Abstract
The first reference to the “C-value paradox” reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.
Highlights
Unlike in prokaryotes, genomes in eukaryotes exhibit a large variability in their size [1,2], which does not always correlate with the number of protein-coding genes nor the developmental complexity of organisms
SEPALLATA 3 (SEP3) is a member of the plant MADS (MCM1-AGAMOUS-DEFICIENS-SRF)-box transcription factor superfamily involved in flower development, and modifications of SEP3 splicing gives rise to floral homeotic phenotypes [52,53]
SEP3 exon 6 circRNA can directly interact with its cognate DNA locus, forming an RNA:DNA hybrid (R-loop), which results in transcriptional pausing and correlates with the recruitment of splicing factors and alternative splicing (AS)
Summary
Genomes in eukaryotes exhibit a large variability in their size [1,2], which does not always correlate with the number of protein-coding genes nor the developmental complexity of organisms. The noncoding genome, long considered silent and declared as “junk DNA” due to its high content in pseudogenes, simple repeats, and transposons [8,9], encodes a plethora of noncoding RNAs (ncRNAs) with unarguable biological functions. LncRNAs form the most diversified group of ncRNAs, exhibiting a large range of sizes varying from 200 bases to over 100 kb in length They are expressed in various tissues, cell-types, and cell-states, and function in the nucleus or cytoplasm [11,12]. We report and integrate recent discoveries about plant lncRNA-mediated regulations of post-transcriptional gene expression
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