A candidate functional SNP rs7074440 in TCF7L2 alters gene expression through C‐FOS in hepatocytes

Abstract

The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies. However, the functional SNPs regulating TCF7L2 expression remain unclear. Here, we show that the SNP rs7074440 is a candidate functional SNP highly linked with rs7903146. A reporter plasmid with rs7074440 normal allele sequence exhibited 15-fold higher luciferase activity compared with risk allele sequence in hepatocytes, demonstrating a strong enhancer activity at rs7074440. Additionally, we identified C-FOS as an activator binding to the rs7074440 enhancer using a TFEL genome-wide screen method. Consistently, knockdown of C-FOS significantly reduced TCF7L2 expression in hepatocytes. Collectively, a novel enhancer regulating TCF7L2 expression was revealed through searching for functional SNPs.

Glucocorticoid receptor suppresses gene expression of Rev‐erbα (Nr1d1) through interaction with the CLOCK complex

“…In order to evaluate whether this promoter region is sufficient to produce circadian oscillation in vivo, we performed animal experiments using the in vivo Ad-luc analytical system originally developed by our laboratory [18,20,28,33]; Nr1d1-promoter-luc adenovirus was administered to mice, and luciferase reporter activities were measured in the liver using an IVIS imaging system. As shown in Fig.…”

FoxO-KLF15 pathway switches the flow of macronutrients under the control of insulin

“…Using our unique intra-organ promoter analysis technique ''in vivo Ad-luc'' analytical system (Murayama et al, 2019;Nishi-Tatsumi et al, 2017;Takeuchi et al, 2010Takeuchi et al, , 2016, we identified two important genomic regions within an unexplored area for the fasting response of the Klf15-1a gene in liver (Figures 1A, 1B, S1I, and S1J); in the previous studies of Klf15 gene promoter analysis (Asada et al, 2011;Shao et al, 2018;Shimizu et al, 2011), they analyzed only 1 k upstream and 1.3 k downstream regions of the exon 1c TSS, which did not cover the sufficient genomic regions required for the fasting response. Moreover, we clarified by a genome-wide screening method ''TFEL scan'' using our original cDNA library named Transcription Factor Expression Library (TFEL) covering nearly all the transcription (Piao et al, 2018;Takeuchi et al, 2016;Yahagi and Takeuchi, 2021) that the genomic regions are activated by FoxOs (FoxO1 and FoxO3a) both in cultured hepatocytes (Figures 2A and 2F) and in mouse liver tissue (Figures 3A,3D,3G,and 3J). Furthermore, it was shown that the FoxO-binding sequences are important for transcriptional activation during fasting (Figures 5A-5D) and FoxOs binding to the two sites increases in correlation with its increase in nuclear protein abundance during fasting (Figures 5C-5F).…”

“…To identify the trans-factors corresponding to the above identified cis-elements, we screened 1,588 genome-wide transcription factor genes included in our original cDNA library named Transcription Factor Expression Library (TFEL) as described previously (Piao et al, 2018;Takeuchi et al, 2016;Yahagi and Takeuchi, 2021). After three rounds of screening in HepG2 cells as shown in Figures 1C and S2A-S2C, FoxO3a transcription factor was identified as a candidate with the ability to up-regulate the luciferase activity of Klf15-core-luc.…”

Functional genomics elucidates regulatory mechanisms of Parkinson’s disease-associated variants

“…Considering that different LD thresholds (r 2 ) were used in different genetic studies to define whether interest SNPs were in LD, for example, Shriner et al [23] and Chen et al [24] used r 2 ≥ 0.3 to select variants in LD with the reported risk variants, Ardlie et al [25] showed that an r 2 of 1/3 might be useful for LD determination for genetic mapping, Lee et al [26] used r 2 > 0.5 and the schizophrenia working group of the Psychiatric Genomics Consortium [27] used r 2 > 0.6 to define whether flanking SNPs were in LD with the reported risk variants, we performed an extensive literature search to select a proper r 2 threshold in this study. We noted that r 2 > 0.6 was widely used to extract SNPs in high LD with the reported lead SNPs in many studies [28][29][30][31][32][33][34][35][36][37][38][39][40][41]. Of note, though r 2 > 0.8 was used to define SNPs in strong LD [42][43][44], we utilized the widely accepted threshold (r 2 > 0.6) in this study based on following considerations: First, r 2 > 0.6 was widely accepted to define SNPs in high LD with the reported index SNPs [28][29][30][31][32][33][34][35][36][37][38][39][40][41].…”