Aims
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,
LOC157273, located 175 kilobases from
PPP1R3B, which encodes a key protein regulating insulin-mediated hepatic glycogen storage in humans. We hypothesized that
LOC157273 regulates expression of
PPP1R3B in human hepatocytes.
Methods
We tested our hypothesis using Stellaris fluorescent
in situ hybridization to assess subcellular localization of
LOC157273; small interfering RNA (siRNA) knockdown of
LOC157273, followed by RT-PCR to quantify
LOC157273 and
PPP1R3B expression; RNA-seq to quantify the whole-transcriptome gene expression response to
LOC157273 knockdown; and an insulin-stimulated assay to measure hepatocyte glycogen deposition before and after knockdown.
Results
We found that siRNA knockdown decreased
LOC157273 transcript levels by approximately 80%, increased
PPP1R3B mRNA levels by 1.7-fold, and increased glycogen deposition by >50% in primary human hepatocytes. An A/G heterozygous carrier (vs. three G/G carriers) had reduced
LOC157273 abundance due to reduced transcription of the A allele and increased PPP1R3B expression and glycogen deposition.
Conclusion
We show that the lncRNA
LOC157273 is a negative regulator of
PPP1R3B expression and glycogen deposition in human hepatocytes and a causal transcript at an insulin-resistant T2D risk locus.
