title: Characterization of the transcriptional machinery bound across the widely presumed type 2 diabetes causal variant, rs7903146, within TCF7L2.
abstract: Resolving the underlying functional mechanism to a given genetic association has proven extremely challenging. However, the strongest associated type 2 diabetes (T2D) locus reported to date, TCF7L2, presents an opportunity for translational analyses, as many studies in multiple ethnicities strongly point to SNP rs7903146 in intron 3 as being the causal variant within this gene. We carried out oligo pull-down combined with mass spectrophotometry (MS) to elucidate the specific transcriptional machinery across this SNP using protein extracts from HCT116 cells. We observed that poly (ADP-ribose) polymerase 1 (PARP-1) is by far the most abundant binding factor. Pursuing the possibility of a feedback mechanism, we observed that PARP-1, along with the next most abundant binding proteins, DNA topoisomerase I and ATP-dependent RNA helicase A, dimerize with the TCF7L2 protein and with each other. We uncovered further evidence of a feedback mechanism using a luciferase reporter approach, including observing expression differences between alleles for rs7903146. We also found that there was an allelic difference in the MS results for proteins with less abundant binding, namely X-ray repair cross-complementing 5 and RPA/p70. Our results point to a protein complex binding across rs7903146 within TCF7L2 and suggests a possible mechanism by which this locus confers its T2D risk.
authors.affiliation: Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Qianghua
authors.initials: Q
authors.lastname: Xia
authors.affiliation: Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Sandra
authors.initials: S
authors.lastname: Deliard
authors.affiliation: Department of Proteomics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Chao-Xing
authors.initials: CX
authors.lastname: Yuan
authors.affiliation: Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Johnson
authors.affiliation: 1] Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA [2] Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA [3] Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Struan F A
authors.initials: SF
authors.lastname: Grant
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D045744:Cell Line, Tumor; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics* / Q000378:metabolism*; D005786:Gene Expression Regulation; D006801:Humans; D009154:Mutation; D000071137:Poly (ADP-Ribose) Polymerase-1; D011065:Poly(ADP-ribose) Polymerases / Q000378:metabolism; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D058118:Transcription Factor 7-Like 2 Protein / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D058118:Transcription Factor 7-Like 2 Protein; C499320:PARP1 protein, human; D000071137:Poly (ADP-Ribose) Polymerase-1; D011065:Poly(ADP-ribose) Polymerases