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Results for “Molecular Biology”

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bioRxiv2023

MicroRNA-423-5p Mediates Cocaine-Induced Smooth Muscle Cell Contraction by Targeting Cacna2d2

BackgroundCocaine abuse increases the risk of atherosclerotic cardiovascular disease (CVD) and causes acute coronary syndromes (ACS) and hypertension (HTN). Significant research has explored the role of the sympathetic nervous system mediating the cocaine effects on the cardiovascular (CV) system. However, the response of the sympathetic nervous system alone is insufficient to completely account for the CV consequences seen in cocaine users. Here, we examined the role of microRNAs (miRNAs) in mediating the effect of cocaine on the CV system. MiRNAs regulate many important biological processes and have been associated with both response to cocaine and CV disease development. Multiple miRNAs have altered expression in the CV system (CVS) upon cocaine exposure. Herein, we examined the role of microRNA-423-5p and the downstream signaling events in regulating cocaine-induced mouse aortic smooth muscle cell (SMC) contraction. MethodsTo understand the molecular mechanisms underlying the cocaine response in the CV system, we studied the role of miRNA-423-5p and its target Cacna2d2 in the regulation of intracellular calcium concentration and SMC contractility, a critical factor in the modulation of blood pressure (BP). We used in vivo models to evaluate BP and aortic stiffness. ResultsIn vitro, Cocaine treatment decreased miR-423-5p expression and increased Cacna2d2 expression, which led to elevated intracellular calcium concentrations and increased SMC contractility. Overexpression of miR-423-5p, silencing of its target Cacna2d2, and treatment with a calcium channel blocker reversed the elevated SMC contractility caused by cocaine. In contrast, suppression of miR-423-5p increased the intracellular calcium concentration and SMC contractibility. In vivo, overexpression of miR-423-5p ameliorated the increase in BP and aortic stiffness associated with cocaine use. ConclusionsMiR-423-5p regulates SMC contraction by modulating Cacna2d2 expression increasing intracellular calcium concentrations. Modulation of miR-423-5p--Cacna2d2--Calcium transport pathway may represent a novel therapeutic strategy to improve cocaine-induced hypertension and aortic stiffness.

molecular biology↗

bioRxiv2018

Bayesian inference and comparison of stochastic transcription elongation models

Transcription elongation can be modelled as a three step process, involving polymerase translocation, NTP binding, and nucleotide incorporation into the nascent mRNA. This cycle of events can be simulated at the single-molecule level as a continuous-time Markov process using parameters derived from single-molecule experiments. Previously developed models differ in the way they are parameterised, and in their incorporation of partial equilibrium approximations.\n\nWe have formulated a hierarchical network comprised of 12 sequence-dependent transcription elongation models. The simplest model has two parameters and assumes that both translocation and NTP binding can be modelled as equilibrium processes. The most complex model has six parameters makes no partial equilibrium assumptions. We systematically compared the ability of these models to explain published force-velocity data, using approximate Bayesian computation. This analysis was performed using data for the RNA polymerase complexes of E. coli, S. cerevisiae and Bacteriophage T7.\n\nOur analysis indicates that the polymerases differ significantly in their translocation rates, with the rates in T7 pol being fast compared to E. coli RNAP and S. cerevisiae pol II. Different models are applicable in different cases. We also show that all three RNA polymerases have an energetic preference for the posttranslocated state over the pretranslocated state. A Bayesian inference and model selection framework, like the one presented in this publication, should be routinely applicable to the interrogation of single-molecule datasets.\n\nAuthor summaryTranscription is a critical biological process which occurs in all living organisms. It involves copying the organisms genetic material into messenger RNA (mRNA) which directs protein synthesis on the ribosome. Transcription is performed by RNA polymerases which have been extensively studied using both ensemble and single-molecule techniques (see reviews: [1, 2]). Single-molecule data provides unique insights into the molecular behaviour of RNA polymerases. Transcription at the single-molecule level can be computationally simulated as a continuous-time Markov process and the model outputs compared with experimental data. In this study we use Bayesian techniques to perform a systematic comparison of 12 stochastic models of transcriptional elongation. We demonstrate how equilibrium approximations can strengthen or weaken the model, and show how Bayesian techniques can identify necessary or unnecessary model parameters. We describe a framework to a) simulate, b) perform inference on, and c) compare models of transcription elongation.

molecular biology↗

bioRxiv2019

Identification of flowering-time genes in mast flowering plants using de novo transcriptomic analysis

Mast flowering is synchronised highly variable flowering by a population of perennial plants over a wide geographical area. High seeding years are seen as a threat to native and endangered species due to high predator density caused by the abundance of seed. An understanding of the molecular pathways that influence masting behaviour in plants could provide better prediction of a forthcoming masting season and enable conservation strategies to be deployed. In this study, a high-throughput large-scale RNA-sequencing was performed on two masting plant species, Celmisia lyallii (Asteraceae), and Chionochloa pallens (Poaceae) to develop a reference transcriptome for functional and molecular analysis. An average total of 33 million 150 base-paired reads, for both species, were assembled using the Trinity pipeline, resulting in 151,803 and 348,649 transcripts respectively for Celmisia and Chionochloa. The two datasets generated were blasted against the publicly available databases, TAIR, Swiss-Prot, non-redundant protein (nr), KEGG and COG for unigene annotations. On average, 56% of the unigenes were finally annotated with gene descriptions mapped to known protein sequences for both the species. Gene ontology analysis was then performed on the assembled reference transcriptomes, categorising the transcripts on the basis of putative biological processes, molecular function, and cellular localisation. A total of 543 transcripts from Celmisia and 470 transcripts from Chionochloa were also mapped to unique flowering-time proteins identified in Arabidopsis, suggesting the conservation of the flowering network in these wild alpine plants, growing in natural field conditions. These genes can further be analysed to understand the molecular regulation of the reproductive phase transition in the masting plants.

plant biology↗

bioRxiv2022

Unexpected growth of a classic yeast auxotroph

Organisms must either synthesize or assimilate essential organic compounds to survive. The homocysteine synthase Met15 has been considered essential for inorganic sulfur assimilation in yeast since its discovery in the 1970s. As a result, MET15 has served as a genetic marker for hundreds of experiments that play a foundational role in eukaryote genetics and systems biology. Nevertheless, we demonstrate here through structural and evolutionary modeling, in vitro kinetic assays, and genetic complementation, that an alternative homocysteine synthase encoded by the previously uncharacterized gene YLL058W enables cells lacking Met15 to assimilate enough inorganic sulfur for survival and proliferation. These cells however fail to grow in patches or liquid cultures unless provided with exogenous methionine or other organosulfurs. We show that this growth failure, which has historically justified the status of MET15 as a classic auxotrophic marker, is largely explained by toxic accumulation of the gas hydrogen sulfide due to a metabolic bottleneck. When patched or cultured with a hydrogen sulfide chelator, and when propagated as colony grids, cells without Met15 assimilate inorganic sulfur and grow, and cells with Met15 achieve even higher yields. Thus, Met15 is not essential for inorganic sulfur assimilation in yeast. Instead, MET15 is the first example of a yeast gene whose loss conditionally prevents growth in a manner that depends on local gas exchange. Our results have broad implications for investigations of sulfur metabolism, including studies of stress response, methionine restriction, and aging. More generally, our findings illustrate how unappreciated experimental variables can obfuscate biological discovery.

molecular biology↗

bioRxiv2022

Core and Flanking bHLH-PAS:DNA interactions mediate specificity and drive obesity

The basic-Helix-Loop-Helix Per-Arnt-Sim (PAS) homology domain (bHLH-PAS) transcription factor (TF) family comprises critical biological sensors of physiological (hypoxia, tryptophan metabolites, neuronal activity, and appetite) and environmental (diet derived metabolites and environmental pollutants) stimuli to regulate genes involved in signal adaptation and homeostasis1. bHLH TFs bind DNA as homo or heterodimers via E-box (CANNTG) response elements, however the DNA binding specificity of the PAS domain-containing bHLH subfamily remains unresolved1. We systematically analysed cognate DNA binding hierarchies of prototypical bHLH-PAS family members (ARNT, ARNT2, HIF1, HIF2, AhR, NPAS4, SIM1) and demonstrate distinct core (NNCGTG) specificities for different heterodimer classes. The results also show that bHLH-PAS TFs bind over a large footprint 12-15bp and recognise preferential DNA sequences flanking the core. For example, specificity beyond otherwise identical core binding by SIM1 and the HIFs is mediated through N-terminal HIF-DNA interactions. We also reveal an intimate relationship between DNA shape and both core and flanking TF binding allowing motif sequence flexibility and underpinning TF binding specificity. Furthermore, DNA-shape affinity relationships revealed that novel downstream PAS-A-loop DNA interactions are associated with AT-rich sequences that lead to high-affinity binding, and that loss of this function underpins a monogenic cause of human hyperphagic obesity in a recapitulated SIM1.R171H knock-in mouse model. Importantly, models of protein-DNA binding accurately predict in vivo occupancy, while response element methylation blocks DNA binding and predicts cell type specific chromatin occupancy. These data provide a definitive and accurate map of bHLH-PAS TF specificity and target selectivity through novel flanking protein-DNA interactions that are crucial for in vivo biological function.

molecular biology↗

bioRxiv2022

Proteomic Analysis Defines the Interactome of Telomerase in the Protozoan Parasite, Trypanosoma brucei

Telomerase is a ribonucleoprotein enzyme responsible for maintaining the telomeric end of the chromosome. The telomerase enzyme requires two main components to function: the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), which provides the template for telomeric DNA synthesis. TR is a long noncoding RNA, which forms the basis of a large structural scaffold upon which many accessory proteins can bind and form the complete telomerase holoenzyme. These accessory protein interactions are required for telomerase activity and regulation inside cells. The interacting partners of TERT have been well studied in yeast, human, and Tetrahymena models, but not in lower eukaryotes, including clinically relevant human parasites. Here, using the protozoan parasite, Trypanosoma brucei (T. brucei) as a model, we have identified the interactome of T. brucei TERT (TbTERT) using a mass spectrometry-based approach. We identified previously known and unknown interacting factors of TbTERT, highlighting unique features of T. brucei telomerase biology. These unique interactions with TbTERT, suggest mechanistic differences in telomere maintenance between T. brucei and other eukaryotes.

molecular biology↗

bioRxiv2023

Human telomere length is chromosome specific and conserved across individuals

Short telomeres cause age-related disease and long telomeres predispose to cancer; however, the mechanisms regulating telomere length are unclear. To probe these mechanisms, we developed a nanopore sequencing method, Telomere Profiling, that is easy to implement, precise, and cost effective with broad applications in research and the clinic. We sequenced telomeres from individuals with short telomere syndromes and found similar telomere lengths to the clinical FlowFISH assay. We mapped telomere reads to specific chromosome end and identified both chromosome end-specific and haplotype-specific telomere length distributions. In the T2T HG002 genome, where the average telomere length is 5kb, we found a remarkable 6kb difference in lengths between some telomeres. Further, we found that specific chromosome ends were consistently shorter or longer than the average length across 147 individuals. The presence of conserved chromosome end-specific telomere lengths suggests there are new paradigms in telomere biology that are yet to be explored. Understanding the mechanisms regulating length will allow deeper insights into telomere biology that can lead to new approaches to disease.

molecular biology↗

bioRxiv2019

Enhancer-promoter association determines Sox2 transcription regulation in mouse pluripotent cells

Distal enhancer-promoter associations are essential for transcription control and emerging as a common epigenetic way to determine gene expression in eukaryotes. However, it remains as an uncultivated land on how their diversity influences gene transcription during development. In this study, we select three defined Sox2 associated enhancers (E1, E2 and E3), representing different distal interaction categories, to further explore their biological effects. We construct three enhancer-knockout cells via CRISPR/Cas9 system in mouse embryonic stem cells. Results show that these associations carry out various biological features. Embryonic stem cell specific association (E1) speeds up cell cycle and involves in cardiac development, which has been validated in vivo. In contrast, the indirect one (E2) restrains nerve differentiation and has potential effect on lipid metabolism. The common one (E3) promotes nerve differentiation and inhibits oxidation-reduction process. Together, these different associations determine Sox2 transcription and function specificity in mouse embryonic stem cells. Our study will enable a way for exploring miscellaneous spatiotemporal gene transcription control and advancing quantitative knowledge by utilizing three-dimensional genomic information.\n\nSummary statementSox2 transcription is complicated in mouse embryonic stem cells. It involves in heavily enhancer-promoter associations, which might make it a suitable model for phase-separation study. To decompose this cooperative regulation, diverse interactions are investigated. The biological effects have been explored in multiple perspectives. This may represent a quantitative way to explore and a potential new strategy to transcription control study.

molecular biology↗

bioRxiv2026

Tumor Suppression across the Human miRNome Associates with Guanine-Rich Precursor Terminal Loops

MicroRNAs (miRNAs) play essential regulatory roles in controlling cell growth, proliferation, and differentiation in cancer. While functional studies have identified numerous oncogenic (oncomiRs) and tumor suppressor (TS) miRNAs, the structural features that differentiate these groups remain poorly understood. Here, we performed a comprehensive sequence analysis of 955 human pre-miRNA terminal loops (TLs), focusing on enrichment of single guanine (G) and GG dinucleotides. A quantitative G enrichment score was used to define 42 G-rich TL miRNAs and 17 G-free TL miRNAs as controls. Functional roles of these miRNAs were curated from 757 publications. The results show that G-rich TL miRNAs consistently display higher TS/oncomiR ratios than G-free TL miRNAs across most cancer types, with a significant enrichment observed in lung cancer (p = 0.023). Focusing on miR-139, a TS miRNA with a G-rich TL, integrative analysis of publicly available transcriptomic and proteomic data revealed its consistent downregulation across all stages of lung adenocarcinoma (LUAD), accompanied by reciprocal overexpression of its validated oncogenic target, CCNB1. These findings highlight the biological relevance of G-rich TL structures in miRNA-mediated tumor suppression in lung cancer, suggesting their consideration in future therapeutic strategies aimed at restoring vulnerable TS miRNAs.

molecular biology↗

bioRxiv2026

Expanded Proteome Coverage Powered by Advanced Ion Processing Enables Deep Single-Cell Drug Response Subtyping in Human Stem Cell Derived Cardiomyocytes

Single-cell proteomics (SCP) enables the study of cellular heterogeneity at the functional level but remains limited by incomplete proteome coverage and high data missingness. Here, we present an enhanced label-free SCP workflow that leverages the timsUltra AIP mass spectrometry platform equipped with the Athena Ion Processor (AIP). Across a controlled dilution series of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), AIP-enabled acquisition consistently increased proteome depth and detection consistency across cells at all input levels. In single iPSC-CMs, the timsUltra AIP quantified up to 3,858 protein groups, averaging [~]1,300 proteins per cell, enabling robust proteome-level classification of cardiomyocyte subtypes. Using a reference-based protein classifier, cells were stratified into mature cardiomyocytes and less differentiated cell states, revealing substantial baseline heterogeneity. Importantly, increased single-cell sensitivity translated directly into biological insight, as approximately 30% of differentially expressed proteins associated with subtype-specific drug responses were detected exclusively by timsUltra AIP. Application of this workflow to PR-364 (a mitophagy boosting drug) dose-response experiment uncovered distinct, subtype-dependent pathway adaptations. Mature cardiomyocytes exhibited dose-dependent increases in mitochondrial and metabolic pathway activity, while immature cells showed enrichment of cytoskeletal and developmental programs. These effects were partially obscured in simulated bulk analyses, highlighting the value of single-cell resolution. Together, these results demonstrate that improved fragment ion transmission and utilization translate directly into enhanced biological insight, enabling more comprehensive and functionally relevant single-cell proteomics.

molecular biology↗

bioRxiv2026

Nitrogen-Responsive Extracellular Proteomics Reveals Evidence for a Novel Heterocyst-Specific Protein Secretion Pathway in Anabaena

Nitrogen availability is a major factor governing the physiology, ecology, and metabolism of cyanobacteria. Here, we performed a comparative extracellular proteomic analysis of Anabaena sp. PCC 7120 grown under nitrate-replete and diazotrophic conditions. Using LC-MS/MS, we identified 115 extracellular proteins in nitrate-grown cultures and 113 proteins under N2-fixing conditions. Remarkably, SignalP 6.0 predicted canonical signal peptides in only [~]22% of the identified proteins, suggesting that extracellular protein export in Anabaena predominantly occurs through non-classical secretion mechanisms, potentially involving extracellular vesicles or other unrecognized pathways. Six highly abundant extracellular proteins (Alr2938, Alr4550, Alr2328, All4121, Alr0528, and Alr0529) were detected under both nitrogen regimes. In contrast, All4337, Alr0608, and All3093 were preferentially enriched under nitrate-replete conditions, whereas Alr0267 and Alr1050 emerged among the most abundant extracellular proteins during diazotrophic growth. Notably, an Alr0267-GFP fusion protein was detected exclusively in heterocysts, the specialized N2-fixing cells of Anabaena, with GFP fluorescence concentrated at the cell periphery. The extracellular localization of Alr0267 is particularly intriguing because heterocysts are surrounded by specialized polysaccharide and glycolipid envelope layers that establish the microoxic environment required for nitrogenase activity. The apparent export of Alr0267 across these barriers provides evidence for a previously unrecognized heterocyst-associated protein secretion pathway. Together, these findings reveal a nitrogen-responsive extracellular proteome and provide the first evidence for heterocyst-specific extracellular protein secretion. This work advances our understanding of heterocyst biology and protein trafficking while laying a foundation for engineering Anabaena as a sustainable photosynthetic platform for secreting high-value proteins using sunlight, CO2, N2, and mineralized water.

molecular biology↗

bioRxiv2026

Adeno-Associated Virus (AAV) Synthetic Inverted Terminal Repeats Enhance Tissue-Specific Transduction and Alter the Vector Induced Stress Response

While adeno-associated virus (AAV) vectors have shown therapeutic benefit in clinical applications, noted challenges include low transduction efficiencies, poor cellular targeting, and vector related adverse events. Recently, it was demonstrated that a rationally designed synthetic inverted terminal repeat (SynITR) altered the AAV vector-induced DNA damage response and abrogated apoptosis in human embryonic stem cells. To explore the utility of AAV-SynITR for diverse gene therapy applications, vector production, transduction, and the cellular response were evaluated in various contexts. Regarding production, SynITR preparations exhibited comparable titers to wtITR in a serotype/transgene-independent manner. Despite slightly decreased transduction efficiency in various cell lines, intravenous administration of AAV8 vectors showed SynITR enhanced transduction in a tissue-specific manner in liver (>7-fold) and kidney and pancreas (>2-fold) at equivalent vector copy numbers; however, no differences were observed in muscle/heart/spleen tissues. Interestingly, persistent {gamma}H2AX, a marker of aging/chronic inflammation, was abundant in the liver and spleen following wtITR (but not SynITR) transduction. In human corneas, SynITR enhanced transduction up to 16-fold over wtITRs. These data demonstrate that SynITRs elicit tissue-specific transduction enhancement and alter the cellular stress response. Importantly, the SynITRs offer an alternative context to elucidate wtITR biology for targeted, enhanced, and potentially safer human gene therapy.

molecular biology↗

bioRxiv2026

A multi-scale structural and biophysical atlas of TCR-peptide-HLA recognition dynamics

Dynamic interactions between T cell receptor (TCR) and peptide-human leukocyte antigen (pHLA) complexes are central to peptide-specific immune recognition, influencing T cell activation and immune responses. While structural biology has provided valuable static structures of TCR-pHLA complexes, systematic datasets capturing their dynamic and interaction patterns remain limited. Here, we present DynaTPH, a curated structural dynamics dataset of human TCR-pHLA complexes. DynaTPH integrates TCR-pHLA structures, covering both HLA class I and class II complexes, and extends these static structural resources with standardized molecular dynamics simulations and derived biophysical properties. Through a multi-stage filtering procedure, we identified 256 representative complexes and performed standardized all-atom molecular dynamics simulations for each system, corresponding to a cumulative simulation time of 38.4 s. The dataset includes static structures, trajectories, corresponding frames, and derived physicochemical properties, including hydrogen bonds, intermolecular contacts, solvent accessibility, and backbone flexibility. By capturing the conformational flexibility and dynamic interaction patterns across diverse TCR-pHLA interfaces, DynaTPH extends static structural resources with multidimensional biophysical information. This dataset enables systematic investigation of TCR-pHLA recognition dynamics and supports applications in TCR engineering, vaccine design, and immune tolerance research and artificial intelligence-driven computational immunology.

molecular biology↗

bioRxiv2017

The small non-coding vault RNA1-1 acts as a riboregulator of autophagy

Vault RNAs (vtRNA) are small, 88-100nt non-coding RNAs found in many eukaryotes. Although they have been linked to drug resistance, apoptosis and nuclear transport, their function remains unclear. Here we show that a human vtRNA, RNA1-1, specifically binds to the autophagy receptor sequestosome-1/p62. Antisense-mediated depletion of vault RNA1-1 augments, whereas increased vault RNA1-1 expression restricts, autophagic flux in a p62-dependent manner. Bulk autophagy induced by starvation reduces the levels of vault RNA1-1 and the fraction of RNA-bound p62. These findings show that RNAs can act as riboregulators of biological processes by interacting with proteins, and assign a function to a vault RNA.

molecular biology↗

bioRxiv2020

Post-transcriptional modulation of the SigF regulon in Mycobacterium smegmatis by the PhoH2 toxin-antitoxin.

PhoH2 proteins are highly conserved across bacteria and archaea yet their biological function is poorly characterised. We examined the growth profiles of Mycobacterium smegmatis strains mc2155 and mc2155 {Delta}phoH2 and observed the same growth profile and growth rate in a variety of conditions. In light of the comparable growth rates, we used RNAseq to provide a snapshot of the differences between the transcriptomes of M. smegmatis mc2155 and M. smegmatis mc2155 {Delta}phoH2 during normal growth. At 48 hours, elevated expression of the sigF regulon and its predicted regulatory cascade was observed in{Delta} phoH2 relative to wild type. In biochemical assays, PhoH2 showed specific activity toward sigF mRNA insinuating a role of PhoH2 in modulating the pool of sigF mRNA in the cell during normal growth, adding further complexity to the repertoire of reported mechanisms of post-translational regulation. Multiple copies of the preferred target site of PhoH2 were identified in loops of the sigF mRNA structure, leading us to propose a mechanism for the activity of PhoH2 that is initiated after assembly on specific single-stranded loops of RNA. We hypothesise that PhoH2 is a toxin-antitoxin that contributes to the regulation of SigF at a post-transcriptional level through targeted activity on sigF mRNA. This work presents the first evidence for post-transcriptional regulation of SigF along with the biological function of PhoH2 from M. smegmatis. This also has implications for the highly conserved PhoH2 toxin-antitoxin module across the mycobacteria including the important human pathogen M. tuberculosis.

molecular biology↗

bioRxiv2020

Ethylenediaminetetraacetic acid promotes the accumulation of nitric oxide

Ethylenediaminetetraacetic acid (EDTA) is a well-established chelating agent used in industry, agriculture, food, and medicine. However, the analysis of an EDTA-sensitive Arabidopsis thaliana mutant revealed that EDTA can significantly promote nitric oxide (NO) accumulation, indicating that EDTA has unexpected biological functions beyond its chelating activity. This finding challenges our current understanding about the effects of EDTA on biological systems. One Sentence SummaryAn analysis of ethylenediaminetetraacetic acid (EDTA)-sensitive mutants suggests that EDTA can promote the accumulation of nitric oxide.

molecular biology↗

bioRxiv2021

Determination of m6A frequency utilizing 4SedTTP-RT Ligation Assisted PCR (SLAP) in viral and cellular long non-coding RNAs

N6-methyladenosine is one of the most abundant epitranscriptomic signatures that can affect every aspect of RNA biology, from structure and stability to intra- and intermolecular interactions. The accurate quantitative assessment of RNA stoichiometry at single-nucleotide resolution is a prerequisite to evaluate the biological significance of m6A in the context of specific RNA. We have developed a new method, termed 4-Selenothymidine 5-triphosphate reverse transcription and Ligation Assisted PCR analysis (SLAP), for quantitative and unbiased assessment of the m6A fraction on target RNA. The inclusion of thymidine triphosphate derivative during reverse transcription discourages base pair formation with m6A resulting in the reactions cessation, while maintaining normal A-T base pairing. The site-specific ligation of the resulting cDNAs with adapters, followed by amplification, generates two distinct products that reflect the modified and unmodified fraction of the analyzed RNA. These PCR products are subsequently separated by gel electrophoresis and quantified using densitometric analysis. We applied the SLAP to verify the position and assess the frequency of m6A sites present on two exemplary long non-coding RNAs. We assessed the SLAP specificity, accuracy, and sensitivity, proving the applicability of this method for the m6A analysis on less abundant transcripts. Overall, this method constitutes an extension of the birds-eye view of RNA m6A landscape provided by epitranscriptome-wide analyses by delivering quantitative assessment of modification frequency and can therefore aid the understanding of the consequences of m6A on biological processes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/460679v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@15845aeorg.highwire.dtl.DTLVardef@46a95aorg.highwire.dtl.DTLVardef@118633dorg.highwire.dtl.DTLVardef@1b52f9_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2021

PlantRNA 2.0 : an updated database dedicated to tRNAs of photosynthetic eukaryotes

PlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 51 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. Transfer RNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, circa 37 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, non-canonical splicing sites in the D- or T- regions of tRNA molecules were identified and experimentally validated. As for PlantRNA 1.0, comprehensive biological information including 5- and 3-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included.

molecular biology↗