Regulation of mature mRNA levels by RNA processing efficiency

The enigma of introns: Intronic miRNA-directed mechanisms and alternative splicing diversify alternative oxidase potential in Vitis vinifera

Alternative oxidase (AOX) transcript levels were associated with efficiently balanced respiration and validated to assist selection on multiple-resilience. Consistently, AOX has also been identified as a target for weakening the survival capabilities of parasites and microorganisms responsible for severe human diseases. Despite the unique features of AOX in Vitis vinifera, particularly intense constitutive expression of AOX2 in the presence of unusually large introns that challenge the dogma of gene expression in eukaryotes, V. vinifera has been overlooked in AOX research. This study uncovered two distinct alternative splicing variants of the AOX: AOX1a-Alternative variant attributed to unusual retention of the intron-4 in the 3´UTR, and AOX2-alternative variant, which is intron-1-dependent, involving the skipping of exon-1. The AOX2-alternative variant differed in that cystine-I changed to serine, which is linked to different metabolite stimulation. However, molecular docking suggested that AOX2 and the variant proteins exhibit the same catalytic activities and binding affinities for ubiquinol. The unique large introns in AOX2 exhibited 16 miRNAs, including the master regulator of development and stress responses, mir-398. Among these, nine were conserved and validated in other plant species, whereas seven were considered potential novel miRNA candidates. Transcriptome analyses revealed down- and up-regulation of AOX1a-Alternative during shrivelling and water deficiency, and up-regulation of AOX2-Alternative with increasing temperatures. Consistent with previous studies, AOX1a and AOX1d were linked to biotic and abiotic stress, whereas AOX2 showed constitutive or developmental regulation. This study encourages hypothesis-driven advanced research on early mechanisms and functionality of newly discovered alternative splicing events and intronic miRNAs. Given functional marker-assisted breeding, it strengthened the requirement to consider overall AOX transcript levels as markers for predicting multiple-resilient phenotypes.

Nuclear mRNA decay: regulatory networks that control gene expression

Proper regulation of mRNA production in the nucleus is critical for the maintenance of cellular homoeostasis during adaptation to internal and environmental cues. Over the past 25 years, it has become clear that the nuclear machineries governing gene transcription, pre-mRNA processing, pre-mRNA and mRNA decay, and mRNA export to the cytoplasm are inextricably linked to control the quality and quantity of mRNAs available for translation. More recently, an ever-expanding diversity of new mechanisms by which nuclear RNA decay factors finely tune the expression of protein-encoding genes have been uncovered. Here, we review the current understanding of how mammalian cells shape their protein-encoding potential by regulating the decay of pre-mRNAs and mRNAs in the nucleus.

DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3'-end of genes and involved in the recycling of cleavage factors

mRNA biogenesis in the eukaryotic nucleus is a highly complex process. The numerous RNA processing steps are tightly coordinated to ensure that only fully processed transcripts are released from chromatin for export from the nucleus. Here, we present the hypothesis that fission yeast Dbp2, a ribonucleoprotein complex (RNP) remodelling ATPase of the DEAD-box family, is the key enzyme in an RNP assembly checkpoint at the 3'-end of genes. We show that Dbp2 interacts with the cleavage and polyadenylation complex (CPAC) and localises to cleavage bodies, which are enriched for 3'-end processing factors and proteins involved in nuclear RNA surveillance. Upon loss of Dbp2, 3'-processed, polyadenylated RNAs accumulate on chromatin and in cleavage bodies, and CPAC components are depleted from the soluble pool. Under these conditions, cells display an increased likelihood to skip polyadenylation sites and a delayed transcription termination, suggesting that levels of free CPAC components are insufficient to maintain normal levels of 3'-end processing. Our data support a model in which Dbp2 is the active component of an mRNP remodelling checkpoint that licenses RNA export and is coupled to CPAC release.