Long non-coding RNA: its evolutionary relics and biological implications in mammals: a review

Abstract

The central dogma of gene expression propounds that DNA is transcribed to mRNA and finally gets translated into protein. Only 2–3% of the genomic DNA is transcribed to protein-coding mRNA. Interestingly, only a further minuscule part of genomic DNA encodes for long non-coding RNAs (lncRNAs) which are characteristically more than 200 nucleotides long and can be transcribed from both protein-coding (e.g. H19 and TUG1) as well as non-coding DNA by RNA polymerase II. The lncRNAs do not have open reading frames (with some exceptions), 3`-untranslated regions (3’-UTRs) and necessarily these RNAs lack any translation-termination regions, however, these can be spliced, capped and polyadenylated as mRNA molecules. The flexibility of lncRNAs confers them specific 3D-conformations that eventually enable the lncRNAs to interact with proteins, DNA or other RNA molecules via base pairing or by forming networks. The lncRNAs play a major role in gene regulation, cell differentiation, cancer cell invasion and metastasis and chromatin remodeling. Deregulation of lncRNA is also responsible for numerous diseases in mammals. Various studies have revealed their significance as biomarkers for prognosis and diagnosis of cancer. The aim of this review is to overview the salient features, evolution, biogenesis and biological importance of these molecules in the mammalian system.

Transcriptome Analyses of lncRNAs in A2E-Stressed Retinal Epithelial Cells Unveil Advanced Links between Metabolic Impairments Related to Oxidative Stress and Retinitis Pigmentosa

“…These lncRNAs interact with Cyclin D1 (CCND1) mRNA, whose encoding gene is already known to transcribe a specific lncRNA in DNA damage condition, and that exists on chromatin both as RNA:DNA hybrids and ssRNA, acting as transcription repressor [83]. Furthermore, various lncRNAs could exert their role outside the nucleus, hybridizing with the 3 untranslated regions (3 UTRs) of mRNAs to regulate their stability in the cytoplasm and/or interacting with miRNAs and RNA decay factors [84]. We found at least 40 lncRNAs, the most of which are antisense lncRNAs, acting as miRNA sponges, and they were mostly down-regulated.…”

Prospects and challenges of multi-omics data integration in toxicology

“…However, a significant portion of the transcriptional response controlled by a specific pathway can consist of non-protein-coding RNAs (ncRNAs), e.g., Hackermüller et al (2014). NcRNAs have been shown to participate in a range of different cellular pathways and seem to be particularly relevant for fine tuning the gene expression of eukaryotic cells (Cech and Steitz 2014;Dhanoa et al 2018). For more than a decade, transcriptomics mainly relied on microarrays as a measurement technique.…”

The cellular landscape of mid‐size noncoding RNA

“…Noncoding RNAs are often subdivided into long and small RNAs around a cut‐off of 200 nucleotides. The long noncoding RNAs over 200 nucleotides are mostly generated from intergenic regions (Brosnan & Voinnet, ; Dhanoa, Sethi, Verma, Arora, & Mukhopadhyay, ; Zampetaki, Albrecht, & Steinhofel, ). However, the small noncoding RNAs are a disparate and heterogeneous group of distinct RNA families.…”

“…Finally, we provide a portrait of the challenges facing their detection and annotation in databases. (Brosnan & Voinnet, 2009;Dhanoa, Sethi, Verma, Arora, & Mukhopadhyay, 2018;Zampetaki, Albrecht, & Steinhofel, 2018). However, the small noncoding RNAs are a disparate and heterogeneous group of distinct RNA families.…”