title: The transcriptional regulator BCL6 participates in the secondary gene regulatory response to vitamin D.
abstract: The vitamin D metabolite 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) is the high affinity ligand of the transcription factor vitamin D receptor (VDR) and therefore a direct regulator of transcription. Transcriptome-wide analysis of THP-1 human monocytes had indicated more than 600 genes to be significantly (p<0.05) stimulated after 4h incubation with 1,25(OH)2D3, but only 67 of them where more than 1.5-fold up-regulated. These include the genes encoding for the transcription factors BCL6, NFE2, POU4F2 and ELF4, which are controlled by one or two VDR binding sites within their chromosomal domains. The latter are defined via DNA loop formation mediated by the transcription factor CTCF that is highly conserved in its genome-wide loci. We found BCL6 being most responsive to 1,25(OH)2D3 and selected it for further analysis. An incubation of THP-1 cells with 1,25(OH)2D3 for 24 h resulted in a significant (p<0.001) change in the mRNA expression of more than 1600 genes, of which 132 were at least 2-fold up-regulated. About half of the latter genes are secondary 1,25(OH)2D3 targets, since they do not carry any VDR binding site within their chromosomal domain. Chromatin immunoprecipitation sequencing datasets indicated that the majority of these domains contain a BCL6 binding site. We followed the secondary transcriptional response to 1,25(OH)2D3 for eight representative gene examples and confirmed the binding of CTCF and BCL6 to their respective chromosomal domains. In conclusion, our study indicated that in monocytes most of the physiological responses to 1,25(OH)2D3 involve the action of the transcription factor BCL6.
authors.affiliation: School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
authors.forename: Veijo
authors.initials: V
authors.lastname: Nurminen
authors.affiliation: School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
authors.forename: Antonio
authors.initials: A
authors.lastname: Neme
authors.affiliation: School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
authors.forename: Jussi
authors.initials: J
authors.lastname: Ryynänen
authors.affiliation: School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
authors.forename: Sami
authors.initials: S
authors.lastname: Heikkinen
authors.affiliation: School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
authors.forename: Sabine
authors.initials: S
authors.lastname: Seuter
authors.affiliation: School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland. Electronic address: carsten.carlberg@uef.fi.
authors.forename: Carsten
authors.initials: C
authors.lastname: Carlberg
mesh_terms: D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002460:Cell Line; D004268:DNA-Binding Proteins / Q000096:biosynthesis* / Q000378:metabolism; D005786:Gene Expression Regulation / Q000187:drug effects; D006801:Humans; D050984:NF-E2 Transcription Factor, p45 Subunit / Q000096:biosynthesis* / Q000378:metabolism; D011485:Protein Binding; D051560:Proto-Oncogene Proteins c-bcl-6; D012333:RNA, Messenger / Q000096:biosynthesis; D018167:Receptors, Calcitriol / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D050820:Transcription Factor Brn-3B / Q000096:biosynthesis* / Q000378:metabolism; D014157:Transcription Factors / Q000096:biosynthesis* / Q000378:metabolism; D015533:Transcriptional Activation / Q000187:drug effects; D014807:Vitamin D / Q000008:administration & dosage* / Q000031:analogs & derivatives
chemical_list: C084103:BCL6 protein, human; D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D004268:DNA-Binding Proteins; C111931:ELF4 protein, human; D050984:NF-E2 Transcription Factor, p45 Subunit; C494692:NFE2 protein, human; C494190:POU4F2 protein, human; D051560:Proto-Oncogene Proteins c-bcl-6; D012333:RNA, Messenger; D018167:Receptors, Calcitriol; D012097:Repressor Proteins; D050820:Transcription Factor Brn-3B; D014157:Transcription Factors; C579457:VDR protein, human; C118756:dihydroxy-vitamin D3; D014807:Vitamin D
keywords: BCL6; ChIP-seq; FAIRE-seq; Secondary transcriptional response; VDR; Vitamin D