title: Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer.
abstract: HOXB7 encodes a transcription factor that is overexpressed in a number of cancers and encompasses many oncogenic functions. Previous results have shown it to promote cell proliferation, angiogenesis, epithelial-mesenchymal transition, DNA repair and cell survival. Because of its role in many cancers and tumorigenic processes, HOXB7 has been suggested to be a potential drug target. However, HOXB7 binding sites on chromatin and its targets are poorly known. The aim of our study was to identify HOXB7 binding sites on breast cancer cell chromatin and to delineate direct target genes located nearby these binding sites. We found 1,504 HOXB7 chromatin binding sites in BT-474 breast cancer cell line that overexpresses HOXB7. Seventeen selected binding sites were validated by ChIP-qPCR in several breast cancer cell lines. Furthermore, we analyzed expression of a large number of genes located nearby HOXB7 binding sites and found several new direct targets, such as CTNND2 and SCGB1D2. Identification of HOXB7 chromatin binding sites and target genes is essential to understand better the role of HOXB7 in breast cancer and mechanisms by which it regulates tumorigenic processes.
authors.affiliation: Research Programs' Unit, Genome-Scale Biology and Institute of Biomedicine, Medical Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors.forename: Henna
authors.initials: H
authors.lastname: Heinonen
authors.affiliation: Research Programs' Unit, Genome-Scale Biology and Institute of Biomedicine, Medical Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Lepikhova
authors.affiliation: Institute of Biomedicine/Physiology, University of Helsinki, Helsinki, Finland.
authors.forename: Biswajyoti
authors.initials: B
authors.lastname: Sahu
authors.affiliation: Research Programs' Unit, Genome-Scale Biology and Institute of Biomedicine, Medical Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors.forename: Henna
authors.initials: H
authors.lastname: Pehkonen
authors.affiliation: Institute of Biomedicine/Physiology, University of Helsinki, Helsinki, Finland.
authors.forename: Päivi
authors.initials: P
authors.lastname: Pihlajamaa
authors.affiliation: Research Programs' Unit, Genome-Scale Biology and Institute of Biomedicine, Medical Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors.forename: Riku
authors.initials: R
authors.lastname: Louhimo
authors.affiliation: Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
authors.forename: Ping
authors.initials: P
authors.lastname: Gao
authors.affiliation: Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
authors.forename: Gong-Hong
authors.initials: GH
authors.lastname: Wei
authors.affiliation: Research Programs' Unit, Genome-Scale Biology and Institute of Biomedicine, Medical Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors.forename: Sampsa
authors.initials: S
authors.lastname: Hautaniemi
authors.affiliation: Institute of Biomedicine/Physiology, University of Helsinki, Helsinki, Finland.
authors.forename: Olli A
authors.initials: OA
authors.lastname: Jänne
authors.affiliation: Research Programs' Unit, Genome-Scale Biology and Institute of Biomedicine, Medical Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland.
authors.forename: Outi
authors.initials: O
authors.lastname: Monni
mesh_terms: D001665:Binding Sites; D001943:Breast Neoplasms / Q000378:metabolism*; D051177:Catenins / Q000378:metabolism; D045744:Cell Line, Tumor; D002843:Chromatin / Q000235:genetics* / Q000473:pathology; D047369:Chromatin Immunoprecipitation / Q000379:methods; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D061986:MCF-7 Cells; D060765:Secretoglobins / Q000378:metabolism; D000095002:Delta Catenin
chemical_list: D051177:Catenins; D002843:Chromatin; C490538:HOXB7 protein, human; D018398:Homeodomain Proteins; C556464:SCGB1D2 protein, human; D060765:Secretoglobins; D000095002:Delta Catenin; C000722348:CTNND2 protein, human
keywords: ChIP-seq; HOXB7; binding site; breast cancer; target gene