AUTHOR=Manning Alisa K. , Goustin Anton Scott , Kleinbrink Erica L. , Thepsuwan Pattaraporn , Cai Juan , Ju Donghong , Leong Aaron , Udler Miriam S. , Brown James Bentley , Goodarzi Mark O. , Rotter Jerome I. , Sladek Robert , Meigs James B. , Lipovich Leonard 

TITLE=A Long Non-coding RNA, LOC157273, Is an Effector Transcript at the Chromosome 8p23.1-PPP1R3B Metabolic Traits and Type 2 Diabetes Risk Locus

JOURNAL=Frontiers in Genetics

VOLUME=Volume 11 - 2020

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00615

DOI=10.3389/fgene.2020.00615

ISSN=1664-8021

ABSTRACT=<sec><title>Aims</title><p>Causal transcripts at genomic loci associated with type 2 diabetes (T2D) are mostly unknown. The chr8p23.1 variant rs4841132, associated with an insulin-resistant diabetes risk phenotype, lies in the second exon of a long non-coding RNA (lncRNA) gene, <italic>LOC157273</italic>, located 175 kilobases from <italic>PPP1R3B</italic>, which encodes a key protein regulating insulin-mediated hepatic glycogen storage in humans. We hypothesized that <italic>LOC157273</italic> regulates expression of <italic>PPP1R3B</italic> in human hepatocytes.</p></sec><sec><title>Methods</title><p>We tested our hypothesis using Stellaris fluorescent <italic>in situ</italic> hybridization to assess subcellular localization of <italic>LOC157273</italic>; small interfering RNA (siRNA) knockdown of <italic>LOC157273</italic>, followed by RT-PCR to quantify <italic>LOC157273</italic> and <italic>PPP1R3B</italic> expression; RNA-seq to quantify the whole-transcriptome gene expression response to <italic>LOC157273</italic> knockdown; and an insulin-stimulated assay to measure hepatocyte glycogen deposition before and after knockdown.</p></sec><sec><title>Results</title><p>We found that siRNA knockdown decreased <italic>LOC157273</italic> transcript levels by approximately 80%, increased <italic>PPP1R3B</italic> mRNA levels by 1.7-fold, and increased glycogen deposition by &gt;50% in primary human hepatocytes. An A/G heterozygous carrier (vs. three G/G carriers) had reduced <italic>LOC157273</italic> abundance due to reduced transcription of the A allele and increased PPP1R3B expression and glycogen deposition.</p></sec><sec><title>Conclusion</title><p>We show that the lncRNA <italic>LOC157273</italic> is a negative regulator of <italic>PPP1R3B</italic> expression and glycogen deposition in human hepatocytes and a causal transcript at an insulin-resistant T2D risk locus.</p></sec>