scholarly journals Genome-wide analysis of canonical Wnt target gene regulation inXenopus tropicalischallenges β-catenin paradigm

genesis ◽  
2017 ◽  
Vol 55 (1-2) ◽  
pp. e22991 ◽  
Author(s):  
Yukio Nakamura ◽  
Stefan Hoppler
Keyword(s):  
Gene Regulation ◽  
Target Gene ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Canonical Wnt

scholarly journals Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Jen-Hao Cheng ◽  
David Zhi-Chao Pan ◽  
Zing Tsung-Yeh Tsai ◽  
Huai-Kuang Tsai
Keyword(s):  
Gene Regulation ◽  
Genome Wide Analysis ◽  
Enhancer Rna ◽  
Genome Wide ◽  
Mouse Tissues

scholarly journals Pinpointing miRNA and genes enrichment over trait-relevant tissue network in Genome-Wide Association Studies

2020 ◽  
Vol 13 (S11) ◽  
Author(s):  
Binze Li ◽  
Julian Dong ◽  
Jiaqi Yu ◽  
Yuqi Fan ◽  
Lulu Shang ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Binding Affinity ◽  
Gene Network ◽  
Mirna Target ◽  
Target Gene ◽  
Genome Wide Association ◽  
Untranslated Regions ◽  
Regulation Mechanism ◽  
Mirna Target Gene ◽  
Genome Wide

Abstract Background Understanding gene regulation is important but difficult. Elucidating tissue-specific gene regulation mechanism is even more challenging and requires gene co-expression network assembled from protein–protein interaction, transcription factor and gene binding, and post-transcriptional regulation (e.g., miRNA targeting) information. The miRNA binding affinity could therefore be changed by SNP(s) located at the 3′ untranslated regions (3′UTR) of the target messenger RNA (mRNA) which miRNA(s) interacts with. Genome-wide association study (GWAS) has reported significant numbers of loci hosting SNPs associated with many traits. The goal of this study is to pinpoint GWAS functional variants located in 3′UTRs and elucidate if the genes harboring these variants along with their targeting miRNAs are associated with genetic traits relevant to certain tissues. Methods By applying MIGWAS, CoCoNet, ANNOVAR, and DAVID bioinformatics software and utilizing the gene expression database (e.g. GTEx data) to study GWAS summary statistics for 43 traits from 28 GWAS studies, we have identified a list of miRNAs and targeted genes harboring 3′UTR variants, which could contribute to trait-relevant tissue over miRNA-target gene network. Results Our result demonstrated that strong association between traits and tissues exists, and in particular, the Primary Biliary Cirrhosis (PBC) trait has the most significant p-value for all 180 tissues among all 43 traits used for this study. We reported SNPs located in 3′UTR regions of genes (SFMBT2, ZC3HAV1, and UGT3A1) targeted by miRNAs for PBC trait and its tissue association network. After employing Gene Ontology (GO) analysis for PBC trait, we have also identified a very important miRNA targeted gene over miRNA-target gene network, PFKL, which encodes the liver subunit of an enzyme. Conclusions The non-coding variants identified from GWAS studies are casually assumed to be not critical to translated protein product. However, 3′ untranslated regions (3′UTRs) of genes harbor variants can often change the binding affinity of targeting miRNAs playing important roles in protein translation degree. Our study has shown that GWAS variants could play important roles on miRNA-target gene networks by contributing the association between traits and tissues. Our analysis expands our knowledge on trait-relevant tissue network and paves way for future human disease studies.

scholarly journals The mechanisms of genome-wide target gene regulation by TCF7L2 in liver cells

2014 ◽  
Vol 42 (22) ◽  
pp. 13646-13661 ◽  
Author(s):  
Luke Norton ◽  
Xi Chen ◽  
Marcel Fourcaudot ◽  
Nikhil K. Acharya ◽  
Ralph A. DeFronzo ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Target Gene ◽  
Liver Cells ◽  
Genome Wide
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