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At least 19 recordsLinked to original sources
PubMed2025

The small nucleolar RNA NON-CODING RNA 1 negatively regulates drought tolerance in Arabidopsis thaliana.

Small nucleolar RNAs (snoRNAs) function in ribosome biogenesis, and many ribosome biogenesis-related genes were downregulated by osmotic stress, implying a negative role of snoRNAs in drought tolerance. A snoRNA, namely, the NON-CODING RNA 1 (NCR1) was studied for its roles in drought tolerance in Arabidopsis. In comparison with wild-type (WT) plants, the loss-of-function ncr1 mutant plants showed enhanced drought tolerance, which was restored in the NCR1-complemented plants, whereas the NCR1-overexpressing plants revealed a drought-sensitive phenotype. Physiological analyses revealed that the ncr1 plants had a higher leaf surface temperature, lower water loss rates, and improved cell membrane integrity compared with WT. Comparative leaf transcriptomics and proteomics suggested that wax biosynthesis, anthocyanin metabolism, and leaf senescence processes are regulated by NCR1 under both normal and water-deficit conditions. Under drought, an increase in wax and anthocyanin accumulations and a delay in leaf senescence in ncr1 plants, when compared with WT, supported the transcriptome and proteomics data. Additionally, the ncr1 plants exhibited higher abscisic acid (ABA) sensitivity and longer root hairs than WT. Collectively, our results suggest that NCR1 negatively regulates drought tolerance through modification of wax biosynthesis, anthocyanin accumulation, leaf senescence, cell membrane integrity, ABA responses, and root hair development.

Arabidopsis↗
PubMed2026

Small nucleolar RNA HIDDEN TREASURE 2 reduces drought tolerance via multiple pathways in Arabidopsis.

Small nucleolar RNAs (snoRNAs) contribute to ribosome biogenesis and modulate various aspects of plant growth and development. Given that osmotic stress downregulates numerous genes associated with ribosome biogenesis in roots, we hypothesize that snoRNAs might function in modulating plant responses to osmotic and drought stresses. To prove this hypothesis, we assessed the role of a C/D-box snoRNA, namely the HIDDEN TREASURE 2 (HID2), in Arabidopsis thaliana responses to drought using both loss-of-function and overexpression approaches. Under drought conditions, the Arabidopsis hid2 mutant displayed a significantly higher survival rate than both wild-type (WT) and HID2-complemented plants, while HID2-overexpressing plants showed a lower survival rate than WT. A series of physiological assays indicated that the hid2 mutant maintained a slower rate of water loss and more intact cell membranes than WT plants under drought, which supported their drought-tolerant phenotype. Comparative leaf transcriptome and proteome analyses revealed that processes related to wax biosynthesis, senescence, and anthocyanin accumulation were differentially regulated between hid2 and WT plants under water-deficit conditions. Consistently, the hid2 mutant accumulated higher amounts of wax and anthocyanins and exhibited delayed leaf senescence relative to WT plants under drought. Additionally, the hid2 mutant showed improved ability to increase sensitivity to abscisic acid (ABA), scavenge reactive oxygen species (ROS), and extended root hairs. Overall, these findings demonstrate HID2's role as a negative modulator in Arabidopsis drought tolerance by negatively affecting cell membrane stability, wax and anthocyanin biosynthesis, senescence, ROS-scavenging capacity, ABA responsiveness, and root hair formation.

Arabidopsis↗
PubMed2026

A muskrat tissue atlas of small non-coding RNAs and their regulatory roles in muskrat musk secretion.

Muskrat musk, secreted by the male muskrat scent gland during the secretion period, is a valuable natural product with promising pharmacological activities. Its synthesis is regulated not only by coding genes but also by small non-coding RNAs (sncRNAs). However, a comprehensive tissue atlas of sncRNAs in muskrats has been lacking. To address this issue, we systematically profiled the expression levels of 6 sncRNA categories (piRNA [PIWI-interacting RNA], miRNA [microRNA], snoRNA [small nucleolar RNA], snRNA [small nuclear RNA], tRNA [transfer RNA], and other RNAs) across 13 tissues of the muskrat via deep sequencing. We identified 23,957 sncRNAs (∼ 65%) exhibiting tissue-specific expression patterns throughout the body. The results show that miRNA is the main contributor to tissue specificity. Eleven tissues showed a significantly higher number of miRNA-5p arm expressions compared to the 3p arm, although the brain was an exception. Quantitative results imply that miR-477-3p/5p and miR-794-3p are potentially involved in the regulation of muskrat musk synthesis and secretion in the muskrat scent glands. Their target genes were enriched in pathways related to energy supply, lipid metabolism, and cyclic morphological changes of the scent gland. Furthermore, we constructed a set of co-expressed miRNAs based on the hormone-dominated "brain-testis-scent gland" axis and the energy metabolism-dominated "brain-liver-scent gland" axis. These results provide the most comprehensive description to date of tissue-specific and ubiquitous sncRNAs in individual muskrat tissues. We anticipate that these data will enhance the understanding of the molecular regulation underlying muskrat musk synthesis and secretion.

Animals↗
PubMed2025

Quantitative Real-Time PCR for Circular RNA Detection and Analysis.

In eukaryotes, nearly 2% of the genome represented by the coding proteins. However, emerging evidence suggest more than 75% of the human genome referred to as noncoding part also plays a crucial role in governing major regulatory pathways. Noncoding RNAs can be categorized into several groups, such as microRNAs (miRNAs), small nuclear RNA (snRNAs), small nucleolar RNA (snoRNAs), transfer RNA (tRNA), and circular RNA (circRNAs), which contribute to this regulatory landscape. Circular RNAs (circRNAs) are identified as a new class of regulatory noncoding RNAs with gene regulatory roles by acting as miRNA or RNA binding protein sponges or interacting with proteins. Researchers employ quantitative real-time PCR methods to examine circular RNA expression utilizing divergent primers for identification and quantification.

RNA, Circular↗
PubMed2025

Identification and Analysis of Small Nucleolar RNAs by Real-Time Quantitative PCR.

One of the greatest scientific achievements of the twenty-first century is the completion of The Human Genome Project (HGP). Thereafter, we came to know that the human genome codes nearly 2% for making proteins and thus named as coding genes, suggesting the rest of the genome as noncoding or junk. However, research in the past two decades has shown and established that noncoding RNAs are major contributors of regulating and modulating the various function of cells as well as tissues. Noncoding RNAs can be classified as basis of their sizes in two categories, long noncoding RNAs (>200&#xa0;nt) and small noncoding RNAs (<200&#xa0;nt). Small nucleolar RNAs (snoRNAs) are part of the small noncoding RNA family and primarily reside inside the nucleus of eukaryotes. Sno RNAs can be divided into two major categories based on their distinguished structure and function; these are C/D box and HACA box snoRNAs. They participate in the posttranscriptional modifications on ribosomal RNAs (r-RNAs), transfer RNAs (t-RNAs), messenger RNAs (m-RNAs), and small nuclear RNAs (snRNAs). Sno RNAs act as guide RNAs to modify other noncoding RNAs by pseudouridylation or 2'O ribomethylation. We discussed in this protocol about one of the widely used techniques for detection and analysis of snoRNAs, i.e., real-time quantitative PCR (RT-qPCR).

RNA, Small Nucleolar↗
PubMed2026

Development and optimization of T-ARMS PCR assays for detection of lethal haplotypes of TADA2A, UR1B, and PORL1B in pigs in Vietnam.

Marker-assisted selection has increasingly relied on single-nucleotide polymorphisms (SNPs) as robust genetic markers, particularly in livestock breeding programs. In pig farming, embryonic mortality significantly affects litter size, and SNPs in reference genes have been implicated as potential causal factors. We developed and optimized a tetra-primer amplification refractory mutation system (T-ARMS) PCR assay for rapid, cost-effective detection of SNPs in 3 candidate genes-TADA2A, PORL1B, URB1-that are associated with embryonic lethality and reproductive performance. Primer sets were designed based on known mutation sites and validated using synthetic gene constructs and porcine genomic DNA from pigs of Duroc and Landrace breeds. Optimization of annealing temperatures and primer concentration ratios yielded distinct and reproducible allele-specific amplicon patterns that were corroborated by PCR-RFLP and Sanger sequencing. Our T-ARMS PCR protocol, which requires minimal equipment and reduces processing time to <3&#x2009;h, had high specificity and efficiency in differentiating wild-type, heterozygous, and homozygous mutant genotypes in 20 Duroc and 20 Landrace pigs. Our Tetra-ARMS PCR assay is a robust and economically viable tool for SNP genotyping in pig breeding programs, potentially contributing to the reduction of embryonic lethality and the improvement of overall reproductive outcomes.

Sus scrofa↗
PubMed2025

RNase III cleavage sites spread across splice junctions enforce sequential snoRNA processing.

Small nucleolar RNAs (snoRNAs) are a class of eukaryotic non-coding RNA molecules whose precursor transcripts are capped and polyadenylated. However, these end modifications are detrimental to snoRNA function and must be removed, a process typically involving excision from introns and/or endonucleolytic cleavage. For RNA precursors that host multiple snoRNAs, the sequence of maturation events is potentially important, but not well understood. Here, we report a new mode of maturation concerning snoRNA pairs that are co-hosted in the intron and the adjacent 3' exon of a precursor transcript. For a snoRNA pair with this arrangement in Schizosaccharomyces pombe, we found that the sequence surrounding an exon-exon junction within their precursor transcript folds into a hairpin after splicing of the intron. This hairpin recruits the RNase III ortholog Pac1, which participates in the maturation of the downstream snoRNA by cleaving the precursor. Our findings suggest that conditional RNase III cleavage signals hidden in an exon-exon junction evolved to enforce sequential snoRNA processing. Sequence analysis suggests that this mechanism is conserved in animals and plants.

RNA, Small Nucleolar↗
PubMed2025

SNORA47 affects stemness and chemotherapy sensitivity via EBF3/RPL11/c-Myc axis in luminal A breast cancer.

Chemotherapy sensitivity is an important factor that restricts the prognosis of breast cancer, and breast cancer stem cells (BCSCs) are the root cause of chemotherapy sensitivity. SNORA47, a member of the small nucleolar RNAs, has not been documented in the context of breast cancer, although it has been reported in lung cancer. In this study, high SNORA47 expression was linked to unfavorable survival outcomes among patients with Luminal A breast cancer in The Cancer Genome Atlas (TCGA). Among Luminal A patients, an elevated expression of SNORA47 correlated with high TNM stage (P&#x2009;=&#x2009;0.049). SNORA47 was strongly associated with breast cancer stemness phenotype and tumor sensitivity in vivo and in vitro. Our findings demonstrated that SNORA47, through its interaction with early B-cell factor 3(EBF3), facilitated the translocation of ribosomal protein L11(RPL11), which as a modulator that subsequently regulates the expression levels of the oncogene c-Myc. These discoveries provided novel insights into the molecular mechanisms of breast cancer progression and suggested potential therapeutic targets for overcoming drug sensitivity by disrupting the SNORA47-EBF3-RPL11 axis.

Humans↗
PubMed2026

Altered neural electrophysiological properties in the anterior cingulate cortex in a mouse model of Prader-Willi syndrome.

Prader-Willi syndrome (PWS) is a neurodevelopmental genetic disease associated with multiple metabolic and behavioural abnormalities converging into a distinctive clinical phenotype characterized by insatiable appetite leading to hyperphagia and eventual morbid obesity. The PWS spectrum results from deficiencies in paternally imprinted chromosome 15q11-13 region clustering around non-coding RNA multiple-repeat gene Snord116. A PWS mouse model with paternal Snord116 deletion (Snord116del) revealed multiple expected behavioural traits but failed to reproduce obesity in experimental paradigms designed to uncover homeostatic hypothalamic mechanisms of hyperphagia, while the possibility for pathologic hedonic overdrive underlying hyperphagic behaviours was not studied. In Snord116del mice, we examined functional properties of pyramidal neurons (PyNs) in the anterior cingulate cortex (ACC), the brain area commonly associated with goal-oriented and choice-outcome processing, including the value assessment of food items. We found indications of higher dendritic complexity and stronger afferent excitatory connectivity compared to controls. A strong excitatory input into Snord116del PyNs was balanced by a more hyperpolarized resting membrane potential, rendering lower soma excitability, improved signal-to-noise discrimination and stronger low-pass filtering. The enhanced excitatory network-tuning ability originating from Snord116 deficiency may explain the previously reported better performance of Snord116del over wild-type mice in working-for-food behavioural tests, whereas in humans it might entail exaggerated reward-seeking behaviour since early childhood when food is the main attractant. Our analysis of previously published genomic databases revealed candidate genes responsible for the abnormal functional neuronal phenotype caused by Snord116 deletion, including K+ and Na+ voltage-dependent ion channels, protein kinases, phosphatases and components of the mechanistic target of rapamycin (mTOR) intracellular signalling pathway. KEY POINTS: Altered biophysical characteristics and parameters of neuronal connectivity in pyramidal neurons in the anterior cingulate cortex (ACC) in Snord116 deletion mice. Alterations include augmented afferent synaptic input, altered resting state and firing properties of ACC pyramidal neurons. Our findings uncover a possible mechanistic basis for altered ACC functionality in Prader-Willi syndrome.

Animals↗
PubMed1976

Small RNA species of the HeLa cell: metabolism and subcellular localization.

The small molecular weight RNAs of the HeLa cell have been located in specific subcellular fractions. SnA is located in the nucleolus and is partially bonded to nucleolar 28S RNA. SnD, the most abundant of the small nuclear RNAs, is partially released from the nucleus when the nuclear preparation is briefly warmed. SnF is released from the nuclei when chromatin is digested with the micrococcal nuclease and not when pancreatic DNAase is used. The remainder of the small nuclear species remain in the nucleus following the digestion of chromatin and are concluded to be elements of the "nuclear skeleton." SnK is found predominantly in the cytoplasm, but migrates quantitatively to the nuclear fraction in the presence of high levels of actinomycin D. ScL is totally cytoplasmic and is partially bound to cell membranes. It is the 7S RNA found in oncornavirus virions. All the small nuclear RNAs appear initially in the cytoplasmic fraction before fixation in the nucleus. Two short-lived cytoplasmic species behave kinetically as precursors to the stable nuclear RNAs.

Cell Fractionation↗
PubMed1976

The similarities of ribosomal and basic chromosomal proteins from fungi.

We have compared the physical and chemical properties of yeast and fungal ribosomal proteins with those of higher eukaryotic histones. We have found that acidic urea gel electrophoresis, sodium dodecyl sulfate gel electrophoresis or chromatography on carboxymethylcellulose columns failed to distinguish ribosomal proteins from histones. The majority of the ribosomal proteins did not adsorb to an amberlite CG-50 column in the presence of 8% guanidine hydrochloride. Histones quantitatively adsorbed to an amberlite CG-50 column in the presence of 8% guanidine hydrochloride. A small number of fungal acid-soluble nuclear proteins, which coelectrophoresed with histones, were identified in a presumed nucleolar and nuclear membrane fraction. This fraction contained large amounts of RNA and small amounts of DNA. It is suggested that contamination of yeast and fungal chromosome preparations by a small number of ribosomal proteins can occur. Furthermore, several commonly employed criteria did not distinguish contaminating ribosomal proteins from authentic histones.

Binding Sites↗
PubMed1978

Studies on pulse-labelled RNA during the mitotic cycle of Physarum polycephalum by subnuclear fractionation.

A method is described for the isolation of pulse-labelled RNA from nuclei and subnuclear fractions of Physarum polycephalum. At all times during interphase the nucleolar RNA consisted mainly of a 34-S rRNA precursor with only small amounts of 26-S and 19-S rRNAs. The nucleoplasmic RNA consisted of predominantly mature 26-S rRNA with small amounts of 19-S rRNA and a 30-S RNA species. The 30-S RNA component displayed different labelling kinetics from the rRNA precursors. A low molecular weight RNA fraction (4-8 S) appeared to accumulate in the nucleus as interphase progressed.

Cell Nucleus↗
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↗
PubMed1978

Characterization of proteins from nucleolar preribosomes of mouse leukemia cells by two-dimensional polyacrylamide gel electrophoresis.

Proteins of isolated 80-S and 60-S nucleolar preribosomal particles were characterized by means of two-dimensional polyacrylamide gel electrophoresis, in the lymphocytic mouse leukemia cells L5178Y. Their identification and metabolic relationships with ribosomal subunit proteins were investigated using co-electrophoresis of unlabeled polysomal proteins with labeled proteins of either nucleolar preribosomes or ribosomal subunits. The large and small ribosomal subunits contain 40 and 31 proteins, respectively. The nucleolar 80-S preribosomes were analysed after 2 and 5 h of incubation with tritiated valine and leucine and were shown to contain about 55 proteins. Most of them were identical to cytoplasmic ribosomal subunit proteins. The nucleolar 60-S preribosomes contain all the proteins which are common to 80-S preribosomes and large ribosomal subunits, and one additional protein (L10). The ribosomal proteins which were absent from nucleolar particles were found to be labeled in the cytoplasmic ribosomes after the same incubation period. Thus, in addition to the association of the bulk of ribosomal proteins with 45-S RNA within the 80-S preribosomes, results indicate that a group of ribosomal proteins and particularly from the small subunits, become associated at later stages of the maturation process of mammalian ribosomes. It was further shown that a set of 10 proteins, different from ribosomal polypeptides, were present in nucleolar preribosomal particles. Several of them were associated with polyribosomes in the cytoplasm, whereas the others were unique to the nucleolus.

Cell Line↗
PubMed1975

Preferential inhibition by homopolyribonucleotides of the methylation of ribosomal ribonucleic acid and disruption of the production of ribosomes in a rat tumor.

The literature indicates that some mechanism other than the interferon or host-mediated immune enhancement might also be responsible for an antitumor effect of polyinosinate-polycytidylate [poly(I)-poly(C)]. We have examined the effect of this drug on the synthesis of ribosomes and other macromolecules in a rat tumor, the Novikoff ascites hepatoma. The nucleolus was one of the primary targets affected by the administration of poly(I)-poly(C) in vivo. A progressive decline of the activity of nucleolar ribosomal RNA methylases began within 2 hr, followed by a decline of the nucleolar RNA content. The activity of nucleolar RNA polymerase was inhibited only at later time intervals. Labeling of tumor macromolecules in vivo revealed that the methylation of ribosomal RNA and the production of ribosomes, particularly in the small subunits, were immediately and progressively affected, followed by inhibition of the synthesis of DNA, RNA, and protein at later times. In addition, poly(I)-poly(C) also induced disaggregation of polyribosomes and restricted the movements of nuclear RNA to cytoplasm and of cytoplasmic protein to nucleus. These in vivo effects of poly(I)-poly(C) on tumor cells was observed neither on the host livers nor on livers of normal rats. Studies on isolated nucleoli showed that the in vitro addition of polyinosinate and several other compounds actively inhibited tumor ribosomal RNA methylases but were devoid of inhibitory effect against liver ribosomal RNA methylases; these results augment other studies in the literature in suggesting a selective effect of the polyinosinate moiety on tumor cells. We conclude from this study that initial impairment of the methylation of ribosomal precursor RNA, following exposure of tumor cells to poly(I)-poly(C), is responsible for the destruction of ribosomes, preferentially the small subunits, during the maturation processes. Failure to provide new ribosomes thus triggers the events limiting the growth of tumor cells.

Animals↗
PubMed1975

[Preliminary data on "fibrillary centers" of the nucleolus of various cells of the ovarian follicle of a lizard Lacerta muralis Laur].

The nucleolus of the thecal cells and little cells of the granulosa contains generally a single "fibrillar center" surrounded by the dense fibrous material of the nucleolus. The "fibrillar centers" are in contact with nucleolar associated heterochromatin. Cytochemical results show that "fibrillar centers" are chiefly composed of proteins which are revealed as ribonucleoproteins with the EDTA method, but the amount of RNA associated with these proteins seems to be small. It is possible that the fibrillar center also contains a little DNA.

Animals↗
PubMed1978

Nucleolar size in parallel with ribosomal RNA synthesis at diapause termination in the eggs of Bombyx mori.

The eggs of Bombyx mori, both in diapause and nondiapause, were subjected to cytological examination of nucleoli and measurement of RNA precursor incorporation (2 hours) into ribosomal RNA. In diapause eggs, the nucleoli were very small and the rate of ribosomal RNA synthesis was the lowest of the samples tested. Most cells in diapause possessed nuclei with one nucleolus. In contrast, the eggs activated from diapause by long chilling attained the largest size of nucleoli and the highest rate of ribosomal RNA synthesis. A significant proportion of the cell nuclei still had only one nucleolus at this stage. Three days after activation, the eggs exhibited intermediate levels in both the size of nucleoli and the rate of ribosomal RNA sythesis. At this stage, about half of the egg cell nuclei had two nucleoli.

Animals↗
PubMed1976

Fine structural observations on oocyte development in monogeneans.

The ultrastructural changes accompanying oocyte differentiation in the ovaries of the monogeneans, Diclidophora merlangi, Diplozoon paradoxum and Calicotyle kröyeri have been described. In each case, oogenesis in the ovary proceeds as far as meiotic prophase in the primary oocyte. A three-stage sequence of development based on oocyte morphology is proposed: (1) Oogonia and early, immature primary oocytes are typically undifferentiated, with chromatin-laden nuclei occupying most of the cell volume. The cytoplasm contains small clumps of mitochondria and unattached ribosomal aggregates. There is evidence of mitosis and, in later stages, meiotic prophase is indicated by the appearance of nuclear synaptonemal complexes. (2) Maturing primary oocytes are characterized by increased nucleolar volume associated with the production of RNA for export to the cytoplasm. An organized GER and Golgi apparatus are established and involved in the synthesis and packaging of membrane-limited cortical granules. Annulate lamellae and nucleolus-like bodies appear in the cytoplasm and, with development, the cells increase in size and, peripherally, become interdigitated. (3) Mature primary oocytes represent a resting phase when cellular activity is minimal. Golgi disappear and the ER fragments or becomes reduced in dimensions. Mitochondria and free ribosomes are numerous and cortical granules move to the cell periphery. The cells separate and, when mature, are released from the ovary. There are minor species differences in oocyte ultrastructure and development.

Animals↗