Fig. 1.

Human HNF4A-AS1, a liver-enriched lncRNA with a stable structure, is predominantly located in the nucleus. (A) Schematic representation of HNF4A-AS1 on chromosome 20 based on the University of California, Santa Cruz Genome Browser tracks showing peak signals of H3K4me1, H3K4me3, H3K27Ac, DNase, and mammalian conservation. (B) The mfe structure of HNF4A-AS1. The secondary structure of HNF4A-AS1 was predicted based on mfe (−223.01 kcal/mol). The base colors in the figure change with the entropy value. The more biased to red, the smaller the entropy of the corresponding base and the greater the probability offorming a pair. (C) A mountain plot of HNF4A-AS1. A mountain plot containing the mfe structure, partition function (pf) structure, and centroid structures. These curves are closely related, which indicates that the secondary structure of HNF4A-AS1 is stable. The height (y-axis) of the mountain plot represents the base pairs containing sequence positions in the x-axis. (D) RNA levels of HNF4A-AS1 across 27 different human tissues from NCBI database. (E and F) qRT-PCR Real-time qRT-PCR was used to reveal the enrichment levels of HNF4A-AS1 and HNF4A in the nuclei and cytoplasm of both Huh7 and HepG2 cells. U1 and GAPDH were used as nuclear and cytoplasmic markers, respectively. Data are shown as the means ± S.D. of three independent experiments.