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Results for “Molecular Biology”

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bioRxiv2020

Combined degradome and replicated small RNA sequencing identifies Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

BackgroundSmall RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed Brassica napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem. ResultsWe identified different classes of sRNAs from B. napus by high throughput sequencing of replicated mock and infected samples at 24 hours post-inoculation (HPI). Overall, 3,999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. Degradome sequencing identified numerous likely sRNA targets that were enriched for immunity-related GO terms, including those related to jasmonic acid signalling, during infection. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 434 unique cleaved mRNA products from these miRNAs, of which 50 were unique to the infected library. A novel miR1885-triggered disease resistance gene-derived secondary sRNA locus was identified and verified with degradome sequencing. We also experimentally validated silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5-RACE. ConclusionsThe findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.

molecular biology↗

bioRxiv2023

How do biomarkers dance? Specific moves of defense and damage biomarkers for biological interpretation of dose-response model trends.

Omics and multi-omics studies are currently increasingly used in ecotoxicology to highlight the induction of known or new biomarkers when an organism is exposed to one (or more) contaminant(s). Although it is virtually impossible to identify all biomarkers from all possible organisms, biomarkers can be grouped into two categories, defense or damage biomarkers and they have a limited number of response trends. Our working hypothesis is that defense and damage biomarkers show different dose-response patterns. A meta-analysis of 156 articles and 2,595 observations of dose-response curves of well-known defense and damage biomarkers was carried out in order to characterize the response trends of these biological parameters in a large panel of living organisms (18 phyla) exposed to a wide variety of inorganic or organic contaminants. Defense biomarkers describe biphasic responses (bell-shaped and U-shaped) to a greater extent than damage biomarkers. In contrast, damage biomarkers varied mainly monotonically (decreasing or increasing). Neither the nature of the contaminant nor the type of organisms, whatever the kingdom (Plantae, Animalia, Chromista or Bacteria), influence these specific responses. This result suggests that cellular defense and damage mechanisms are not specific to stressors and are conserved throughout life. The meta-analysis results confirm the usefulness of trend analysis in dose-response models as a biological interpretation of biomarkers in large dataset and their application in determining the concentration ranges inducing defense responses (CRIDeR) and the concentration ranges inducing damage responses (CRIDaR) regardless of the contaminant tested or the organism studied. HighlightsO_LIWe interpreted 2,595 biomarker dose-response curves generated by chemical exposure. C_LIO_LIDefense biomarkers mainly describe biphasic (bell- or U-shaped) trends. C_LIO_LIDamage biomarkers mainly describe monotonic (decreasing or increasing) trends. C_LIO_LICellular defense and damage responses appear to have been conserved during evolution. C_LIO_LIResponse trend analysis is a promising tool for environmental risk assessment. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/551999v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@14b19c4org.highwire.dtl.DTLVardef@188ae31org.highwire.dtl.DTLVardef@643ed6org.highwire.dtl.DTLVardef@15953cd_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

A tRNA-specific function for tRNA methyltransferase Trm10 is associated with a new tRNA quality control mechanism in Saccharomyces cerevisiae

In Saccharomyces cerevisiae a single homolog of the tRNA methyltransferase Trm10 performs m1G9 modification on 13 different tRNAs. Here we provide evidence that the m1G9 modification catalyzed by S. cerevisiae Trm10 plays a biologically important role for one of these tRNA substrates, tRNATrp. Overexpression of tRNATrp (and not any of 38 other elongator tRNAs) rescues growth hypersensitivity of the trm10{Delta} strain in the presence of the antitumor drug 5-fluorouracil (5FU). Mature tRNATrp is depleted in trm10{Delta} cells, and its levels are further decreased upon growth in 5FU, while another Trm10 substrate (tRNAGly) is not affected under these conditions. Thus, m1G9 in S. cerevisiae is another example of a tRNA modification that is present on multiple tRNAs but is only essential for the biological function of one of those species. In addition to the effects of m1G9 on mature tRNATrp, precursor tRNATrp species accumulate in the same strains, an effect that is due to at least two distinct mechanisms. The levels of mature tRNATrp are rescued in the trm10{Delta}met22{Delta} strain, consistent with the known role of Met22 in tRNA quality control, where deletion of met22 causes inhibition of 5-3 exonucleases that catalyze tRNA decay. However, none of the known Met22-associated exonucleases appear to be responsible for decay of hypomodified tRNATrp, based on inability of mutants of each enzyme to rescue growth of the trm10{Delta} strain in the presence of 5FU. Thus, the surveillance of tRNATrp appears to constitute a distinct tRNA quality control pathway in S. cerevisiae.

molecular biology↗

bioRxiv2025

How many (distinguishable) classes can we identify in Single Particle Analysis?

Heterogeneity in cryoEM is essential for capturing macromolecule structural variability, reflecting their functional states and biological significance. However, estimating heterogeneity remains challenging due to particle misclassification and algorithmic biases, which can lead to reconstructions that blend distinct conformations or fail to resolve subtle differences. Furthermore, the low signal-to-noise ratio (SNR) inherent in cryo-EM data makes it nearly impossible to detect minute structural changes, as noise often obscures subtle variations in macromolecular projections. In this paper, we investigate the use of p-values associated with the null hypothesis that the observed classification differs from a random partition of the input dataset, thereby providing a statistical framework for determining the number of distinguishable classes present in a given dataset.

molecular biology↗

bioRxiv2018

Error-correcting DNA barcodes for high-throughput sequencing

Many large-scale high-throughput experiments use DNA barcodes--short DNA sequences prepended to DNA libraries--for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely-used error-correcting codes borrowed from computer science (e.g., Hamming and Levenshtein codes) do not properly account for insertions and deletions in DNA barcodes, even though deletions are the most common type of synthesis error. Here, we present and experimentally validate FREE (Filled/truncated Right End Edit) barcodes, which correct substitution, insertion, and deletion errors, even when these errors alter the barcode length. FREE barcodes are designed with experimental considerations in mind, including balanced GC content, minimal homopolymer runs, and reduced internal hairpin propensity. We generate and include lists of barcodes with different lengths and error-correction levels that may be useful in diverse high-throughput applications, including >106 single-error correcting 16-mers that strike a balance between decoding accuracy, barcode length, and library size. Moreover, concatenating two or more FREE codes into a single barcode increases the available barcode space combinatorially, generating lists with > 1015 error-correcting barcodes. The included software for creating barcode libraries and decoding sequenced barcodes is efficient and designed to be user-friendly for the general biology community.\n\nSIGNIFICANCE STATEMENTModern high-throughput biological assays study pooled populations of individual members by labeling each member with a unique DNA sequence called a \"barcode.\" DNA barcodes are frequently corrupted by DNA synthesis and sequencing errors, leading to significant data loss and incorrect data interpretation. Here, we describe a novel error-correction strategy to improve the efficiency and statistical power of DNA barcodes. To our knowledge, this is the first report of an error-correcting method that accurately handles insertions and deletions in DNA barcodes, the most common type of error encountered during DNA synthesis and sequencing, resulting in order-of-magnitude increases in accuracy, efficiency, and signal-to-noise. The accompanying software package makes deployment of these barcodes effortless for the broader experimental scientist community.

molecular biology↗

bioRxiv2017

Affinity-mass spectrometric technologies for quantitative proteomics in biological fluids

Proteins are the functional molecules in organisms and are therefore excellent biomarker candidates for a diversity of diseases. Immunoassays and mass spectrometry (MS) are two major technologies being used in proteomics; however, they either lack specificity or sensitivity. An emerging trend is to combine immunoassays with MS (which we call \"affinity-MS\"). This is an important milestone in quantitative proteomics, making it possible to measure low-abundance proteins with high specificity. The targeted enrichment and the assignment of mass-to-charge ratios to different molecules provide two selection criteria, making affinity-MS highly specific. Picogram-per-milliliter limits of detection have been obtained for many proteins. Furthermore, multiplexing capacity of >150 proteins has been achieved. This article reviews different formats of affinity-enrichment methods, and demonstrates how they are interfaced with both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) MS. The pros and cons of these techniques are compared, and future prospectives are discussed.

molecular biology↗

bioRxiv2019

Alteration of the premature tRNA landscape by gammaherpesvirus infection

Transfer RNAs (tRNAs) are transcribed by RNA polymerase III (RNAPIII) and play a central role in decoding our genome, yet their expression and non-canonical function remain understudied. Many DNA tumor viruses enhance the activity of RNAPIII, yet whether infection alters tRNA expression is largely unknown. Here, we present the first genome-wide analysis of how viral infection alters the tRNAome. Using a tRNA-specific sequencing method (DM-tRNA-seq), we find that the murine gammaherpesvirus MHV68 induces global changes in pre-tRNA expression with 14% of tRNA genes upregulated more than 3-fold, indicating that differential tRNA gene induction is a characteristic of DNA virus infection. Elevated pre-tRNA expression corresponds to increased RNAPIII occupancy for the subset of tRNA genes tested; additionally, post-transcriptional mechanisms contribute to the accumulation of pre-tRNA species. We find increased abundance of tRNA fragments derived from pre-tRNAs upregulated by viral infection, suggesting that non-canonical tRNA cleavage is also affected. Further, pre-tRNA accumulation, but not RNAPIII recruitment, requires gammaherpesvirus-induced degradation of host mRNAs by the virally encoded mRNA endonuclease muSOX. We hypothesize that depletion of pre-tRNA maturation or turnover machinery contributes to robust accumulation of full-length pre-tRNAs in infected cells. Collectively, these findings reveal pervasive changes to tRNA expression during DNA virus infection and highlight the potential of using viruses to explore tRNA biology. SignificanceViral infection can dramatically change the gene expression landscape of the host cell, yet little is known regarding changes in non-coding gene transcription by RNA polymerase III (RNAPIII). Among these are transfer RNAs (tRNAs), which are fundamental in protein translation, yet whose gene regulatory features remain largely undefined in mammalian cells. Here, we perform the first genome-wide analysis of tRNA expression changes during viral infection. We show that premature tRNAs accumulate during infection with the model gammaherpesvirus MHV68 as a consequence of increased transcription, but that transcripts do not undergo canonical maturation into mature tRNAs. These findings underscore how tRNA expression is a highly-regulated process and that cells have strategies to balance tRNA pools during conditions of elevated RNAPIII activity.

molecular biology↗

bioRxiv2023

The Unexpected Match: STAT3-NORAD Interaction, a Novel Link in Antiviral Defense

In the intricate biological landscape, evolution often repurposes familiar elements for novel roles. This study reveals an interaction between the long non-coding RNA NORAD, noted for its role in DNA stability, and the immune-related transcription factor STAT3. Our findings indicate that NORADs binding to STAT3 facilitates its nuclear entry, suppressing the antiviral response. In the absence of NORAD, STAT3 remains cytoplasmic, enabling STAT1 to activate this response. Evidence from viral infections and clinical samples reinforces this unique role for NORAD. Intriguingly, while other functions of NORAD are conserved in evolution, this newly discovered role is unique to humans, owing to the introduction of an ALU element in hominoids. This discovery sheds new light on the evolution of antiviral defenses.

molecular biology↗

bioRxiv2023

Characterization of gene regulatory elements and dynamic antimicrobial immune responses in mosquito cells using PRO-seq

Aedes aegypti mosquitoes are the principal vectors for epidemic arboviruses, including dengue, Zika, and chikungunya viruses. In these insect vectors, the concerted action of immune pathways shapes virus replication and transmission; yet, mechanistic and dynamic understanding of the transcriptional immune responses in mosquitoes remain limited. To address this knowledge gap, we profiled nascent transcription in mosquito cells and midgut tissue using Precision Run-On sequencing (PRO-seq). We identified exact transcription start nucleotides (TSNs), characterized promoter architectures, and generated the first genome-wide list of putative enhancers in Aedes aegypti, substantially expanding the regulatory annotation of this non-model organism. To investigate dynamic immune responses, we stimulated Aag2 cells with heat-inactivated E. coli and measured RNA synthesis and mRNA levels from matched samples. Bacterial stimulation induced rapid and temporally organized transcriptional responses associated with distinct biological functions and transcription factor motifs. Integration with mRNA-seq revealed that temporal patterns of mRNA accumulation were shaped by RNA synthesis, gene length, and stability, indicating multilayered regulation of mosquito immune responses. Implementing PRO-seq for mosquito midgut enabled characterization of tissue-specific transcription and TSN usage. Importantly, we demonstrate for the first time that PRO-seq captures in vivo microbial transcription within an organism, co-profiling host and microbiome nascent RNA synthesis. Altogether, this study substantially expands the regulatory annotation and functional genomic landscape of Aedes aegypti, reveals multilayered regulation of mosquito immune responses, and extends transcriptional profiling to host and microbiome activity in vivo. These insights advance understanding of gene regulation and immunity in this important arbovirus vector.

molecular biology↗

bioRxiv2024

First report of astroviruses in Tanzanian bats

Emerging and re-emerging infectious diseases have posed significant global health threats, with many attributed to zoonotic RNA viruses. These pathogens can, under some conditions, cross species barriers, facilitating transmission from animal hosts to humans. Bats, characterised by unique physiological and ecological features, and remarkable species diversity, are recognized to host numerous viruses with cross-species transmission potential. This study aimed to investigate the presence of RNA viruses from a broad diversity of Tanzanian bats while valorising archived biological samples. RNA was extracted from 125 samples (28 faeces and 97 oral swabs) of 17 bat species, followed by PCR amplification targeting five distinct viral genera (Filovirus, Coronavirus, Hantavirus, Paramyxovirus and Astrovirus). Overall, 1.6 % (3/125) of the samples from two bat species (Scotophilus dinganii and Miniopterus fraterculus) tested positive for astrovirus, with the coinfection of one bat with two AstV strains. No samples tested positive for Filovirus, Coronavirus, Hantavirus and Paramyxovirus. Phylogenetic analysis based on RNA-dependent RNA polymerase sequences revealed these sequences are respectively clustering with astroviruses detected in other bat species from the genus Scotophilus from East Asia and with astroviruses detected in Miniopterus bats from Africa and Asia. Altogether, these results are the first report of astroviruses in Tanzanian bats.

molecular biology↗

bioRxiv2025

Twist and Scout: Analysis and Curation of Particles in Cryo-Electron Tomography Using TANGO

Cryo-electron tomography (cryo-ET) enables the visualization of cellular structures in near-native environments, but its potential for spatial analysis has been underutilized due to a lack of versatile tools accommodating biological sample diversity. Available solutions often rely on case-specific or hypothesis-driven approaches, while holistic analyses remain challenging. In this work, we introduce TANGO (Twist-Aware Neighborhoods for Geometric Organization), a novel framework leveraging point cloud descriptors to analyze spatial arrangements of particles, such as macromolecular complexes, in cryo-ET. By encoding relative positions and orientations of particles as twist vectors, TANGO enables rotationally invariant feature extraction, including structured neighborhood occupancy, lattice topology, or angular deviations. Its modular design and user-friendly interface allow for customization of features, facilitating exploratory analyses of spatial patterns in diverse experimental datasets. With its open-source Python implementation, TANGO advances the ability to decode complex cellular architectures and their functional relationships, offering a valuable tool for the cryo-ET community.

molecular biology↗

bioRxiv2025

Donor Sex and Platelet Storage Influence the Therapeutic Effects of Platelet-Derived Extracellular Vesicles on Endothelial Barrier Function

Platelet-derived extracellular vesicles (PEVs) play an active role in vascular protection and repair and are being explored as a viable alternative to platelet therapy. Because platelet function and stability are shaped by donor sex and storage conditions, these same factors are likely to influence the PEVs they release. Understanding these influences is key to developing PEVs into a safe and dependable therapeutic option. In this study, we investigated how donor sex and platelet storage affect the therapeutic properties of PEVs. To address this, PEVs were isolated from platelets of healthy male and female donors. Platelets were either processed immediately after blood collection to represent a resting state or stored overnight at room temperature on a rocker to mimic platelet storage conditions. PEVs isolated from these preparations displayed similar size, morphology, and cellular uptake across groups, but their biological effects diverged. Female PEVs, particularly from resting platelets, provided the strongest protection against thrombin-induced endothelial barrier disruption, stabilized junctional proteins, and reduced oxidative stress. Male PEVs showed weaker barrier protection compared to female-derived PEVs but more pronounced modulation of certain inflammatory mediators. In addition, PEVs derived from resting platelets (RP-PEVs) consistently showed stronger protective effects than those from stored platelets (SP-PEVs), regardless of donor sex. These results highlight that donor sex and platelet storage influence PEVs function and underscore the need to account for both when developing PEV-based therapies. Key PointThe endothelial-protective effects of platelet-derived extracellular vesicles are modulated by platelet storage conditions and donor sex.

molecular biology↗

bioRxiv2018

Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing

Oligonucleotides and nucleic acid analogues that alter gene expression are showing therapeutic promise for selected human diseases. The modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, however, such modifications may also confer unexpected physicochemical and biological properties. Here we report backbone-specific effects of modified oligonucleotides on subnuclear organelles, altered distribution of nuclear proteins, the appearance of novel structured nuclear inclusions, and modification of RNA processing in cultured cells transfected with antisense oligonucleotides on a phosphorothioate backbone. Phosphodiester and phosphorodiamidate morpholino oligomers elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of fibroblasts exhibiting such disruption. These data suggest that the toxic effects and adverse events reported after clinical evaluation of phosphorothioate nucleic acid drugs may be mediated, at least in part, by non-specific interaction of nuclear components with the phosphorothioate backbone.

molecular biology↗

bioRxiv2026

HInt: interaction-based homology discovery through accelerated genome-scale AlphaFold screening

Identifying homologous proteins across deep evolutionary distances remains a major challenge because sequence and structural similarity progressively become undetectable over time. Although protein-protein interactions (PPIs) are often constrained by function and evolution, whether conserved interaction interfaces can provide an independent signal for homology detection has remained largely unexplored owing to the computational cost of proteome-scale interaction prediction. Here we introduce HInt (Homology by Interaction), an accelerated AlphaFold-based framework that enables practical proteome-scale PPI prediction through biologically informed pre-filtering and optimised high-throughput structure modelling. Using HInt, we establish interaction-based similarity as a third axis of homology detection. We show that conserved interaction interfaces reveal homologous relationships that remain inaccessible to conventional sequence- and structure-based approaches. Application of HInt to both prokaryotic and eukaryotic systems, together with experimental validation, uncovered a previously unrecognised VirB5 pilus-tip protein in the F-plasmid type IV secretion system and a previously unannotated F-box-like protein in the Saccharomyces cerevisiae ubiquitin-proteasome system. By enabling practical proteome-scale interaction screening, HInt provides a general framework for uncovering hidden homologues and expands the conceptual landscape of protein homology inference.

molecular biology↗

bioRxiv2021

The lncRNA EPB41L4A-AS1 regulates gene expression in the nucleus and exerts cell type-dependent effects on cell cycle progression

The long non-coding RNA (lncRNA) EPB41L4A-AS1 is aberrantly expressed in various cancers and has been reported to be involved in metabolic reprogramming and as a repressor of the Warburg effect. Although the biological relevance of EPB41L4A-AS1 is evident, its functional role seems to vary depending on cell type and state of disease. By combining RNA sequencing and ChIP sequencing of cell cycle synchronized HaCaT cells we previously identified EPB41L4A-AS1 to be one of 59 lncRNAs with potential cell cycle functions. Here, we demonstrate that EPB41L4A-AS1 exists as bright foci and regulates gene expression in the nucleus in both cis and trans. Specifically, we find that EPB41L4A-AS1 positively regulates its sense overlapping gene EPB41L4A and influences expression of hundreds of other genes, including genes involved in cell proliferation. Finally, we show that EPB41L4A-AS1 affects cell cycle phase distribution, though these effects vary between cell types.

molecular biology↗

bioRxiv2021

Combinations of Peptides Synergistically Activate the Regenerative Capacity of Skin Cells In Vitro

OBJECTIVETo explore synergistic effects related to skin regeneration, peptides with distinct biological mechanisms of action were evaluated in combination in different skin cell lines in the presence or absence of niacinamide (Nam). Furthermore, the synergistic responses of peptide combinations on global gene expression were compared to the changes that occur with fractional laser resurfacing treatment, a gold standard approach for skin rejuvenation, to further define optimal peptide combinations. METHODSMicroarray profiling was used to characterize the biological responses of peptide combinations (+/- Nam) relative to the individual components in epidermal keratinocyte and dermal fibroblast cell lines. Cellular functional assays were utilized to confirm the synergistic effects of peptide combinations. Bioinformatics approaches were used to link the synergistic effects of peptide combinations on gene expression to the transcriptomics of the skin rejuvenation response from fractional laser treatment. RESULTSMicroarray analysis of skin cells treated with peptide combinations revealed synergistic changes in gene expression compared to individual peptide controls. Bioinformatic analysis of synergy genes in keratinocytes revealed activation of NRF2-mediated oxidative stress responses by a combination of Ac-PPYL, Pal-KTTKS, and Nam. Additional analysis revealed direct downstream transcriptional targets of NRF2/ARE exhibiting synergistic regulation by this combination of materials, which was corroborated by a cellular reporter assay. NRF2-mediated oxidative stress response pathways were also found to be activated in the transcriptomics of the early skin rejuvenation response to fractional laser treatment, suggesting the importance of this biology in the early stages of tissue repair. Additionally, a second combination of peptides (pal-KT and Ac-PPYL) was found to synergistically restore cellular ATP levels that had been depleted due to the presence of ROS, indicating an additional mechanism whereby peptide synergies may accelerate skin repair. CONCLUSIONThrough combinatorial synergy studies, we have identified additional in vitro skin repair mechanisms beyond the previously described functions of individual peptides and correlated these to the transcriptomics of the skin rejuvenation response of fractional laser treatment. These findings suggest that specific peptides can act together, via complementary and synergistic mechanisms, to holistically enhance the regenerative capacity of in vitro skin cells.

molecular biology↗

bioRxiv2023

Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development

Ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ribosome ubiquitination is crucial for translational regulation and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To explore ribosome ubiquitination during animal development, we generated a zebrafish strain that expresses a FLAG-tagged ribosomal protein Rpl36/eL36 from its endogenous locus. We examined ribosome ubiquitination during zebrafish development by combining affinity purification of ribosomes from rpl36-FLAG zebrafish embryos with immunoblotting analysis. Our findings showed that ubiquitination of ribosomal proteins dynamically changed as development proceeded. We also showed that during zebrafish development, the ribosome was ubiquitinated by Znf598, an E3 ubiquitin ligase that activates RQC. Ribosomal protein Rps10/eS10 was found to be a key ubiquitinated protein during development. Furthermore, we showed that Rps10/eS10 ubiquitination-site mutations reduced the overall ubiquitination pattern of ribosome. These results demonstrate the complexity and dynamics of ribosome ubiquitination during zebrafish development.

molecular biology↗

bioRxiv2018

Single-molecule imaging of mRNA localization and regulation during the integrated stress response

Biological phase transitions form membrane-less organelles that generate distinct cellular environments. How molecules are partitioned between these compartments and the surrounding cellular space and the functional consequence of this localization is not well understood. Here, we report the localization of mRNA to stress granules(SGs) and processing bodies(PBs), which are distinct biomolecular condensates, and its effect on translation and mRNA degradation during the integrated stress response. Using single mRNA imaging in living human cells, we find that the interactions of mRNAs with SGs and PBs have different dynamics and that specific RNA binding proteins can anchor mRNAs within these compartments. During recovery from stress, mRNAs that were within SGs and PBs are translated and degraded at similar rates as their cytosolic counterparts.

molecular biology↗