Genomes and Genes
Affiliation: University of Eastern Finland
Location: Kuopio, Finland
- Polly P, Herdick M, Moehren U, Baniahmad A, Heinzel T, Carlberg C. VDR-Alien: a novel, DNA-selective vitamin D(3) receptor-corepressor partnership. FASEB J. 2000;14:1455-63 pubmed..Taken together, association of the VDR with corepressor proteins provides a further level of transcriptional regulation, which is emerging as a complex network of protein-protein interaction-mediated control. ..
- Frank C, Gonzalez M, Oinonen C, Dunlop T, Carlberg C. Characterization of DNA complexes formed by the nuclear receptor constitutive androstane receptor. J Biol Chem. 2003;278:43299-310 pubmed..This points to a physiological role for CAR monomers. Therefore, both CAR-RXR heterodimers and CAR monomers can contribute to the gene activating function of PBREMs in CAR target genes. ..
- Väisänen S, Dunlop T, Sinkkonen L, Frank C, Carlberg C. Spatio-temporal activation of chromatin on the human CYP24 gene promoter in the presence of 1alpha,25-Dihydroxyvitamin D3. J Mol Biol. 2005;350:65-77 pubmed....
- Thorne J, Maguire O, Doig C, Battaglia S, Fehr L, Sucheston L, et al. Epigenetic control of a VDR-governed feed-forward loop that regulates p21(waf1/cip1) expression and function in non-malignant prostate cells. Nucleic Acids Res. 2011;39:2045-56 pubmed publisher..Dissection of this feed-forward loop in a non-malignant prostate cell system illuminates mechanisms of sensitivity and therefore possible resistance in prostate and other VDR responsive cancers. ..
- Carlberg C, Dunlop T. The impact of chromatin organization of vitamin D target genes. Anticancer Res. 2006;26:2637-45 pubmed..These results will have an impact on the development of therapeutic regimes for diseases, such as cancer, that use 1alpha,25(OH)2D3 and its analogs. ..
- Carlberg C. Molecular basis of the selective activity of vitamin D analogues. J Cell Biochem. 2003;88:274-81 pubmed..This provides them with some selectivity for DNA-dependent and -independent signaling pathways and VDRE structures. ..
- Martens K, Ver Loren van Themaat E, van Batenburg M, Heinaniemi M, Huyghe S, Van Hummelen P, et al. Coordinate induction of PPAR alpha and SREBP2 in multifunctional protein 2 deficient mice. Biochim Biophys Acta. 2008;1781:694-702 pubmed publisher..These data demonstrate a tight interrelationship between induction of PPAR alpha by endogenous ligands and up-regulation of genes of cholesterol biosynthesis through increased expression of SREBP2. ..
- Jokela T, Makkonen K, Oikari S, Kärnä R, Koli E, Hart G, et al. Cellular content of UDP-N-acetylhexosamines controls hyaluronan synthase 2 expression and correlates with O-linked N-acetylglucosamine modification of transcription factors YY1 and SP1. J Biol Chem. 2011;286:33632-40 pubmed publisher....
- Turunen M, Dunlop T, Carlberg C, Väisänen S. Selective use of multiple vitamin D response elements underlies the 1 alpha,25-dihydroxyvitamin D3-mediated negative regulation of the human CYP27B1 gene. Nucleic Acids Res. 2007;35:2734-47 pubmed..This data explains, in part, why the human CYP27B1 gene is repressed in HEK-293 but not in MCF-7 cells. ..
- Seuter S, Väisänen S, Radmark O, Carlberg C, Steinhilber D. Functional characterization of vitamin D responding regions in the human 5-Lipoxygenase gene. Biochim Biophys Acta. 2007;1771:864-72 pubmed..This indicates DNA looping of the TSS to even very distant gene regions. In summary, we suggest that the upregulation of the primary 1alpha,25(OH)(2)D(3) target 5-LO is mediated in vivo by a prominent VDRE in intron 4. ..
- Makkonen K, Malinen M, Ropponen A, Väisänen S, Carlberg C. Cell cycle regulatory effects of retinoic Acid and forskolin are mediated by the cyclin C gene. J Mol Biol. 2009;393:261-71 pubmed publisher..This suggests that the primary regulation of Cyclin C by all-trans RA and Forskolin mediates some of the cell cycle control actions of these compounds. ..
- Degenhardt T, Matilainen M, Herzig K, Dunlop T, Carlberg C. The insulin-like growth factor-binding protein 1 gene is a primary target of peroxisome proliferator-activated receptors. J Biol Chem. 2006;281:39607-19 pubmed..We also show that these additional PPAR binding genes contain a number of candidate PPREs and that their mRNA levels respond quickly to the presence of PPAR ligands, indicating that they are also primary PPAR target genes. ..
- Heikkinen S, Väisänen S, Pehkonen P, Seuter S, Benes V, Carlberg C. Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy. Nucleic Acids Res. 2011;39:9181-93 pubmed publisher..In conclusion, ligand binding shifts the locations of VDR occupation to DR3-type REs that surround its target genes and occur in a large variety of regulatory constellations. ..
- Kriebitzsch C, Verlinden L, Eelen G, van Schoor N, Swart K, Lips P, et al. 1,25-dihydroxyvitamin D3 influences cellular homocysteine levels in murine preosteoblastic MC3T3-E1 cells by direct regulation of cystathionine β-synthase. J Bone Miner Res. 2011;26:2991-3000 pubmed publisher..In conclusion, this study showed that cbs is a primary 1,25(OH)(2) D(3) target gene which renders HCY metabolism responsive to 1,25(OH)(2) D(3). ..
- Matilainen J, Malinen M, Turunen M, Carlberg C, Väisänen S. The number of vitamin D receptor binding sites defines the different vitamin D responsiveness of the CYP24 gene in malignant and normal mammary cells. J Biol Chem. 2010;285:24174-83 pubmed publisher..In conclusion, our data suggest that in comparison to normal cells, clearing of 1alpha,25(OH)(2)D(3) is enhanced in malignant cells due to differences in transcriptional regulation of CYP24 and metabolism of CYP24 mRNA. ..
- Lou Y, Molnár F, PERAKYLA M, Qiao S, Kalueff A, St Arnaud R, et al. 25-Hydroxyvitamin D(3) is an agonistic vitamin D receptor ligand. J Steroid Biochem Mol Biol. 2010;118:162-70 pubmed publisher..In conclusion, 25-hydroxyvitamin D(3) is an agonistic vitamin D receptor ligand with gene regulatory and anti-proliferative properties. ..
- Dunlop T, Väisänen S, Frank C, Molnár F, Sinkkonen L, Carlberg C. The human peroxisome proliferator-activated receptor delta gene is a primary target of 1alpha,25-dihydroxyvitamin D3 and its nuclear receptor. J Mol Biol. 2005;349:248-60 pubmed....
- Singh P, van den Berg P, Long M, Vreugdenhil A, Grieshober L, Ochs Balcom H, et al. Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes. BMC Genomics. 2017;18:132 pubmed publisher..Our work provides a framework for the combination of ChIP-seq and GWAS findings to provide insight into the underlying phenotype-associated biology of a given transcription factor. ..