The evolution of lncRNA repertoires and expression patterns in tetrapods

Abstract

Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.

The human RBPome: From genes and proteins to human disease

“…Further, tissue specificity of the expression pattern was estimated using an index that varies between zero (for housekeeping genes) and one (observed for tissue specific genes) [25,26]. We then calculated the tissue specificity scores for 17 well known housekeeping genes [27] and these resulted in an average tissue specificity score of 0.63.…”

“…A complete linkage hierarchical clustering of the expression levels ( Figure 4A) groups tissues exhibiting similar levels of expression. Further, the tissue specificity of the expression pattern was estimated using an index [25,26] that varies between zero (for housekeeping genes) and one (observed for tissue specific genes). Genes that resulted in an index of 0.7 or higher were termed tissue-specific and the rest of them were classified as ubiquitous (Materials and Methods, Supplementary Table 4).…”

Biotin-Lys-His Blocks Aggregation of RNA-binding Protein TLS, a Cause of Amyotrophic Lateral Sclerosis

“…Mutations in TLS might cause these RNA metabolic functions, suggesting its function as a mediator for biologically active RNA molecules. a Cause of Amyotrophic Lateral Sclerosis Biology of RNA has been highlighting more impact on modern science extending the previous views for the RNA metabolism that is just oriented to a step of gene expression at the process of the Central Dogma [10][11][12][13][14][15][16][17][18][19]. The extensive works on transcriptome inspections of the human genome-derived RNAs enlighten huge numbers of RNAs transcribed from noncoding regions of the human genome [20][21][22].…”

Deep homology in the age of next-generation sequencing

“…As a consequence, comparative large-scale transcriptome studies, covering different species and tissue types, have emerged in recent years as a powerful approach to address questions of morphological evolution and homology [43]. These approaches have been used across several taxonomic levels, from comparing transcriptomes of closely related species in a given genus, to spanning the entire metazoan kingdom [44][45][46]. Such studies are a powerful proof of how one can now go far beyond the standard realm of model organisms, eliminating the need to focus on just a select few taxa [47,48].…”