with gene promoters. However, several YY2 binding sites are linked to long noncoding RNA (lncRNA) genes and we show that the expression levels of a few of those are Yy2-dependent.
authors.affiliation: Instituto Aragonés de Ciencias de la Salud and Instituto de Investigación Sanitaria de Aragón (IIS-Aragón), Zaragoza, Spain.
authors.forename: Raquel
authors.initials: R
authors.lastname: Pérez-Palacios
authors.affiliation: Instituto Aragonés de Ciencias de la Salud and Instituto de Investigación Sanitaria de Aragón (IIS-Aragón), Zaragoza, Spain.
authors.forename: Sofía
authors.initials: S
authors.lastname: Macías-Redondo
authors.affiliation: Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza, C/ Miguel Servet 177, 50013 Zaragoza, Spain.
authors.forename: María
authors.initials: M
authors.lastname: Climent
authors.affiliation: ARAID Foundation, Zaragoza, Spain.|Estación Experimental de Aula Dei /CSIC, Av. Montañana 1.005, 50059 Zaragoza, Spain.
authors.forename: Bruno
authors.initials: B
authors.lastname: Contreras-Moreira
authors.affiliation: Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza, C/ Miguel Servet 177, 50013 Zaragoza, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Muniesa
authors.affiliation: Instituto Aragonés de Ciencias de la Salud and Instituto de Investigación Sanitaria de Aragón (IIS-Aragón), Zaragoza, Spain.|ARAID Foundation, Zaragoza, Spain.
authors.forename: Jon
authors.initials: J
authors.lastname: Schoorlemmer
mesh_terms: D000818:Animals; D001665:Binding Sites; D002460:Cell Line; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D053595:Embryonic Stem Cells / Q000378:metabolism*; D020077:Endogenous Retroviruses / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D011485:Protein Binding; D062085:RNA, Long Noncoding / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism*; D014327:Trophoblasts / Q000378:metabolism*; D050986:YY1 Transcription Factor / Q000378:metabolism
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding; C513672:Zfp42 protein, mouse; D014157:Transcription Factors; D050986:YY1 Transcription Factor; C509847:YY2 protein, mouse