Abstract
Long non-coding RNAs (lncRNAs) are usually located in the nucleus and cytoplasm of cells. The transcripts of lncRNAs are >200 nucleotides in length and do not encode proteins. Compared with small RNAs, lncRNAs have longer sequences, more complex spatial structures, and more diverse and complex mechanisms involved in the regulation of gene expression. LncRNAs are widely involved in the biological processes of cells, and in the occurrence and development of many human diseases. Many studies have shown that lncRNAs can induce the occurrence of diseases, and some lncRNAs undergo specific changes in tumor cells. Research into the roles of lncRNAs has covered the diagnosis of, for example, cardiovascular, cerebrovascular, and central nervous system diseases. The bioinformatics of lncRNAs has gradually become a research hotspot and has led to the discovery of a large number of lncRNAs and associated biological functions, and lncRNA databases and recognition models have been developed. In this review, the research progress of lncRNAs is discussed, and lncRNA-related databases and the mechanisms and modes of action of lncRNAs are described. In addition, disease-related lncRNA methods and the relationships between lncRNAs and human lung adenocarcinoma, rectal cancer, colon cancer, heart disease, and diabetes are discussed. Finally, the significance and existing problems of lncRNA research are considered.
Highlights
A long transcription product was discovered and identified by Okazaki in 2002 (Okazaki et al, 2003) when sequencing a mouse cDNA library
They have been classified according to the position of the Long non-coding RNAs (lncRNAs) in the genome relative to the target protein-coding gene as 1) antisense lncRNA, which is partially or completely complementary to the transcription product on the opposite strand; 2) enhancer lncRNA, which is produced from the enhancer region of a protein coding gene; 3) bidirectional lncRNA, which shares the same promoter with protein-coding genes, LncRNAs and Related Diseases but the transcription direction is opposite; 4) intronic lncRNA, which is produced by introns of genes; and 5) large intergenic non-coding RNA, which is independently transcribed from sequences located between protein-coding genes (Figure 1)
In 2013, Chen et al (Chen and Yan, 2013) developed a semi-supervised learning framework LRLSLDA based on Laplace regularization least squares by integrating lncRNA expression profiles and known lncRNA–disease associations
Summary
A long transcription product was discovered and identified by Okazaki in 2002 (Okazaki et al, 2003) when sequencing a mouse cDNA library. 3) NRED (Dinger et al, 2009) provides the expression information of thousands of lncRNAs of humans and mice from microarray and in situ hybridization data, as well as auxiliary information such as secondary structure evidence, antisense relationships, evolutionary conservation, and genome-related text links LncRNAs can regulate gene expression at the epigenetic (Mercer and Mattick, 2013), transcriptional (Bonasio and Shiekhattar, 2014), and post-transcriptional (Yoon et al, 2013) levels They participate in important regulatory processes such as X chromosome silencing, genome imprinting, chromatin modification, transcription activation and inhibition, and nuclear transport. LncRNAs bind to proteins that have transcriptional regulatory functions (e.g., transcription factors and chromosome folding proteins), thereby regulating the transcriptional activation and inhibition of related genes by controlling the activity of molecules and signal pathways. The 5′ end of HOTAIR combines with the PRC2 complex (acting on H3 and H27 to methylate them) to promote gene expression (Rinn et al, 2007), whereas the 3′ end of HOTAIR combines with LSD1 (acting on H3K4 to demethylate it) to antagonize gene expression activation (Tsai et al, 2010), thereby inducing the interaction between the PRC2 and LSD1 complexes
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