SEARCH · PubMed Health

Results for “RNA granules”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed2024

An Intrinsically Disordered RNA Binding Protein Modulates mRNA Translation and Storage.

Proteins with intrinsically disordered regions (IDR) play diverse functions in regulating gene expression in the cell. Many of these proteins interact with cytoplasmic ribosomes. However, the molecular functions related to the interactions are largely unclear. In this study, using an abundant RNA-binding protein, Sbp1, with a structurally well-defined RNA recognition motif and an intrinsically disordered RGG domain as a model system, we investigated how an RNA binding protein with IDR modulates mRNA storage and translation. Using genomic and molecular approaches, we show that Sbp1 slows ribosome movement on cellular mRNAs and promotes polysome stacking or aggregation. Sbp1-associated polysomes display a ring-shaped structure in addition to a beads-on-string morphology visualized under the electron microscope, likely to be an intermediate slow translation state between actively translating polysomes and the translation-sequestered RNA granule. Moreover, the binding of Sbp1 to the 5'UTRs of mRNAs represses both cap-dependent and cap-independent translation initiation of proteins, many are functionally important for general protein synthesis in the cell. Finally, post-translational modifications at the arginine in the RGG motif change the Sbp1 protein interactome and play important roles in directing cellular mRNAs to either translation or storage. Taken together, our study demonstrates that under physiological conditions, intrinsically disordered RNA binding proteins promote polysome aggregation and regulate mRNA translation and storage using multiple distinctive mechanisms. This research also establishes a framework with which functions of other IDR-containing proteins can be investigated and defined.

RNA-Binding Proteins↗

PubMed2026

Genome-Wide Impact of Human DBR1 Depletion on RNA Processing Networks Reveal a Connection Between Pre-mRNA Splicing, mRNA Surveillance and Stress Granule Dynamics.

The RNA lariat debranching enzyme DBR1 is essential for intron turnover and RNA metabolism, yet its broader impact on transcriptome regulation remains incompletely defined. To elucidate the consequences of DBR1 depletion, we performed transcriptome-wide RNA sequencing of DBR1-knockdown and wild-type HEK293 cells. Differential expression analysis revealed widespread perturbations in pathways linked to RNA splicing, mRNA surveillance, translational control, and stress-granule biology. Many of the most significantly altered transcripts encode splicing factors and RNA quality-control components, underscoring DBR1's influence on post-transcriptional regulation. Alternative splicing analysis showed changes across multiple event types, with exon skipping accounting for >50% of events, followed by mutually exclusive exons, alternative 5' and 3' splice sites, and retained introns, indicating that DBR1 depletion induces pervasive splicing defects. Direct spliceosome inhibition using isoginkgetin (blocks tri-snRNP recruitment) and pladienolide B (targets SF3B1) reproduced the DBR1-KD mis-splicing patterns of cell signaling genes and factors involved in RNA metabolism, supporting a functional link between DBR1 activity and alternative splicing. Notably, DBR1 knockdown revealed a subset of transcripts that are both NMD-sensitive and enriched within stress granules. Consistent with this observation, G3BP1 immunopurification and confocal microscopy further support a role for DBR1 and UPF1 in stress-granule dynamics, suggesting that these factors may participate at distinct stages to influence mRNA fate under stress conditions. Together, these findings indicate that DBR1 functions beyond lariat RNA turnover as a common regulator of RNA processing, transcriptome stability, and stress granule homeostasis, revealing intricate crosstalk between RNA splicing and RNA quality control pathways in human cells.

Humans↗

PubMed1978

High resolution autoradiographic studies of RNA, protein and DNA synthesis during human eosinophil granulocytopoiesis: evidence for the presence of RNA on or within eosinophil granules.

Human bone marrow cells which had been incubated with [3H]uridine or [3H]leucine for I h were studied using the technique of electron microscope-autoradiography. The autoradiographs revealed the presence of newly-synthesized RNA and protein molecules within or on a proportion of (I) the primary and secondary granules in all classes of eosinophil precursors and (2) the secondary granules in eosinophil granulocytes. It is suggested that the granule-associated RNA molecules may be concerned with the synthesis of at least some of the new protein molecules which were incorporated into the limiting membrane or substance of eosinophil granules long after the immature primary granule stage. Studies of eosinophil precursors which had been incubated with [3H]thymidine for I h showed that the eosinophil granules do not label with this DNA precursor.

Autoradiography↗

PubMed2026

Systematic identification of germ granule proteins reveals specialized roles in RNAi and small RNA inheritance.

Biomolecular condensates, such as germ granules, organize RNAi pathways critical for fertility and genome regulation. However, the protein composition and functional contributions of these condensates remain poorly defined. Here, we applied TurboID proximity labeling to the Caenorhabditis elegans germ granule protein SIMR-1, integrating mass spectrometry with genetic screening, CRISPR-based tagging, and small RNA sequencing. This systematic approach identified several previously uncharacterized germ granule proteins that contribute to fertility, germline immortality, exogenous RNAi, and transgenerational inheritance. Small RNA sequencing of 21 mutants revealed broad and class-specific defects in siRNA and miRNA biogenesis, with distinct factors associated with defects in WAGO-class 22G-RNAs, CSR-class 22G-RNAs, or histone-directed small RNAs. Among these, we identified PINT-1, a highly disordered protein that directly interacts with and is recruited to germ granules by the PIWI Argonaute PRG-1. PINT-1 is required for piRNA-dependent and -independent secondary siRNA biogenesis and germline development. Comparative genomics revealed that PINT-1 has coevolved with PRG-1 across clade V nematodes, with a conserved structured N terminus and a rapidly diverging repeat-rich intrinsically disordered region. Together, our findings expand the germ granule proteome and reveal how distinct condensate components contribute to specialized functions within the small RNA pathways, while highlighting an evolutionarily coadapted PIWI interactor critical for siRNA biogenesis.

Animals↗

PubMed2026

Phosphoproteomics identifies the DYRK1B protein kinase as a regulator of processing bodies.

Dual-specificity tyrosine-phosphorylation-regulated kinase 1B (DYRK1B) modulates the cell cycle and cell fate during development, and is deregulated in cancer and metabolic syndrome. However, only a few DYRK1B substrates have been defined, so we undertook a phosphoproteomics screen in cells that exhibit inducible DYRK1B expression. Motif analysis revealed enrichment for proline-directed serine or threonine phosphorylation sites (pSer-Pro or pThr-Pro), consistent with the consensus motif of class I DYRKs. Gene Ontology (GO) analysis revealed enrichment of proteins involved in mRNA binding, mRNA processing and ribonucleoprotein complexes. Several processing body (PB) components, including DCP1A, PATL1 (PAT1B), EDC3 and 4E-T (also known as EIF4ENIF1), were identified as DYRK1B-inducible phosphoproteins. DYRK1B also co-immunoprecipitated with DCP1A, PAT1B, EDC3, EDC4, DDX6 and XRN1. Super-resolution microscopy demonstrated that DYRK1B co-localised with DCP1A, DCP1B and DDX6 in PBs. Expression of DYRK1B increased PB abundance, whereas inhibition, depletion or knockout of DYRK1B reduced phosphorylation of DCP1A and 4E-T and decreased PB number. Re-expression of wild-type but not kinase-dead DYRK1B restored PB numbers in knockout cells. These findings reveal novel DYRK1B targets and establish DYRK1B as a regulator of PB abundance.

Dyrk Kinases↗

PubMed1978

[Characteristics of mitosis pathology in a Chinese hamster cell culture with disorders of the protein-synthesizing system].

Disturbance of protein synthesis with puromycin and transcription of chromosomal and ribosomal RNA with actinomycin D was followed by marked changes in the normal course of mitosis. There was noted an increase in number of colchicin-like mitoses (C-mitoses), and particularly, sometimes, fragmentation of their cytoplasm with the formation of cluster-like structures. It is suggested that development of C-mitosis was connected not only with destruction in the mitotic apparatus formation system, but also with the block of synthesis of one of the chromosomal proteins, stabilizing DNA strands spiralization. Another form of pathological mitosis occurring under conditions of suppression of the metabolic processes ("hollow metaphase plate") was linked not only with the chromosomal alterations. Selective suppression of the ribosomal RNA transcription led to an evident anaphase delay and to coupling of telomere regions of chromosomes. This phenomenon is apparently associated with destruction of the "protective cover" of chromosomes, formed by RNA of the disintegrating nucleoli and RNA of perichromatin granules.

Animals↗

PubMed1979

Further cytochemical studies on the perichromatin granules.

The perichromatin granules were studied in hepatocytes of experimental rats injected with cycloheximide because the increased number of these nuclear components after such treatment facilitated their cytochemical investigation. Most perichromatin granules were sensitive to the digestion with pepsin and ribonuclease. In contrast, small population of perichromatin granules was resistent to such digestion under conditions which remove known RNA containing components such as ribosomes, nucleolar RNP components and interchromatin granules. The size of these resistent perichromatin granules was reduced and they consisted of filaments the width of which was similar to that of filaments in the chromatin. Moreover, a small population of perichromatin granules was sensitive to the digestion with pepsin and deoxyribonuclease. The size of these granules was only slightly reduced. All these observations indicate that most perichromatin granules contain the RNA and some the DNA. A possibility also exists that the perichromatin granules might contain both RNA and DNA but in various proportions. In addition, partial digestion with pepsin followed by a complete digestion with ribonuclease and deoxyribonuclease removed perichromatin granules as well as other nucleoprotein structures. On the other hand, such digestion facilitated the visualization of the nuclear and cytoplasmic skeleton (matrix) in situ.

Animals↗

PubMed1979

Ultrastructural and autoradiographic study of the effects of bleomycin on the interphase nucleus of cultured normal cells.

Primary cultures of hepatocytes and epithelial endometrial cells were treated with bleomycin (10 to 200 microgram/ml) for 30 to 300 min. Structural changes were studied with a staining method which contrasts ribonucleoproteins. The earliest visible alteration was the accumulation of perichromatin granules in association with the nucleolus. This disturbance was frequently accompanied by modifications in the nucleolar architecture. After larger treatments, the most striking changes were nucleolar segregation and the appearance of spherical clear bodies in the nucleolus. In the extranucleolar area, a remarkable diminution of ribonucleoprotein fibrils and clustering of interchromatin granules were observed. Functional disturbances in the synthesis and transporting of RNA to the cytoplasm were studied by high-resolution quantitative autoradiography after labeling with tritiated uridine. Bleomycin produces a strong inhibition of RNA synthesis in nucleolar and extranucleolar areas. Important decreases of [3H]uridine incorporation were observed as early as 30 min after the administration of drug. Alterations of processing and/or transporting of RNA to the cytoplasm were found after treatments with bleomycin (100 microgram/ml) for 30 to 300 min. It is suggested that the diminution of ribonucleoprotein fibrils is related to the inhibition of RNA synthesis while the accumulation of perichromatin granules is connected to alteration of the transporting and/or processing.

Animals↗

PubMed2026

Differential assembly of RNP granules via activation of distinct dsRNA sensors by adenovirus mutants.

Recognition of double-stranded RNA (dsRNA) triggers antiviral defense mediated by PKR and OAS3/RNase L pathways through translational arrest and RNA decay. This is accompanied by assembly of distinct cytoplasmic ribonucleoprotein (RNP) condensates termed stress granules (SGs) and RNase L-dependent bodies (RLBs). Here we show that adenovirus mutants engage distinct RNA-sensing pathways and promote differential assembly of cytoplasmic RNP granules. Infection with splicing-defective ∆E4 mutant leads to dsRNA accumulation and activation of both PKR and OAS3/RNase L, promoting formation of RLB-like granules. In contrast, mutants lacking virus-associated (VA) RNAs trigger PKR activation and assembly of SGs despite absence of detectable dsRNA. Proximity labeling proteomic analysis revealed distinct protein compositions of canonical SGs and RLBs, which were reflected in virus-induced granules. While ∆VA-induced granules were PKR-dependent, ∆E4 mutants induced RLB-like granules independently of PKR and RNase L. In cells lacking these sensors, granule assembly during ∆E4 infection coincided with translational arrest independent of eIF2α phosphorylation, indicating additional pathways linking nuclear dsRNA sensing to translational control and RNP granule assembly during viral infection. These findings provide novel insights into how distinct dsRNA sensors modulate translation and RNP condensates in response to stress.

RNA, Double-Stranded↗

PubMed1979

Induction of androgen-dependent protease and serous-like granules by tri-iodothyronine in the submandibular gland of mice with testicular feminization.

Esteroprotease, an androgen-dependent enzyme of the mouse submandibular gland, was increased by injection of tri-iodothyronine (T3) in mice with testicular feminization (Tfm) which are genetically deficient in androgen receptors. Histochemical and electron microscopic studies also demonstrated increases of RNA and serous-like granules in cells of the convoluted tubules of the gland. These findings suggest that the esteroprotease gene in Tfm mice is normal and that T3 can induced both esteroprotease and serous-like granules independently of androgen.

Androgen-Insensitivity Syndrome↗

PubMed1978

Alkaline ribonuclease associated with polyribosomes in fibroblasts of experimental granulation tissue.

Alkaline ribonuclease (RNase) from polyribosomes derived from experimental granulation tissue has been purified 1900-fold through affinity chromatography. The preparation was homogeneous in sodium dodecyl sulfate (SDS) polyacrylamide-gel electrophoresis with an estimated molecular weight of 15 000. Purified RNase was completely inhibited in the presence of divalent ions Mg2+(100 mM) and Ca2+(100 mM) but activated slightly with Na+(50 mM). The enzyme is an endonuclease and the best substrates were poly(U), mixed RNA from yeast, rRNA from granulation tissue and poly(C). The estimated apparent Km-values were 0.037, 0.064, 0.13 and 0.27 g1-1, respectively. In polyribosomes RNase occurred in both free and p-chloromercuribenzoate (pCMB)-liberated forms. The total activity was at the highest but the proportion of the free activity minimal in the granulation tissue during the maximal synthesis of collagen.

Animals↗

PubMed1977

On the relationship between the perichromatin granules and cellular ageing as well as cell differentiation.

Current hypotheses ascribe the role of pre-RNA storage or transport structures to the perichromatin granules. Their numerical density is directly related to the transcription activity of the nucleus. The perichromatin granules (P.K.) can be demonstrated in ultrathin sections with the stain used by Bernhard (1969) for ribonucleo-proteins. We have established the numerical density per unit of area in nuclear cross-sections of cells in young rats (1-2 months), old rats (26-29 months) and in relation to various cell function types. Cell aging causes a reduction in the numerical density of perichomatin granules in the big neurons of the cerebral cortex, the cerebellar granulocytes, the hepatocytes and the parotid cells. No age-related changes were found in the myocardial cells and erythroblasts of the same maturity. However, at the end of maturation, the number of perichromatin granules both in young and old erythroblasts was nil. (1) There is a quantitative reduction of perichromatin granules primarily in postmitotic and relatively postmitotic cells; (2) cell types showing no age-related reduction in perichromatin granules maintain high synthetic activity throughout their life; (3) the results confirm that relationships exist between numerical density of the perichromatin granules and cell activity; (4) the big fluctuations in the numbers of perichromatin granules in various cell types are probably connected with cell function.

Aging↗

PubMed1978

In vivo stimulation of nerve cells by phytohemagglutinin. I. Alterations of some cytological aging parameters in rat brain cells.

Phytohemagglutinin P (PHA-P) was administered in form of intralumbar injection to old (24-27 months) female Wistar rats. PHA-P has an inductive effect also on the nerve cells. The thermal denaturation characteristics of the DNA in situ as well as the numerical density of perichromatin granules being connected to the extranucleolar RNA synthesis returned practically to the young levels in the large brain cortical cells and in the cerebellar granular cells 20 h after the injection. The reversal of these aging phenomena was accompanied by a significant decrease of intranuclear and intracytoplasmic K+ content measured by X-ray microanalysis in the dry mass, whereas Na+ and Cl- remained unchanged. If PHA-P causes also some (1-2%) rehydration of the old neurons, the total ionic strength in the cell due to the monovalents may even reach the young level. The possible regulatory role of the ionic strength and the Na+/K+ ratio in the chromatin function is discussed on the basis of experimental data. It is the first time that the reversibility of some cytological aging parameters has been demonstrated in vivo.

Animals↗

PubMed2026

Acetic acid-induced translational repression involves eIF2B body formation and Ded1 sequestration into stress granules in yeast.

Elucidating the physiological impact of acetic acid stress and the corresponding yeast responses is essential for advancing fundamental biology and improving industrial alcoholic fermentation. Despite numerous genome-wide studies, information on the effects of acetic acid stress on yeast translational regulation remains limited. We found that a sublethal concentration of acetic acid (35 mM, 0.2% v/v) causes translational repression, accompanied by the formation of eIF2B bodies and the phosphorylation of eIF2α, both of which are involved in the regulation of translation initiation. Acetic acid also caused the sequestration of Ded1, a DEAD-box RNA helicase crucial for translation initiation, into stress granules. Removal of acetic acid restored translational activity and the proper localization of eIF2B and Ded1, indicating the reversibility of acetic acid-induced translational repression. Furthermore, when yeast cells were pretreated with 0.05% acetic acid, translational repression under subsequent 0.2% acetic acid stress was attenuated in wild-type cells but not in hrk1Δ cells. This indicates that Hrk1, a Pma1 activator, is required to sufficiently enhance tolerance to acetic acid-induced translational repression. These findings provide novel insights into the physiological effects of acetic acid stress on translational activity and translation-related factors in yeast cells.

Saccharomyces cerevisiae↗

PubMed1976

[Autoradiographic study of the rate of collagen synthesis under conditions of stimulation of the wound process].

A study was made of the rate of the tropocollagen synthesis by the granulation tissue fibroblasts and of its passage into the intercellular space in control animals and under conditions of stimulation of the wound process by potassium orotate, one of the pyrimidine series derivatives. It appeared that the process of tropocollagen synthesis became accelerated under the effect of the stimulant; collagen fiber precursor appeared in the intercellular space earlier than in control and became included into the fibrous structures of the granulation tissue, this correlating with the intensification of the RNA synthesis in the fibroblast nuclei and an accelerated passage of the newly-synthesized RNA from the nucleus into the cell cytoplasm under analogous conditions. There was noted no sharp excess of collagen in the granulation tissue of animals given potassium orotate.

Animals↗

PubMedDate not supplied

Neuromelanin and RNA in cells of substantia nigra.

We have found that with accumulation of neuromelanin granules within cell bodies of neurones of the human substantia nigra there is a reduction in cytoplasmic RNA and a decrease in nucleolar volume. These observations imply a gradual decrease in the functional capacity of the cell such that eventually, the cell is unable to produce sufficient protein to maintain its metabolic economy with atrophy and death ensuing. This reduction in protein synthesis may result from the mechanical displacement and disruption of the endoplasmic reticulum by the accumulated pigment granules.

Brain Chemistry↗

PubMed1977

Age-dependent alterations of the rate of RNA synthesis in rat brain cell nuclei.

Endogenous Mn2+ and Mg2+ activated RNA polymerase activity was measured in isolated cell nuclei of brain from rats of different age-groups. It was established that the activity of the nucleoplasmic RNA polymerase is maintained at the level of young animals up to an age of 16 months but is decreased after 24 months. The nucleolar RNA polymerase activity decreases already at 16 months and a higher ratio of the Mn2+:Mg2+ activated RNA polymerase activities has been found to be characteristic for the older animals. By means of stepwise sucrose density gradient centrifugation fractions were obtained from the nuclear preparations highly enriched in cell nuclei of neuronal and glial origin respectively. By measuring the activity of the nucleoplasmic and nucleolar RNA polymerases in these fractions it was found that the elevated ratio of the nucleoplasmic to nucleolar RNA polymerase activity at 16 months of age is a characteristic of the neuronal nuclei while the glial nuclei behave by the opposite manner. A parallelism existing between the age-dependent change of the endogenous RNA polymerase activity and that of perichromatic granules of rat brain cortical cells is discussed.

Age Factors↗

PubMed1976

Effects of nuclease and protease digestion on the ultrastructure of Paramecium basal bodies.

The action of deoxyribonuclease, ribonuclease, perchloric acid, and pronase on the fine structure of basal bodies of sectioned Paramecium was observed as part of a more extensive autoradiographic electron microscope analysis directed toward the problem of basal body DNA. DNase was found to have no detectable effect on basal body fine structure. Pronase first solubilized the linkers and C tubules of the triplets, then attacked the protein portion of the axosome, a localized portion of the ciliary axoneme adjacent to the distal end of the basal body, the rim fiber, and newly described lumen spiral complex. Prolonged pronase treatment disrupted the remaining microtubular elements, basal body plates, and cartwheel. RNase removed material from the axosome and the lumen complex, a conspicuous structure occupying the central portion of the basal body and consisting of a twisted or looped 90-A diam fiber or, more probably, pair of fibers, in association with large, dense granules. The apparent removal of both RNA and protein from this basal body structure by either of the two corresponding enzymes suggests an unusual organization of the two components. Observations from this and other laboratories suggest that the basal body RNA is single stranded. Its function is unknown but alternatives are discussed.

Animals↗