Plants use RNA interference for basal antiviral immunity, but emerging evidence suggests that additional RNA-targeting defense mechanisms also defend against invading viruses. Recent advancements in the understanding of RNA decay, RNA quality control, and N6-methyladenosine (m6A) RNA modifications have unveiled new insights into the molecular arms race between plants and viruses.

mRNA surveillance pathways are essential for accurate gene expression and to maintain translation homeostasis, ensuring the production of fully functional proteins. Future insights into mRNA quality control pathways will enable us to understand how cellular mRNA levels are controlled, how defective or unwanted mRNAs can be eliminated, and how dysregulation of these can contribute to human disease. Here we review translation-coupled mRNA quality control mechanisms, including the non-stop and no-go mRNA decay pathways, describing their mechanisms, shared trans-acting factors, and differences. We also describe advances in our understanding of the nonsense-mediated mRNA decay (NMD) pathway, highlighting recent mechanistic findings, the discovery of novel factors, as well as the role of NMD in cellular physiology and its impact on human disease.

Plant varieties exhibiting unstable or variegated phenotypes, or showing virus recovery have long remained a mystery. It is only with the development of transgenic plants 40 years ago that the epigenetic features underlying these phenomena were elucidated. Indeed, the study of transgenic plants that did not express the introduced sequences revealed that transgene loci sometimes undergo transcriptional gene silencing (TGS) or post-transcriptional gene silencing (PTGS) by activating epigenetic defenses that naturally control transposable elements, duplicated genes or viruses. Even when they do not trigger TGS or PTGS spontaneously, stably expressed transgenes driven by viral promoters set apart from endogenous genes in their epigenetic regulation. As a result, transgenes driven by viral promoters are capable of undergoing systemic PTGS throughout the plant, whereas endogenous genes can only undergo local PTGS in cells where RNA quality control is impaired. Together, these results indicate that the host genome distinguishes self from non-self at the epigenetic level, allowing PTGS to eliminate non-self, and preventing PTGS to become systemic and kill the plant when it is locally activated against deregulated self.
Les phénotypes instables ou mosaïques de certaines variétés de plantes, et la capacité de certaines plantes à récupérer après une infection virale sont longtemps demeurés des mystères. Ce n’est qu’avec le développement des plantes transgéniques il y a 40 ans que les caractéristiques épigénétiques de ces phénomènes ont été élucidées. En effet, l’étude de plantes transgéniques qui n’exprimaient pas les séquences introduites a révélé que les transgènes pouvaient parfois subir une extinction transcriptionnelle (TGS) ou post-transcriptionnelle (PTGS) en activant des défenses épigénétiques endogènes naturellement dirigées contre les éléments transposables, les gènes dupliqués ou les virus. Même lorsqu’ils ne subissent pas le TGS ou le PTGS spontanément, les transgènes exprimés de façon stable sous le contrôle de promoteurs viraux se distinguent des gènes endogènes par leurs caractéristiques épigénétiques. Il en résulte que les transgènes exprimés sous le contrôle de promoteurs viraux sont capables de subir un PTGS systémique dans l’ensemble de la plante, alors que les gènes endogènes ne peuvent subir qu’un PTGS restreint aux cellules où le contrôle de qualité des ARN (RQC) est défectueux. L’ensemble de ces données indique que le génome des plantes distingue le soi du non-soi au niveau épigénétique, permettant d’une part au PTGS d’éliminer le non-soi, et d’autre part d’empêcher le PTGS de devenir systémique et de tuer la plante quand il est activé localement pour éliminer le soi défectueux.

Cellular senescence, a hallmark of aging, is defined as irreversible cell cycle arrest in response to various stimuli. It plays both beneficial and detrimental roles in cellular homeostasis and diseases. Quality control (QC) is important for the proper maintenance of cellular homeostasis. The QC machineries regulate the integrity of RNA and protein by repairing or degrading them, and are dysregulated during cellular senescence. QC dysfunction also contributes to multiple age-related diseases, including cancers and neurodegenerative, muscle, and cardiovascular diseases. In this review, we describe the characters of cellular senescence, discuss the major mechanisms of RNA and protein QC in cellular senescence and aging, and comprehensively describe the involvement of these QC machineries in age-related diseases. There are many open questions regarding RNA and protein QC in cellular senescence and aging. We believe that a better understanding of these topics could propel the development of new strategies for addressing age-related diseases.

The transcriptome of a tissue can be acquired both by single-cell RNAseq (scRNA-seq) and by spatial transcriptomics (ST). The dissociation step, which is mandatory in scRNA-seq methods, might lead to the loss of fragile cells and of spatial information, thus limiting the acquisition of the tissue cellular organization. Spatial transcriptomics methods moderate the above-mentioned issues and provide single-cell transcripts detection over an intact fresh frozen tissue section. Visium platform, commercialized from 10× Genomics, provides a whole transcriptome spatial transcriptomics platform, which does not require dedicated instruments, other than those available in any pathology laboratory. In spatial transcriptomics, proper tissue handling is mandatory to preserve the morphological quality of the tissue sections and the integrity of mRNA transcripts. Proper tissue handling is critical for downstream library preparation and sequencing performance. In this chapter, we describe the most critical steps of Visium protocol on fresh frozen tissues and we provide indications on how to interpret the data obtained from the quality control analysis recommended during the workflow.

Transcriptome-wide interrogation of eukaryotic genomes has unveiled the pervasive nature of RNA polymerase II transcription. Virtually, any DNA region with an accessible chromatin structure can be transcribed, resulting in a mass production of noncoding RNAs (ncRNAs) with the potential of interfering with gene expression programs. Budding yeast has proved to be a powerful model organism to understand the mechanisms at play to control pervasive transcription and overcome the risks of hazardous disruption of cellular functions. In this review, we focus on the actors and strategies yeasts employ to govern ncRNA production, and we discuss recent findings highlighting the dangers of losing control over pervasive transcription.

RNA quality control pathways are critical for cell survival. Here, we describe a new surveillance process involved in the degradation of highly structured and stable ribosomal RNAs. The results demonstrated that the RNA chaperone Hfq and the 3\'-5\' exoribonuclease R mediate the elimination of detrimental rRNA fragments and are required for the correct processing of rRNA precursors. Escherichia coli cells lacking both Hfq and RNase R accumulate a high level of 16S- and 23S-derived rRNA fragments. Hfq and RNase R were also shown to participate in the maturation of 16S and 23S rRNA precursors. This correlates with the fact that in the absence of Hfq and RNase R, there are severe ribosome assembly defects and a sharp reduction in 70S ribosome levels. Hfq and RNase R may act independently or in a complex, as protein interaction studies revealed that these RNA-binding proteins can associate. This is the first demonstration that the well-conserved Hfq and RNase R proteins act on common regulatory pathways, unraveling previously unknown mechanisms of rRNA surveillance with important consequences for translation and cell survival.IMPORTANCE Quality control pathways that oversee the quality of stable RNA molecules are critical for the cell. In this work, we demonstrate, for the first time, a functional link between Hfq and RNase R in the processing and degradation of the highly structured rRNAs. These RNA-binding proteins are required for the maturation of 16S and 23S rRNAs and correct ribosome assembly. Furthermore, they participate in the degradation of rRNAs and clearance of toxic rRNA fragments from the cell. Our studies have also shown that Hfq and RNase R can form a complex. In summary, the cooperation between Hfq and RNase R in metabolic pathways of stable RNAs may represent a broader mechanism of RNA quality control, given the high conservation of these RNA-binding proteins throughout evolution.

RNA is a crucial component of every living organism and is necessary for gene expression and its regulation in the cell. Mechanisms of RNA synthesis (especially mRNA synthesis) were a subject of extensive study for a long time. More recently, RNA degradation pathways began to be considered as equally important part of eukaryotic cell metabolism. These pathways have been studied intensely, and ample information accumulated about RNA degradation systems and their role in cell life. It is currently obvious that RNA decay is of no less importance as RNA synthesis and contributes to regulating the RNA level in the cell. The review considers the main RNA degradation enzymes, the decay pathways of various coding and non-coding RNAs, the mechanisms providing RNA quality control in the nucleus and cytoplasm, and certain structural elements responsible for RNA stability or short life in the cell.

Nonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the endoplasmic reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Furthermore, we show that NBAS fulfills an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 coregulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER-protective function by ensuring quality control of ER-translated mRNAs.

PI3K-related kinases (PIKKs) are large Serine/Threonine (Ser/Thr)-protein kinases central to the regulation of many fundamental cellular processes. PIKK family member SMG1 orchestrates progression of an RNA quality control pathway, termed nonsense-mediated mRNA decay (NMD), by phosphorylating the NMD factor UPF1. Phosphorylation of UPF1 occurs in its unstructured N- and C-terminal regions at Serine/Threonine-Glutamine (SQ) motifs. How SMG1 and other PIKKs specifically recognize SQ motifs has remained unclear. Here, we present a cryo-electron microscopy (cryo-EM) reconstruction of a human SMG1-8-9 kinase complex bound to a UPF1 phosphorylation site at an overall resolution of 2.9 Å. This structure provides the first snapshot of a human PIKK with a substrate-bound active site. Together with biochemical assays, it rationalizes how SMG1 and perhaps other PIKKs specifically phosphorylate Ser/Thr-containing motifs with a glutamine residue at position +1 and a hydrophobic residue at position -1, thus elucidating the molecular basis for phosphorylation site recognition.
The instructions for producing proteins in the cell are copied from DNA to molecules known as messenger RNA. If there is an error in the messenger RNA, this causes incorrect proteins to be produced that could potentially kill the cell. Cells have a special detection system that spots and removes any messenger RNA molecules that contain errors, which would result in the protein produced being too short. For this error-detecting system to work, a protein called UPF1 must be modified by an enzyme called SMG1. This enzyme only binds to and modifies the UPF1 protein at sites that contain a specific pattern of amino acids – the building blocks that proteins are made from. However, it remained unclear how SMG1 recognizes this pattern and interacts with UPF1. Now, Langer et al. have used a technique known as cryo-electron microscopy to image human SMG1 bound to a segment of UPF1. These images were then used to generate the three-dimensional structure of how the two proteins interact. This high-resolution structure showed that protein building blocks called leucine, serine and glutamine are the recognized pattern of amino acids. To further understand the role of the amino acids, Langer et al. replaced them one-by-one with different amino acids to see how each affected the interaction between the two proteins. This revealed that SMG1 preferred leucine at the beginning of the recognized pattern and glutamine at the end when binding to UPF1. SMG1 is member of an important group of enzymes that are involved in various error detecting systems. This is the first time that a protein from this family has been imaged together with its target and these findings may also be relevant to other enzymes in this family. Furthermore, the approach used to determine the structure of SMG1 and the structural information itself could also be used in drug design to improve the accuracy with which drugs identify their targets.