Case 1 Characterization and identification of lncRNA in maize
Background
lncRNAs play an important regulatory role in gene expression at multiple levels in eukaryotes, but the amount, characteristics and genetic pattern of expression of lncRNAs in maize remain largely unknown at present
Study
By analyzing maize EST, whole genome, and RNA-seq data, 20,163 lncRNAs were predicted from them, and it was hypothesized that more than 90% of them might be precursors of small RNAs, and 1704 were highly plausible lncRNAs. RNA-Seq data results from 13 different tissues and 105 maize recombinant self-incompatibility lines showed that lncRNAs have a strong of tissue specificity. This study provides a unique resource of maize genome annotation and genome-wide characterization of maize lncRNAs, and the genetic pattern of maize lncRNA expression pattern was obtained using eQTL analysis.
Results
The highly plausible 1704 lncRNAs were found to have an average length of 463 bp, and the lncRNAs contained fewer exons compared to functional genes, with 81% containing only one exon.
RNA-seq results in 13 tissues and 105 RILs materials showed that more than 50% of these lncRNAs had tissue expression specificity.
The eQTL localization analysis revealed that lncRNAs in maize are more regulated by trans than cis.

图1. lncRNA在玉米的10条染色体的分布

Figure 2. Location of lncRNA eQTL in maize seeds
Case 2 PVT1 promotes gallbladder cancer proliferation by inhibiting miR-18b-5p through DNA methylation
Background
Gallbladder cancer (GBC) is the most common biliary tract cancer, and the lack of early diagnosis, abnormal invasiveness, and chemoresistance has led to its poor overall prognosis with a 5-10% 5-year survival rate. With the rapid development of sequencing technology, a novel type of regulatory genes with lengths exceeding 200 nucleotides, long noncoding RNAs (lncRNAs), have been recognized to play important biological roles in physiological and pathological development. In recent years, there is increasing evidence that dysregulation of lncRNAs is involved in cancer progression.
Study
The novel lncRNA PVT1 plays an important role in the progression of GBC as an oncogene. PVT1 is upregulated in GBC tissues and cells, and its upregulation is associated with poor prognosis in GBC patients. PVT1 promotes GBC cell proliferation and increases tumorigenicity in nude mice. In addition, miR-18b-5p down-regulated by PVT1 was screened by miRNA microarray analysis. Mechanistically, PVT1 promotes miR-18b-5p DNA promoter methylation by recruiting DNMT1 through EZH2 and then represses its expression.
Results.
lncRNA PVT1 expression was upregulated in GBC tissues and cells, and high PVT1 expression correlated with the prognosis of GBC patients. lncRNA PVT1 knockdown inhibited GBC cell proliferation in vitro and in vivo. In addition, PVT1 facilitated DNA promoter methylation of miR-18b-5p through recruitment of DNMT1 by EZH2, which in turn attenuated the inhibitory effect of miR-18b-5p on HIF1A and ultimately mediated GBC progression.

Figure 1: miR-18b-5p down-regulates HIF1A and promotes GBC cell proliferation in vitro
reference:
1. Li L, Eichten S R, Shimizu R, et al. Genome-wide discovery and characterization of maize long non-coding RNAs[J]. Genome Biology, 2014, 15(2):R40.
2.Jin, L., Cai, Q., Wang, S. et al. Long noncoding RNA PVT1 promoted gallbladder cancer proliferation by epigenetically suppressing miR-18b-5p via DNA methylation[J]. Cell Death Dis 11, 871 (2020).