title: Characterisation of genome-wide PLZF/RARA target genes.
abstract: The PLZF/RARA fusion protein generated by the t(11;17)(q23;q21) translocation in acute promyelocytic leukaemia (APL) is believed to act as an oncogenic transcriptional regulator recruiting epigenetic factors to genes important for its transforming potential. However, molecular mechanisms associated with PLZF/RARA-dependent leukaemogenesis still remain unclear.We searched for specific PLZF/RARA target genes by ChIP-on-chip in the haematopoietic cell line U937 conditionally expressing PLZF/RARA. By comparing bound regions found in U937 cells expressing endogenous PLZF with PLZF/RARA-induced U937 cells, we isolated specific PLZF/RARA target gene promoters. We next analysed gene expression profiles of our identified target genes in PLZF/RARA APL patients and analysed DNA sequences and epigenetic modification at PLZF/RARA binding sites. We identify 413 specific PLZF/RARA target genes including a number encoding transcription factors involved in the regulation of haematopoiesis. Among these genes, 22 were significantly down regulated in primary PLZF/RARA APL cells. In addition, repressed PLZF/RARA target genes were associated with increased levels of H3K27me3 and decreased levels of H3K9K14ac. Finally, sequence analysis of PLZF/RARA bound sequences reveals the presence of both consensus and degenerated RAREs as well as enrichment for tissue-specific transcription factor motifs, highlighting the complexity of targeting fusion protein to chromatin. Our study suggests that PLZF/RARA directly targets genes important for haematopoietic development and supports the notion that PLZF/RARA acts mainly as an epigenetic regulator of its direct target genes.
authors.affiliation: Centre d'Immunologie de Marseille-Luminy, Université de la Méditerranée, Campus de Luminy, Marseille, France.
authors.forename: Salvatore
authors.initials: S
authors.lastname: Spicuglia
authors.forename: Christelle
authors.initials: C
authors.lastname: Vincent-Fabert
authors.forename: Touati
authors.initials: T
authors.lastname: Benoukraf
authors.forename: Guillaume
authors.initials: G
authors.lastname: Tibéri
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Saurin
authors.forename: Joaquin
authors.initials: J
authors.lastname: Zacarias-Cabeza
authors.forename: David
authors.initials: D
authors.lastname: Grimwade
authors.forename: Ken
authors.initials: K
authors.lastname: Mills
authors.forename: Boris
authors.initials: B
authors.lastname: Calmels
authors.forename: François
authors.initials: F
authors.lastname: Bertucci
authors.forename: Michael
authors.initials: M
authors.lastname: Sieweke
authors.forename: Pierre
authors.initials: P
authors.lastname: Ferrier
authors.forename: Estelle
authors.initials: E
authors.lastname: Duprez
mesh_terms: D000107:Acetylation; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D015973:Gene Expression Regulation, Leukemic; D055106:Genome-Wide Association Study; D006657:Histones / Q000378:metabolism; D006801:Humans; D051741:Kruppel-Like Transcription Factors / Q000235:genetics / Q000378:metabolism; D015473:Leukemia, Promyelocytic, Acute / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D008745:Methylation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015514:Oncogene Proteins, Fusion / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D000075722:Promyelocytic Leukemia Zinc Finger Protein; D011485:Protein Binding; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D020298:U937 Cells
chemical_list: D006657:Histones; D051741:Kruppel-Like Transcription Factors; D015514:Oncogene Proteins, Fusion; C118318:PLZF-RARalpha fusion protein, human; D000075722:Promyelocytic Leukemia Zinc Finger Protein; D014157:Transcription Factors; C092037:ZBTB16 protein, human