RNA Biol [JOURNAL]
Sun
200 papers
Multipurpose RNA maturation factors dysregulate multiple mRNA processing steps simultaneously and provide new therapeutic opportunities.
Paira S, Borden KLB
RNA Biol · 2025 Dec · PMID 40485569 · Full text
mRNAs undergo a series of chemical modifications to become competent for nuclear export and translation. This is referred to as mRNA maturation or processing and includes capping, splicing, and 3'end formation. These ste...
mRNAs undergo a series of chemical modifications to become competent for nuclear export and translation. This is referred to as mRNA maturation or processing and includes capping, splicing, and 3'end formation. These steps can be hijacked in cancer to alter proteins' forms and levels in the absence of mutation or changes to transcript levels. Here, we focus on an emerging idea that some factors act in multiple processing events and that their dysregulation in both their canonical and noncanonical functions contributes to cancer with a focus on Acute Myeloid Leukaemia (AML). As examples, we discuss the eukaryotic translation initiation factor (eIF4E), splice factor 3 complex B subunit 1 (SF3B1), U2 small nuclear auxiliary factor (U2AF1), and associated factors. These physically interact with each other and play roles in splicing, export, and translation. Malignant dysregulation of this mRNA processing-export-translation axis diversifies the proteome to support cancer. Finally, we discuss the simultaneous dysregulation of mRNA processing in malignancy and related therapeutic development.
Epitranscriptomic modifications in plant RNAs.
Bhat SS, Paul M, Gregory BD
RNA Biol · 2025 Dec · PMID 40464679 · Full text
A plethora of new and exciting findings have dramatically widened the horizons of plant RNA-related research. Despite being identified decades ago, RNA modifications were largely ignored owing to the immense difficulty i...
A plethora of new and exciting findings have dramatically widened the horizons of plant RNA-related research. Despite being identified decades ago, RNA modifications were largely ignored owing to the immense difficulty in studying them with traditional methods. We now know that these chemical additions to RNA nucleotides affect a myriad of plant biological processes ranging from plant growth and development to stress responses. The field of epitranscriptomics, the study of RNA modifications, has been dominated by mA in messenger RNAs (mRNAs), while modifications other than mA remained largely unstudied. A recent increase in studies investigating other RNA modifications and the development of novel tools has added to the evolving landscape of plant epitranscriptomic research. As this non-mA RNA modification research gathers pace, we use this review to provide a snapshot of the current state-of-the-art regarding these modifications with a focus on those occurring in functional non-coding RNAs as compared to mRNAs.
Systematic analysis of A-to-I RNA editing upon release of ADAR from the nucleolus.
Lattuca R, Bascetin R, Detours V … +1 more , Lafontaine DLJ
RNA Biol · 2025 Dec · PMID 40464638 · Full text
Adenosine-to-inosine (A-to-I) RNA editing, catalysed by two ADAR isoforms (p110 and p150) and ADARB1, is a critical regulatory step in gene expression. Intriguingly, the nucleolus is conspicuously rich in ADAR p110 and A...
Adenosine-to-inosine (A-to-I) RNA editing, catalysed by two ADAR isoforms (p110 and p150) and ADARB1, is a critical regulatory step in gene expression. Intriguingly, the nucleolus is conspicuously rich in ADAR p110 and ADARB1, though the biological reason remains unclear. To investigate a putative role of nucleolar enrichment in ADAR, we released it gradually from the nucleolus into the nucleoplasm by treating cells briefly with low doses of actinomycin D, known to disassemble the nucleolus. Deep sequencing of the transcriptome revealed that as ADAR dissociated from the nucleolus, RNA editing increased significantly, with sharp rises in both the number of edited sites and editing frequency. This co-transcriptional editing, predominantly in intronic regions, was associated with disrupted pre-mRNA splicing, causing exon skipping and intron retention which remodelled gene expression. These findings suggest that the nucleolar localization of ADAR serves to restrain its activity, preventing excessive editing that could lead to splicing errors and cellular dysfunction.
Investigation of possible G-quadruplex formation by GU- and GA-rich repeats and their role in translation.
Morren BM, Marcelis J, Muradin I … +1 more , Olsthoorn RCL
RNA Biol · 2025 Dec · PMID 40454959 · Full text
RNA G-quadruplexes (rG4s) are involved in many aspects of cellular and viral protein expression. rG4s consist of at least two stacks of guanine tetrads that are stabilized by non-Watson-Crick-Franklin base pairs. It is c...
RNA G-quadruplexes (rG4s) are involved in many aspects of cellular and viral protein expression. rG4s consist of at least two stacks of guanine tetrads that are stabilized by non-Watson-Crick-Franklin base pairs. It is currently unknown how single or multiple non-G nucleotide insertions affect the stability or function of rG4s. Here, we investigated the G4-forming potential of GU- and GA-rich sequences by measuring their ability to inhibit ribosomal scanning and induce -1 ribosomal frameshifting (-1 FS) using a cell-free lysate. Our results show that, in contrast to canonical rG4s, GU and GA repeats with eight or more guanines do not affect ribosomal scanning or stimulate -1 FS. However, in the presence of G4-stabilizing ligands PhenDC3 or pyridostatin, GU and GA repeats strongly inhibited scanning and induced -1 FS. These findings have implications for the structural landscape of rG4s and the potential side-effects of G4 targeting drugs in general.
Extracellular vesicle-derived MicroRNAs as potential therapies for spinal cord and peripheral nerve injuries.
Lim YJ, Seo MS, Park WT … +2 more , Park S, Lee GW
RNA Biol · 2025 Dec · PMID 40448270 · Full text
Complete nerve regeneration is limited in current therapeutic approaches for spinal cord injuries (SCIs) and peripheral nerve injuries (PNIs). Extracellular vesicles (EVs) and microRNAs (miRNAs) play a pivotal role in in...
Complete nerve regeneration is limited in current therapeutic approaches for spinal cord injuries (SCIs) and peripheral nerve injuries (PNIs). Extracellular vesicles (EVs) and microRNAs (miRNAs) play a pivotal role in intercellular communication by transporting various biomolecules, including miRNAs, to the recipient cells. Thus, they are promising targets for novel neural regeneration drugs. This comprehensive study examined the roles of EV-derived miRNAs in facilitating neural rejuvenation after SCI and PNI. It also explored the mechanisms by which they augment neuroprotection and promote cell viability. It also discusses their translational potential for treating nerve injury and evaluates their potential impact on advancements in nerve resurrection and prospective research in regenerative medicine. The findings may provide effective treatments and improve outcomes, as well as contribute to addressing the direction for the next studies, for the pathologies of SCI and PNI.
Deciphering the multifaceted role of double-stranded RNA sensor protein kinase R: pathophysiological function beyond the antiviral response.
Chung J, Lee Y, Yoon J … +1 more , Kim Y
RNA Biol · 2025 Dec · PMID 40444707 · Full text
Protein kinase R (PKR) is a serine/threonine kinase that recognizes double-stranded RNAs (dsRNAs) to initiate innate immune signalling during viral infection. PKR dimerizes on long dsRNAs and undergoes autophosphorylatio...
Protein kinase R (PKR) is a serine/threonine kinase that recognizes double-stranded RNAs (dsRNAs) to initiate innate immune signalling during viral infection. PKR dimerizes on long dsRNAs and undergoes autophosphorylation. Phosphorylated/Activated PKR then catalyses the phosphorylation of numerous substrates to control global translation, inflammatory response, and cell signalling pathways. While primarily known for its antiviral role, emerging evidence suggests that PKR can play multifaceted roles in uninfected cells by interacting with cellular dsRNAs and protein regulators. The misactivation of PKR in uninfected cells is associated with many degenerative and inflammatory diseases. Even in healthy cells, PKR can affect gene expression by controlling mRNA splicing and gene-specific translation under stress. In addition, PKR can modulate cell cycle progression and promote cellular differentiation in several tissue types. This review explores PKR function in various pathological and physiological contexts in the absence of viral stimuli. By elucidating these diverse functions, we aim to highlight the perspectives in cellular dsRNA research and the therapeutic implications of targeting PKR, stimulating further research into this versatile and essential RNA-dependent kinase.
Dual synthesis pathways of scaRNA28 via intronic processing of transformation/transcription domain-associated protein transcripts and a novel independent transcription unit.
Izumikawa K, Shida T, Ishikawa H … +6 more , Miyao S, Ohga T, Taoka M, Nobe Y, Nakayama H, Nagahama M
RNA Biol · 2025 Dec · PMID 40444427 · Full text
Small Cajal body-specific RNAs (scaRNAs) are noncoding RNAs involved in the maturation of U-rich small nuclear RNAs. Except for a few that have their own transcription units, most scaRNA genes are embedded in introns and...
Small Cajal body-specific RNAs (scaRNAs) are noncoding RNAs involved in the maturation of U-rich small nuclear RNAs. Except for a few that have their own transcription units, most scaRNA genes are embedded in introns and are predicted to be transcribed with host genes. Herein, we report that scaRNA28 is the first scaRNA with a dual synthesis pathway, and that this RNA is transcribed in an independent transcription unit (ITU) by RNA polymerase II while located in intron 2 of the transformation/transcription domain-associated protein (TRRAP) gene. We evaluated the scaRNA28 synthesis pathway using minigenes containing exon 2, intron 2, and exon 3 of . A minigene with a mutation preventing 5' splicing recognition of the exon 2/intron 2 junction generated scaRNA28, suggesting a pathway processing unspliced transcripts into scaRNA28. Even promoterless minigenes and DNA fragments with regions from exons 2 to 3 of showed RNA polymerase II-dependent synthesis of scaRNA28, indicating a novel synthesis pathway involving an ITU. Linker-scanning mutational analysis revealed that the promoter region required for scaRNA28 expression in the ITU is located within 60 bases including exon 2/intron 2 junction of , and especially the first two bases of intron 2 region, a putative part of the MYC-binding (E-box) motif, are essential for scaRNA28 expression in the ITU. MYC promotes scaRNA28 expression by binding to the promoter region in the ITU. Our findings demonstrated a novel transcriptional pathway for the synthesis of scaRNA28, the first scaRNA with a dual synthesis pathway.
RNA-seq analyses reveal the relevance of RNAs involved in ribosomal complex to induce mammalian prion protein aggregation and phase separation .
Tahira AC, Gomes MPB, Freire MH … +9 more , Muxfeldt M, Prosdocimi F, Passos YM, Sena Amaral M, Felix Valadão LP, Rangel LP, Silva JL, Verjovski-Almeida S, Cordeiro Y
RNA Biol · 2025 Dec · PMID 40438940 · Full text
Conformational conversion of cellular prion protein (PrP) into infectious PrP (PrP) is one of the most intriguing processes in modern Biology. It is well accepted that this transition is catalysed by one or more cofactor...
Conformational conversion of cellular prion protein (PrP) into infectious PrP (PrP) is one of the most intriguing processes in modern Biology. It is well accepted that this transition is catalysed by one or more cofactors that lower the energy barrier between the different PrP forms. Among potential candidates, RNA molecules are strong contenders. Our group has pursued nucleic acids, both DNA and RNA, capable of inducing PrP misfolding, aggregation, and, more recently, phase separation, a process proposed to precede aggregation in degenerative disorders. We found that the interaction between recombinant PrP (rPrP) and total RNA extracted from neuroblastoma cells (N2aRNA) results in significant structural alterations. Here, we use rPrP:N2aRNA as a model to search for RNAs capable of inducing full-length murine rPrP phase separation and/or aggregation. N2aRNA was incubated with rPrP and after that, RNA-seq analysis was conducted with RNAs isolated from the insoluble material using two different protocols. We analysed thousands of RNA-seq reads, most of which represented ribosomal RNA molecules. The set of recovered molecules is heterogeneous; nevertheless, three low-complexity consensus motifs within the sequences of RNAs involved in ribosomal complex were identified as significantly enriched in the RNAs bound to rPrP, suggesting that a population of RNAs is responsible for inducing PrP phase transitions. We hypothesize that RNA transcripts enriched in a set of low complexity motif sequences with predicted structural similarities can be involved in PrP binding. This interaction would lead to phase separation and, ultimately, result in aggregation into scrapie-like species, in a stoichiometry-dependent manner.
The oncogenic microRNA miR-222 promotes human LINE-1 retrotransposition.
Friehmann T, Abu Mohsen Y, Schlesinger Y … +6 more , Ghantous L, Gamaev L, Landau Zenilman C, Harazi A, Galun E, Goldenberg DS
RNA Biol · 2025 Dec · PMID 40421600 · Full text
The Long Interspersed Element-1 (LINE-1) contributes significantly to carcinogenesis and to tumour heterogeneity in many cancer types, including hepatocellular carcinoma (HCC), by its autonomous retrotransposition (RTP)...
The Long Interspersed Element-1 (LINE-1) contributes significantly to carcinogenesis and to tumour heterogeneity in many cancer types, including hepatocellular carcinoma (HCC), by its autonomous retrotransposition (RTP) and by its ability to retrotranspose some non-autonomous transposable elements. Previously, multiple proteins and a few microRNAs (miRs) were described as regulators of LINE-1 RTP. Here, we demonstrate that miR-222, which is oncogenic in HCC, promotes LINE-1 RTP in human HCC and some other cell lines , and that both miR-222-3p and miR-222-5p activate LINE-1 RTP in a cell-type specific manner. We generated miR-222-knockout mutants of the Huh7 and FLC4 hCC cell lines, and performed RNA-seq analysis of Huh7/miR-222-knockout cells and global proteomics analysis of both Huh7 and FLC4 miR-222-knockout mutants. We demonstrate that miR-222 decreases let-7c expression in both Huh7 and FLC4 cells, and that this decrease contributes to promotion of LINE-1 RTP by miR-222 in Huh7 cells.
Computational limitations and future needs to unravel the full potential of 2'-O-methylation and C/D box snoRNAs.
Ramirez C, Perenthaler E, Lauria F … +2 more , Tebaldi T, Viero G
RNA Biol · 2025 Dec · PMID 40377202 · Full text
This review evaluates the current state of C/D snoRNA databases and prediction tools in relation to 2'-O-methylation (2'-O-Me). It highlights the limitations of existing resources in accurately annotating and predicting...
This review evaluates the current state of C/D snoRNA databases and prediction tools in relation to 2'-O-methylation (2'-O-Me). It highlights the limitations of existing resources in accurately annotating and predicting guide snoRNAs, particularly for newly identified 2'-O-Me sites. We emphasize the need for advanced computational approaches specifically tailored to 2'-O-Me to enable the discovery and functional analysis of snoRNAs. Given the growing importance of 2'-O-Me in areas such as cancer epitranscriptomics, ribosome biogenesis, and heterogeneity, existing tools remain inadequate. As 2'-O-Me gains recognition as a potential biomarker and therapeutic target, more sophisticated methods are urgently needed to improve snoRNA annotation and prediction, facilitating biomedical advancements.
Translation elongation: measurements and applications.
Watkins L, Li M, Wu B
RNA Biol · 2025 Dec · PMID 40377059 · Full text
Translation converts genetic information in mRNAs into functional proteins. This process occurs in four major steps: initiation, elongation, termination and ribosome recycling; each of which profoundly impacts mRNA stabi...
Translation converts genetic information in mRNAs into functional proteins. This process occurs in four major steps: initiation, elongation, termination and ribosome recycling; each of which profoundly impacts mRNA stability and protein yield. Over recent decades, regulatory mechanisms governing these aspects of translation have been identified. In this review, we focus on the elongation phase, reviewing the experimental methods used to measure elongation rates and discussing how the measurements shed light on the factors that regulate elongation and ultimately gene expression.
Cleavage sequence specificity of Nsp15.
McGuire JV, Horowitz S
RNA Biol · 2025 Dec · PMID 40326411 · Full text
Nsp15 is an EndoU nuclease that is partially responsible for SARS-CoV-2's ability to evade the immune system response. Despite its importance, the sequence specificity of Nsp15 remains difficult to fully determine. In th...
Nsp15 is an EndoU nuclease that is partially responsible for SARS-CoV-2's ability to evade the immune system response. Despite its importance, the sequence specificity of Nsp15 remains difficult to fully determine. In this work, we use a systematic approach to measure Nsp15's sequence specificity by testing all 16 dinucleotides for cleavage activity. The results show a preference for uridine in the first dinucleotide position, but with varying specificity in the second position. Using Alphafold3 predictions to examine the structural basis of this specificity suggests important contacts 3' of the dinucleotide sequence as well as contacts to the dinucleotides that agree with the cleavage specificity.
Evidence that ribosomal protein bS21 is a component of the OLE ribonucleoprotein complex.
Wencker FDR, Lyon SE, Breaker RR
RNA Biol · 2025 Dec · PMID 40322971 · Full text
OLE RNAs represent a large and highly structured noncoding RNA (ncRNA) class that is mostly found in Gram-positive extremophiles and/or anaerobes of the Bacillota phylum. These ~600-nucleotide RNAs are among the most str...
OLE RNAs represent a large and highly structured noncoding RNA (ncRNA) class that is mostly found in Gram-positive extremophiles and/or anaerobes of the Bacillota phylum. These ~600-nucleotide RNAs are among the most structurally complex and well-conserved large ncRNAs whose precise biochemical functions remain to be established. In , OLE RNA is involved in the adaptation to various unfavourable growth conditions, including exposure to cold (≤20°C), ethanol (≥3% [v/v]), excess Mg (≥4 mM), and non-glucose carbon/energy sources. OLE forms a ribonucleoprotein (RNP) complex with the OLE-associated proteins A, B and C, which are known to be essential for OLE RNP complex function in this species. Bacteria lacking OLE RNA (Δ) or a functional OLE RNP complex exhibit growth defects under the stresses listed above. Here, we demonstrate that ribosomal protein bS21 is a natural component of the OLE RNP complex and we map its precise RNA binding site. The presence of bS21 results in a conformational change in OLE RNA resembling a k-turn substructure previously reported to be relevant to the function of the OLE RNP complex. Mutational disruption of the bS21 protein or its OLE RNA binding site results in growth inhibition under cold and ethanol stress to the same extent as the deletion of the gene for OLE RNA. These findings are consistent with the hypothesis that bS21 is a biologically relevant component of the OLE RNP complex under a subset of stresses managed by the OLE RNP complex.
miRNA-mRNA integrated analysis reveals candidate genes associated with salt stress response in Halophytic .
Chen B, Zhen L, Yang Z … +5 more , Liu T, Yang S, Mu W, Xiao X, Chen J
RNA Biol · 2025 Dec · PMID 40296366 · Full text
is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. How...
is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. However, limited attempt has been made to uncover the underlying molecular mechanism of their saline adaptation. Here, we integrated mRNA and microRNA (miRNA) sequencing to identify the genes and pathways that may be involved in salt stress-response in the roots of . A comprehensive full‑length transcriptome containing 295,501 high‑quality unigenes was obtained by PacBio sequencing technology. Of these, 6,686 genes exhibited significantly differential accumulation after salt stress treatment ( < 0.001, < 0.01). They were mainly implicated in plant signal transduction and diverse metabolic pathways, such as those involving phenylpropanoid biosynthesis, plant-pathogen interaction and protein processing. Also, our results identified the regulatory interaction between miRNA-target counterparts during salt stress. Taken together, we present the first global overview of the transcriptome of roots, and identify potentially important genes and pathways associated with salt tolerance for further investigation. This study is expected to deliver novel insights in understanding the regulatory mechanism in response to salt stress.
The implication of non-AUG-initiated N-terminally extended proteoforms in cancer.
Pancsa R, Andreev DE, Dean K
RNA Biol · 2025 Dec · PMID 40276932 · Full text
Dysregulated translation is a hallmark of cancer, and recent genome-wide studies in tumour cells have uncovered widespread translation of non-canonical reading frames that often initiate at non-AUG codons. If an upstream...
Dysregulated translation is a hallmark of cancer, and recent genome-wide studies in tumour cells have uncovered widespread translation of non-canonical reading frames that often initiate at non-AUG codons. If an upstream non-canonical start site is located within a frame with an annotated coding sequence (CDS), such translation events can lead to the production of proteoforms with altered N-termini (PANTs). Certain examples of PANTs from oncogenes (e.g. c-MYC) and tumour suppressors (e.g. PTEN) have been previously linked to cancer. We have performed a systematic computational analysis on recently identified non-AUG initiation-derived N-terminal extensions of cancer-associated proteins, and we discuss how these extended proteoforms may acquire new oncogenic properties. We identified a loss of stability for the N-terminally extended proteoforms of oncogenes TCF-4 and SOX2. Furthermore, we discovered likely functional short linear motifs within the N-terminal extensions of oncogenes and tumour suppressors (SOX2, SUFU, SFPQ, TOP1 and SPEN/SHARP) that could provide an explanation for previously described functionalities or interactions of the proteins. In all, we identify novel cases where PANTs likely show different localization, functions, partner binding or turnover rates compared to the annotated proteoforms. Therefore, we propose that alterations in the stringency of translation initiation, often seen under conditions of cellular stress, may result in reprogramming of translation to generate novel PANTs that influence cancer progression.
Alternative splicing of the Snap23 microexon is regulated by MBNL, QKI, and RBFOX2 in a tissue-specific manner and is altered in striated muscle diseases.
Gentile GM, Blue RE, Goda GA … +12 more , Guzman BB, Szymanski RA, Lee EY, Engels NM, Hinkle ER, Wiedner HJ, Bishop AN, Harrison JT, Zhang H, Wehrens XHT, Dominguez D, Giudice J
RNA Biol · 2025 Dec · PMID 40207498 · Full text
The reprogramming of alternative splicing networks during development is a hallmark of tissue maturation and identity. Alternative splicing of microexons (small, genomic regions ≤ 51 nucleotides) functionally regulate pr...
The reprogramming of alternative splicing networks during development is a hallmark of tissue maturation and identity. Alternative splicing of microexons (small, genomic regions ≤ 51 nucleotides) functionally regulate protein-protein interactions in the brain and is altered in several neuronal diseases. However, little is known about the regulation and function of alternatively spliced microexons in striated muscle. Here, we investigated alternative splicing of a microexon in the synaptosome-associated protein 23 () encoded gene. We found that inclusion of this microexon is developmentally regulated and tissue-specific, as it occurs exclusively in adult heart and skeletal muscle. The alternative region is highly conserved in mammalian species and encodes an in-frame sequence of 11 amino acids. Furthermore, we showed that alternative splicing of this microexon is mis-regulated in mouse models of heart and skeletal muscle diseases. We identified the RNA-binding proteins (RBPs) quaking (QKI) and RNA binding fox-1 homolog 2 (RBFOX2) as the primary splicing regulators of the Snap23 microexon. We found that QKI and RBFOX2 bind downstream of the Snap23 microexon to promote its inclusion, and this regulation can be escaped when the weak splice donor is mutated to the consensus 5' splice site. Finally, we uncovered the interplay between QKI and muscleblind-like splicing regulator (MBNL) as an additional, but minor layer of Snap23 microexon splicing control. Our results are one of the few reports detailing microexon alternative splicing regulation during mammalian striated muscle development.
The LARP6 La module from reveals structural and functional differences from plant and animal LARP6 homologues.
Lewis EM, Becker O, Symons AN … +7 more , LaCoss C, Baclig AJ, Guzman A, Sanders C, Gonzalez L, Warner LR, Lewis KA
RNA Biol · 2025 Dec · PMID 40181506 · Full text
This study identified the LARP6 La Module from (), a four-celled green algae, in an effort to better understand the evolution of LARP6 structure and RNA-binding activity in multicellular eukaryotes. Using a combination...
This study identified the LARP6 La Module from (), a four-celled green algae, in an effort to better understand the evolution of LARP6 structure and RNA-binding activity in multicellular eukaryotes. Using a combination of sequence alignments, domain boundary screens, and structural modelling, we recombinantly expressed and isolated the LARP6 La Module to > 98% purity for biochemical characterization. The La Module is stably folded and exerts minimal RNA binding activity against single-stranded homopolymeric RNAs. Surprisingly, it exhibits low micromolar binding affinity for the vertebrate LARP6 cognate ligand, a bulged-stem loop found in the 5'UTR of collagen type I mRNA, but does not bind double-stranded RNAs of similar size. These result suggests that the LARP6 La Module may prefer structured RNA ligands. In contrast, however, the LARP6 La Module does not exhibit the RNA chaperone activity that is observed in vertebrate homologs. Therefore, we conclude that protist LARP6 may have both distinct RNA ligands and binding mechanisms from the previously characterized LARP6 proteins of animals and vascular plants, thus establishing a distinct third class of the LARP6 protein family.
Release and degradation of dissolved environmental RNAs from zebrafish cells.
Xu Z, Asakawa S
RNA Biol · 2025 Dec · PMID 40167163 · Full text
The sources and degradation profiles of dissolved environmental RNAs from fish in water remain unknown. In this study, laboratory experiments and mathematical modelling were conducted to investigate the permeability of R...
The sources and degradation profiles of dissolved environmental RNAs from fish in water remain unknown. In this study, laboratory experiments and mathematical modelling were conducted to investigate the permeability of RNA extracted from zebrafish cells through filters, the release of dissolved environmental RNAs from live and dying zebrafish cells, and the degradation of RNA extracted from zebrafish cells in a non-sterile aqueous environment. This research aimed to provide biological and ecological insights into fish RNAs dissolved in water. The results showed that most of the RNA extracted from zebrafish cells was detected in the filtrates after passage through 0.45 µm filters. Over the course of the 6-day experiment, dynamic levels of the RNAs in the liquid environment containing live or dying zebrafish cells were determined. The release and degradation rates of dissolved environmental RNA from zebrafish cells were calculated using mathematical modelling. RNA extracted from zebrafish cells degraded in non-sterile water in the tubes, and after 2 months, more than 15% of the RNAs in the water remained detectable. The half-life of the RNA in the tubes was approximately 20 ~ 43 days. The modelling results suggest that the levels of the dissolved environmental fish RNAs in natural waters or aquariums could be so low that it would be difficult to detect them using current techniques. The results obtained in this study will help develop new methods for measuring the dynamics of dissolved environmental fish RNAs in water and determining their significance.
6S-1 pRNA 9-mers are a prominent length species during outgrowth of cells from extended stationary phase.
Damm K, Klemm P, Lechner M … +2 more , Helmecke D, Hartmann RK
RNA Biol · 2025 Dec · PMID 40134231 · Full text
Bacterial RNA polymerases (RNAP) utilize 6S RNAs as templates to synthesize ultrashort transcripts (up to ~14 nt), termed product RNAs (pRNAs), that play a key role in reversing the blockage of RNAP by 6S RNA. Here, we r...
Bacterial RNA polymerases (RNAP) utilize 6S RNAs as templates to synthesize ultrashort transcripts (up to ~14 nt), termed product RNAs (pRNAs), that play a key role in reversing the blockage of RNAP by 6S RNA. Here, we resolved the pRNA length profile of 6S-1 RNA from , a major model system for the study of 6S RNA biology, during outgrowth of cells from extended stationary phase. 9-mers were found to be a particularly abundant pRNA length species, followed by 8-/10-/11-mers and 13-/14-mers. Consistent with data from the system, these findings support the mechanistic model according to which the housekeeping sigma factor (σ or σ) dissociates from 6S RNA:RNAP complexes upon synthesis of pRNA 9-mers, followed by final dissociation of 6S RNA and RNAP upon synthesis of longer pRNAs (13-/14-mers). Methodologically, the identification of such ultrashort RNAs in total cellular extracts by RNA-Seq is inefficient with standard protocols using adapter ligation to RNA 3'-ends for reverse transcription and PCR-based cDNA sequencing. Here, we demonstrate that ultrashort RNAs can instead be incorporated into RNA-Seq libraries by polyA-, polyC- and potentially also polyU-tailing of their 3'-ends. At positions where a non-tailing nucleotide is followed by one or more tailing nucleotides, an algorithm that integrates RNA-Seq results from at least two different 3'-end tailings allows one to approximate the fraction of read counts at such ambiguous positions. Finally, methodological biases and potential applications of our approach to other short RNAs are discussed.
Nucleolar ribosomal RNA synthesis continues in differentiating lens fiber cells until abrupt nuclear degradation required for ocular lens transparency.
Rayêe D, Meier UT, Eliscovich C … +1 more , Cvekl A
RNA Biol · 2025 Dec · PMID 40126102 · Full text
Cellular differentiation requires highly coordinated action of all three transcriptional systems to produce rRNAs, mRNAs and various 'short' and 'long' non-coding RNAs by RNA Polymerase I, II and III systems, respectivel...
Cellular differentiation requires highly coordinated action of all three transcriptional systems to produce rRNAs, mRNAs and various 'short' and 'long' non-coding RNAs by RNA Polymerase I, II and III systems, respectively. RNA Polymerase I catalyzes transcription of about 400 copies of mammalian rDNA genes, generating 18S, 5.8S and 28S rRNA molecules. Lens fiber cell differentiation is a unique process to study transcriptional mechanisms of individual crystallin genes as their very high transcriptional outputs are directly comparable only to globin genes in erythrocytes. Importantly, both terminally differentiated lens fiber cells and mammalian erythrocytes degrade their nuclei through different mechanisms. In lens, the generation of the organelle-free zone (OFZ) includes the degradation of mitochondria, endoplasmic reticulum, Golgi apparatus and nuclei. Here, using RNA fluorescence hybridization (FISH), we evaluated nascent rRNA transcription, located in the nucleoli, during the process of mouse lens fiber cell differentiation. Lens fiber cell nuclei undergo morphological changes including chromatin condensation prior to their denucleation. Remarkably, nascent rRNA transcription persists in all nuclei that are in direct proximity of the OFZ. Additionally, changes in both nuclei and nucleoli shape were evaluated via immunofluorescence detection of fibrillarin, nucleolin, UBF and other proteins. These studies demonstrate for the first time that highly condensed lens fiber cell nuclei have the capacity to support nascent rRNA transcription. Thus, we propose that 'late' production of rRNA molecules and consequently of ribosomes increases crystallin protein synthesis machinery within the mature lens fibers.
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