(RNA-binding motif protein 3) is a stress responsive gene, which maintains cellular homeostasis and promotes survival upon various harmful cellular stimuli. Rbm3 protein shows conserved structural and molecular similarities to heterogeneous nuclear ribonucleoproteins (hnRNPs), which regulate all steps of the mRNA metabolism. Growing evidence is pointing towards a broader role of Rbm3 in various steps of gene expression. Here, we demonstrate that Rbm3 deficiency is linked to transcriptome-wide pre-mRNA splicing alterations, which can be reversed through Rbm3 co-expression from a cDNA. Using an MS2 tethering assay, we show that Rbm3 regulates splice site selection similar to other hnRNP proteins when recruited between two competing 5 splice sites. Furthermore, we show that the N-terminal part of Rbm3 encompassing the RNA recognition motif (RRM), is sufficient to elicit changes in splice site selection. On the basis of these findings, we propose a novel, undescribed function of Rbm3 in RNA splicing that contributes to the preservation of transcriptome integrity.

The estrogen signalling pathway is highly dynamic and primarily mediated by estrogen receptors (ERs) that transcriptionally regulate the expression of target genes. While transcriptional functions of ERs have been widely studied, their roles in RNA biology have not been extensively explored. Here, we reveal a novel biological role of ER alpha (ERα) in mRNA 3' end processing in breast cancer cells, providing an alternative mechanism in regulating gene expression at the post-transcriptional level. We show that ERα activates poly(A) specific ribonuclease (PARN) deadenylase using assays, and that this activation is further increased by tumour suppressor p53, a factor involved in mRNA processing. Consistent with this, we confirm ERα-mediated activation of nuclear deadenylation by PARN in samples from MCF7 and T47D breast cancer cells that vary in expression of ERα and p53. We further show that ERα can form complex(es) with PARN and p53. Lastly, we identify and validate expression of common mRNA targets of ERα and PARN known to be involved in cell invasion, metastasis and angiogenesis, supporting the functional overlap of these factors in regulating gene expression in a transactivation-independent manner. Together, these results show a new regulatory mechanism by which ERα regulates mRNA processing and gene expression post-transcriptionally, highlighting its contribution to unique transcriptomic profiles and breast cancer progression.

Although long noncoding RNAs (lncRNAs) constitute the majority of the human transcriptome, the functional roles of most remain elusive. While protein-coding genes in macrophage biology have been extensively studied, the contribution of lncRNAs in this context is poorly understood. Given the vast number of lncRNAs (>20,000), identifying candidates for functional characterization poses a significant challenge. Here, we present two complementary approaches to pinpoint and investigate lncRNAs involved in monocyte-to-macrophage differentiation: RNA-seq for functional inference and a high-throughput functional screen. These strategies enabled us to identify four lncRNA regulators of monocyte differentiation: , , , and . Preliminary insights suggest these lncRNAs may act in through neighbouring protein-coding genes, although their precise mechanisms remain to be elucidated. We further discuss the strengths and weaknesses of these methodologies, along with validation pipelines crucial for establishing lncRNA functionality.

Approximately 45% of the human genome is comprised of transposable elements (TEs), also known as mobile genetic elements. However, their biological function remains largely unknown. Among them, retrotransposons are particularly abundant, and some of the copies are still capable of mobilization within the genome through RNA intermediates. This review focuses on the life cycle of human retrotransposons and summarizes their regulatory mechanisms and impacts on cellular processes. Retrotransposons are generally epigenetically silenced in somatic cells, but are transcriptionally reactivated under certain conditions, such as tumorigenesis, development, stress, and ageing, potentially leading to genetic instability. We explored the dual nature of retrotransposons as genomic parasites and regulatory elements, focusing on their roles in genetic diversity and innate immunity. Furthermore, we discuss how host factors regulate retrotransposon RNA and cDNA intermediates through their binding, modification, and degradation. The interplay between retrotransposons and the host machinery provides insight into the complex regulation of retrotransposons and the potential for retrotransposon dysregulation to cause aberrant responses leading to inflammation and autoimmune diseases.

Research on the origin of life investigates the transition from abiotic chemistry to the emergence of biology, with the 'RNA world hypothesis' as the leading theory. RNA's dual role in storage and catalysis suggests its importance in this narrative. The discovery of natural ribozymes emphasizes RNA's catalytic capabilities in prebiotic environments, supporting the plausibility of an RNA world and prompting exploration of precellular evolution. Collective autocatalytic sets (CASs) mark a crucial milestone in this transition, fostering complexity through autocatalysis. While modern biology emphasizes sequence-specific polymerases, remnants of CASs persist in primary metabolism highlighting their significance. Autocatalysis, driven by CASs, promotes complexity through mutually interdependent catalytic sets. Yet, the transition from ribonucleotides to complex RNA oligomers remains puzzling. Questions persist about the genesis of the first self-replicating RNA molecule, RNA's stability in prebiotic conditions, and the shift to complex molecular reproduction. This review delves into diverse facets of the RNA world's emergence, addressing critical bottlenecks and scientific advances. Integrating insights from simulation and in vitro evolution research, we illuminate the multistep biogenesis of catalytic RNA from the abiotic world. Through this exploration, we aim to elucidate the journey from the primordial soup to the dawn of life, emphasizing the interplay between chemistry and biology in understanding life's origins.

SRP9/SRP14 is a protein heterodimer that plays a critical role in the signal recognition particle through its interaction with the scaffolding signal recognition particle RNA (7SL). SRP9/SRP14 binding to 7SL is mediated through a conserved structural motif that is shared with the primate-specific Alu RNA. Alu RNA are transcription products of Alu elements, a retroelement that comprises ~10% of the human genome. Alu RNA are involved in myriad biological processes and are dysregulated in several human disease states. This review focuses on the roles SRP9/SRP14 has in regulating Alu RNA diversification, maturation, and function. The diverse mechanisms through which SRP9/SRP14 regulates Alu RNA exemplify the breadth of protein-mediated regulation of non-coding RNA.

2'--ribose methylation (2'--Me) is one of the most common RNA modifications detected in ribosomal RNAs (rRNA) from bacteria to eukaryotic cells. 2'--Me favours a specific RNA conformation and protects RNA from hydrolysis. Moreover, rRNA 2'--Me might stabilize its interactions with messenger RNA (mRNA), transfer RNA (tRNA) or proteins. The extent of rRNA 2'--Me fluctuates between species from 3-4 sites in bacteria to tens of sites in archaea, yeast, algae, plants and human. Depending on the organism as well as the rRNA targeting site and position, the 2'--Me reaction can be carried out by several site-specific RNA methyltransferases (RMTase) or by a single RMTase associated to specific RNA guides. Here, we review current progresses in rRNA 2'--Me (sites/Nm and RMTases) in plants and compare the results with molecular clues from unicellular (bacteria, archaea, algae and yeast) as well as multicellular (human and plants) organisms.

Regulatory non-coding RNAs (ncRNAs) are increasingly recognized as integral to the control of biological processes. This is often through the targeted regulation of mRNA expression, but this is by no means the only mechanism through which regulatory ncRNAs act. The Gene Ontology (GO) has long been used for the systematic annotation of protein-coding and ncRNA gene function, but rapid progress in the understanding of ncRNAs meant that the ontology needed to be revised to accurately reflect current knowledge. Here, a targeted effort to revise GO terms used for the annotation of regulatory ncRNAs is described, focusing on microRNAs (miRNAs), long non-coding RNAs (lncRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). This paper provides guidance to biocurators annotating ncRNA-mediated processes using the GO and serves as background for researchers wishing to make use of the GO in their studies of ncRNAs and the biological processes they regulate.

In an RNA world, the emergence of template-specific self-replication and catalysis necessitated the presence of motifs facilitating reliable recognition between RNA molecules. What did these motifs entail, and how did they evolve into the proteinaceous RNA recognition entities observed today? Direct observation of these primordial entities is hindered by rapid degradation over geological time scales. To overcome this challenge, researchers employ diverse approaches, including scrutiny of conserved sequences and structural motifs across extant organisms and employing directed evolution experiments to generate RNA molecules with specific catalytic abilities. In this review, we delve into the theme of ribonucleotide recognition across key periods of early Earth's evolution. We explore scenarios of RNA interacting with small molecules and examine hypotheses regarding the role of minerals and metal ions in enabling structured ribonucleotide recognition and catalysis. Additionally, we highlight instances of RNA-protein mimicry in interactions with other RNA molecules. We propose a hypothesis where RNA initially recognizes small molecules and metal ions/minerals, with subsequent mimicry by proteins leading to the emergence of proteinaceous RNA binding domains.

In , transport of magnesium ions across the cellular membrane relies on MgtA and CorA transporters. While the expression of is controlled by the two-component system PhoQ/PhoP and 5' upstream region elements, expression is considered to be constitutive and not to depend on cellular factors. Importantly, the 5' upstream region of is predicted to fold into structures highly similar to the magnesium-sensing 5' upstream region. Here using biochemical and genetic assays, we show that the intracellular concentration of magnesium ions affects expression. Similarly to , we find that the effect of magnesium ions on expression is mediated by the 5' upstream region. We demonstrate that the RNA structure is important for regulation and that the Rho transcription factor is involved in the modulation of transcription termination. Consistent with previous studies, we find that translation of , a short ORF located within the 5' upstream region, is important for regulation. Our data indicate that the efficiency of translation is inversely proportional to expression, similar to what has been described for and in . Using a novel assay to control the import of magnesium ions, we show that while the expression of is regulated by both extra- and intracellular magnesium ions, is regulated by variations in intracellular magnesium ions. Our results support a model in which the expression of is regulated by the 5' upstream region that senses variations of intracellular magnesium ions.

Next-generation sequencing has revolutionized cancer genomics by enabling high-throughput mutation screening yet detecting fusion genes reliably remains challenging. Long-read sequencing offers potential for accurate fusion transcript identification, though challenges persist. In this study, we present an optimized workflow using nanopore sequencing technology to precisely identify fusion transcripts. Our approach encompasses a tailored library preparation protocol, data processing, and fusion gene analysis pipeline. We evaluated the performance using Universal Human Reference RNA and human adenocarcinoma cell lines. Our optimized nanopore sequencing workflow generated high-quality full-length transcriptome data characterized by an extended length distribution and comprehensive transcript coverage. Validation experiments confirmed novel fusion events with potential clinical relevance. Our protocol aims to mitigate biases and enhance accuracy, facilitating increased adoption in clinical diagnostics. Continued advancements in long-read sequencing promise deeper insights into fusion gene biology and improved cancer diagnostics.

Circular RNAs (circRNAs) exhibit a wide range of activities that allow them to participate in numerous cellular processes and make them relevant in a variety of diseases. In this regard, a key process in which circRNAs are involved, and which is the focus of this article, is DNA damage repair (DDR). This study aims to illustrate how circRNAs influence different DNA repair pathways, with particular emphasis on the underlying mechanisms. In addition, the potential medical applications of this knowledge are discussed, particularly in the diagnosis, prognosis and treatment of diseases. In this sense, circRNAs were found to play a crucial role in DNA repair processes by regulating the expression and activity of proteins involved in various DNA repair pathways. They influence the expression of DNA repair proteins by interacting with their mRNAs, sponging miRNAs that target these mRNAs, regulating transcription factors that bind to their promoters, modulating upstream signalling pathways, and affecting mRNA translation. Furthermore, circRNAs regulate the activity of DNA repair proteins by interacting directly with them, sequestering them in specific cellular compartments and controlling activation signalling or upstream DDR signalling.

Bulk increases in nucleobase oxidation, most commonly manifesting as the guanine (G) nucleobase modification 8-oxo-7,8-dihydroguanine (8-oxoG), have been linked to several disease pathologies. Elucidating the effects of RNA oxidation on cellular homoeostasis is limited by a lack of effective tools for detecting specific regions modified with 8-oxoG. Building on a previously published method for studying 8-oxoG in DNA, we developed ChLoRox-Seq, which works by covalently functionalizing 8-oxoG sites in RNA with biotin. Importantly, this method enables antibody-free enrichment of 8-oxoG-containing RNA fragments for Next Generation Sequencing-based detection of modified regions transcriptome-wide. We demonstrate the high specificity of ChLoRox-Seq for functionalizing 8-oxoG over unmodified nucleobases in RNA and benchmark this specificity to a commonly used antibody-based approach. Key advantages of ChLoRox-Seq include: (1) heightened resolution of RNA oxidation regions (e.g. exon-level) and (2) lower experimental costs. By applying ChLoRox-Seq to mRNA extracted from human lung epithelial cells (BEAS-2B) after exposure to environmentally relevant stress, we observe that 8-oxoG modifications tend to cluster in regions that are G-rich and within mRNA transcripts possessing longer 5' UTR and CDS regions. These findings provide new insight into the complex mechanisms that bias the accumulation of RNA oxidation across the transcriptome. Notably, our analysis suggests the possibility that most mRNA oxidation events are probabilistically driven and that mRNAs that possess more favourable intrinsic properties are prone to incur oxidation events at elevated rates. ChLoRox-Seq can be readily applied in future studies to identify regions of elevated RNA oxidation in any cellular model of interest.

The vast majority of oxygen-utilizing eukaryotes need to express their own mitochondrial genome, mtDNA, to survive. In comparison to size of their nuclear genome, mtDNA is minimal, even in the most exceptional examples. Having evolved from bacteria in an endosymbiotic event, it might be expected that the process of mtDNA expression would be relatively simple. The aim of this short review is to illustrate just how wrong this assumption is. The production of functional mitochondrial RNA across species evolved in many directions. Organelles use a dizzying array of RNA processing, modifying, editing, splicing and maturation events that largely require the import of nuclear-encoded proteins from the cytosol. These processes are sometimes driven by the unusual behaviour of the mitochondrial genome from which the RNA is originally transcribed, but in many examples the complex processes that are essential for the production of functional RNA in the organelle, are fascinating and bewildering.

Long non-coding RNAs (lncRNAs) have received growing attention due to their diverse regulatory roles in cancer, including in melanoma, an aggressive type of skin cancer. The plasticity and phenotypic adaptability of melanoma cells are crucial factors contributing to therapeutic resistance. The identification of molecules playing key roles in melanoma cell plasticity could unravel novel and more effective therapeutic targets. This review presents current concepts of melanoma cell plasticity, illustrating its fluidity and dismissing the outdated notion of epithelial-mesenchymal-like transition as a simplistic binary process. Emphasis is placed on the pivotal role of lncRNAs in orchestrating cell plasticity, employing various mechanisms recently elucidated and unveiling their potential as promising targets for novel therapeutic strategies. Insights into the molecular mechanisms coordinated by lncRNAs in melanoma pave the way for the development of RNA-based therapies, holding great promise for enhancing treatment outcomes and offering a glimpse into a more effective approach to melanoma treatment.

The process of adenosine deaminase (ADAR)-catalyzed double-stranded RNA (dsRNA) Adenosine-to-Inosine (A-to-I) editing is essential for the correction of pathogenic mutagenesis, as well as the regulation of gene expression and protein function in mammals. The significance of dsRNA A-to-I editing in disease development and occurrence is explored using inferential statistics and cluster analyses to investigate the enzymes involved in dsRNA editing that can catalyze editing sites across multiple biomarkers. This editing process, which occurs in coding or non-coding regions, has the potential to activate abnormal signalling pathways that contributes to disease pathogenesis. Notably, the ADAR family enzymes play a crucial role in initiating the editing process. ADAR1 is upregulated in most diseases as an oncogene during tumorigenesis, whereas ADAR2 typically acts as a tumour suppressor. Furthermore, this review also provides an overview of small molecular inhibitors that disrupt the expression of ADAR enzymes. These inhibitors not only counteract tumorigenicity but also alleviate autoimmune disorders, neurological neurodegenerative symptoms, and metabolic diseases associated with aberrant dsRNA A-to-I editing processes. In summary, this comprehensive review offers detailed insights into the involvement of dsRNA A-to-I editing in disease pathogenesis and highlights the potential therapeutic roles for related small molecular inhibitors. These scientific findings will undoubtedly contribute to the advancement of personalized medicine based on dsRNA A-to-I editing.

Ischaemic stroke is a leading cause of death and life-long disability due to neuronal cell death resulting from interruption of glucose and oxygen supplies. RNA polymerase III (Pol III)-dependent transcription plays a central role in protein synthesis that is necessary for normal cerebral neuronal functions, and the survival and recovery under pathological conditions. Notably, Pol III transcription is highly sensitive to ischaemic stress that is known to rapidly shut down Pol III transcriptional activity. However, its precise role in ischaemic stroke, especially during the acute and recovery phases, remains poorly understood. The microenvironment within the ischaemic brain undergoes dynamic changes in different phases after stroke. Emerging evidence highlights the distinct roles of Pol III transcription in neuroprotection during the acute phase and repair during the recovery phase of stroke. Additionally, investigations into the mTOR-MAF1 signalling pathway, a conserved regulator of Pol-III transcription, reveal its therapeutic potential in enhancing acute phase neuroprotection and recovery phase repair.

RNA helicases are an evolutionary conserved class of nucleoside triphosphate dependent enzymes found in all kingdoms of life. Their cellular functions range from transcription regulation up to maintaining genomic stability and viral defence. As dysregulation of RNA helicases has been shown to be involved in several cancers and various diseases, RNA helicases are potential therapeutic targets. However, for selective targeting of a specific RNA helicase, it is crucial to develop a detailed understanding about its dynamics and regulation on a molecular and structural level. Deciphering unique features of specific RNA helicases is of fundamental importance not only for future drug development but also to deepen our understanding of RNA helicase regulation and function in cellular processes. In this review, we discuss recent insights into regulation mechanisms of RNA helicases and highlight models which demonstrate the interplay between helicase structure and their functions.

N6-methyladenosine (m6A) is widely recognized as the predominant form of RNA modification in higher organisms, with the capability to finely regulate RNA metabolism, thereby influencing a series of crucial physiological and pathological processes. These processes include regulation of gene expression, cell proliferation, invasion and metastasis, cell cycle control, programmed cell death, interactions within the tumour microenvironment, energy metabolism, and immune regulation. With advancing research into the mechanisms of RNA methylation, the pivotal role of m6A modification in the pathophysiology of reproductive system tumours, particularly cervical cancer, has been progressively unveiled. This discovery has opened new research avenues and presented significant potential for the diagnosis, prognostic evaluation, and treatment of diseases. This review delves deeply into the biological functions of m6A modification and its mechanisms of action in the onset and progression of cervical cancer. Furthermore, it explores the prospects of m6A modification in the precision diagnosis and treatment of cervical cancer, aiming to provide new perspectives and a theoretical basis for innovative and advanced treatment strategies for cervical cancer.

General RNA chaperones are RNA-binding proteins (RBPs) that interact transiently and non-specifically with RNA substrates and assist in their folding into their native state. In bacteria, these chaperones impact both coding and non-coding RNAs and are particularly important for large, structured RNAs which are prone to becoming kinetically trapped in misfolded states. Currently, due to the limited number of well-characterized examples and the lack of a consensus structural or sequence motif, it is difficult to identify general RNA chaperones in bacteria. Here, we adapted a previously published RNA regional accessibility probing assay to screen genome wide for intracellular factors in affecting RNA folding, among which we aimed to uncover novel RNA chaperones. Through this method, we identified eight proteins whose deletion gives changes in regional accessibility within the exogenously expressed group I intron ribozyme. Furthermore, we purified and measured properties of two of these proteins, YagL and PepA, which were especially attractive as general chaperone candidates. We showed that both proteins bind RNA and that YagL accelerates native refolding of the ribozyme from a long-lived misfolded state. Further dissection of YagL showed that a putative helix-turn-helix (HTH) domain is responsible for most of its RNA-binding activity, but only the full protein shows chaperone activity. Altogether, this work expands the current repertoire of known general RNA chaperones in bacteria.