Highly conserved and cis-acting lncRNAs produced from paralogous regions in the center of HOXA and HOXB clusters in the endoderm lineage

Long noncoding RNAs (lncRNAs) have been shown to play important roles in gene regulatory networks acting in early development. There has been rapid turnover of lncRNA loci during vertebrate evolution, with few human lncRNAs conserved beyond mammals. The sequences of these rare deeply conserved lncRNAs are typically not similar to each other. Here, we characterize HOXA-AS3 and HOXB-AS3, lncRNAs produced from the central regions of the HOXA and HOXB clusters. Sequence-similar orthologs of both lncRNAs are found in multiple vertebrate species and there is evident sequence similarity between their promoters, suggesting that the production of these lncRNAs predates the duplication of the HOX clusters at the root of the vertebrate lineage. This conservation extends to similar expression patterns of the two lncRNAs, in particular in cells transiently arising during early development or in the adult colon. Functionally, the RNA products of HOXA-AS3 and HOXB-AS3 regulate the expression of their overlapping HOX5–7 genes both in HT-29 cells and during differentiation of human embryonic stem cells. Beyond production of paralogous protein-coding and microRNA genes, the regulatory program in the HOX clusters therefore also relies on paralogous lncRNAs acting in restricted spatial and temporal windows of embryonic development and cell differentiation.     

High throughput deep sequencing elucidates the important role of lncRNAs in Foxtail millet response to herbicides

Long non-coding RNAs (lncRNAs) play an important function in plant growth and development as well as response to stresses. However, little information was known in foxtail millet; no study was reported on lncRNAs in plant response to herbicide treatment. In this study, by using deep sequencing and advanced bioinformatic analysis, a total of 2547 lncRNAs were identified, including 787 known and 1760 novel lncRNAs. These lncRNAs are distributed across all 9 chromosomes, and the majority were located in the intergenic region with 1–2 exons. These lncRNAs were differentially expressed between different genotypes under different herbicide treatments. lncRNAs regulate plant growth and development as well as response to herbicide treatments through targeting protein-coding genes that directly relate to chemical metabolism and defense system. Multiple potential target genes and lncRNA-mRNA-miRNA gene networks were discovered. These results elucidate the potential roles of lncRNAs in plant response to herbicides.     

Sequence Fingerprints of MicroRNA Conservation

It is known that the conservation of protein-coding genes is associated with their sequences both various species, such as animals and plants. However, the association between microRNA (miRNA) conservation and their sequences in various species remains unexplored. Here we report the association of miRNA conservation with its sequence features, such as base content and cleavage sites, suggesting that miRNA sequences contain the fingerprints for miRNA conservation. More interestingly, different species show different and even opposite patterns between miRNA conservation and sequence features. For example, mammalian miRNAs show a positive/negative correlation between conservation and AU/GC content, whereas plant miRNAs show a negative/positive correlation between conservation and AU/GC content. Further analysis puts forward the hypothesis that the introns of protein-coding genes may be a main driving force for the origin and evolution of mammalian miRNAs. At the 5′ end, conserved miRNAs have a preference for base U, while less-conserved miRNAs have a preference for a non-U base in mammals. This difference does not exist in insects and plants, in which both conserved miRNAs and less-conserved miRNAs have a preference for base U at the 5′ end. We further revealed that the non-U preference at the 5′ end of less-conserved mammalian miRNAs is associated with miRNA function diversity, which may have evolved from the pressure of a highly sophisticated environmental stimulus the mammals encountered during evolution. These results indicated that miRNA sequences contain the fingerprints for conservation, and these fingerprints vary according to species. More importantly, the results suggest that although species share common mechanisms by which miRNAs originate and evolve, mammals may develop a novel mechanism for miRNA origin and evolution. In addition, the fingerprint found in this study can be predictor of miRNA conservation, and the findings are helpful in achieving a clearer understanding of miRNA function and evolution.     

Large-scale study of long non-coding RNA functions based on structure and expression features

Mammals and other complex organisms can transcribe an abundance of long non-coding RNAs (lncRNAs) that fulfill a wide variety of regulatory roles in many biological processes. These roles, including as scaffolds and as guides for protein-coding genes, mainly depend on the structure and expression level of lncRNAs. In this review, we focus on the current methods for analyzing lncRNA structure and expression, which is basic but necessary information for in-depth, large-scale analysis of lncRNA functions.