Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans

Abstract

Long non-coding RNAs (lncRNAs) have important regulatory functions across eukarya. It is now clear that many of these functions are related to gene expression regulation through their capacity to recruit epigenetic modifiers and establish chromatin interactions. Several lncRNAs have been recently shown to participate in modulating chromatin within the spatial organization of the genome in the three-dimensional space of the nucleus. The identification of lncRNA candidates is challenging, as it is their functional characterization. Conservation signatures of lncRNAs are different from those of protein-coding genes, making identifying lncRNAs under selection a difficult task, and the homology between lncRNAs may not be readily apparent. Here, we review the evidence for these higher-order genome organization functions of lncRNAs in animals and the evolutionary signatures they display.

Why lncRNAs were not conserved? Is it for adaptation?

“…However, sno-lncRNAs have not been identified yet and, their functions are still unknown. Moreover, sequence analysis among other lncRNAs have also uncovered that these sno-lnRNAs are semiconserved on the contrary the idea of most lncRNAs undergo rapid sequence evolution and may play important roles (Ulitsky et al, 2011;Ramírez-Colmenero et al, 2020). Due to their tissue specific expression nature, products of sno-lncRNAs, which could be snoRNA or lncRNA, should be investigated in further studies, also depending on condition matter.…”

“…To date, there has a passing acquaintance with lncRNA's secondary structure and the interaction between structure and function. In mammals, conservation of lncRNAs in primary sequence, and gene structure are rare at orthologous, indicating lncRNAs undergone rapid turnover during evolution (Kutter et al, 2012;Wood et al, 2013;Ramírez-Colmenero et al, 2020). Some mutations could favor evolutionarily positive selection by stabilizing RNA structures within lncRNAs.…”

“…However, plants are sessile organisms and need to cope with changing environmental conditions throughout their life cycles. Genotypic and phenotypic plasticity are the main components for coping with this variability and unpredictability of stress occurrence (Hilker and Schmülling, 2019;Ramírez-Colmenero et al, 2020). Rapid evolution of lncRNAs may be another force for adaptation to changing environment in plants.…”

“…evolve rapidly based on the comparison of lncRNA exons or mRNA untranslated regions or protein-coding sequences or (Marques and Ponting, 2009;Young et al, 2012;Ramírez-Colmenero et al, 2020).…”

Oncogenic Roles of Small Nucleolar RNA Host Gene 7 (SNHG7) Long Noncoding RNA in Human Cancers and Potentials

“…Thousands of lncRNA-related genes have been identified in the human genome and corresponding transcripts reported in large quantities by a large number ranging from 10,000 to 60,000 in human cells ( Guttman et al, 2009 ; Iyer et al, 2015 ). They have been identified in a wide variety of eukaryotic species, and several show conserved sequences among different organisms suggesting evolution pressure ( Ramírez-Colmenero et al, 2020 ). A number of exclusive properties have made lncRNAs different compared with regular mRNAs.…”