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Frontiers in Plant Science 2023Messenger RNA polyadenylation, the process wherein the primary RNA polymerase II transcript is cleaved and a poly(A) tract added, is a key step in the expression of...
Messenger RNA polyadenylation, the process wherein the primary RNA polymerase II transcript is cleaved and a poly(A) tract added, is a key step in the expression of genes in plants. Moreover, it is a point at which gene expression may be regulated by determining the functionality of the mature mRNA. Polyadenylation is mediated by a complex (the polyadenylation complex, or PAC) that consists of between 15 and 20 subunits. While the general functioning of these subunits may be inferred by extending paradigms established in well-developed eukaryotic models, much remains to be learned about the roles of individual subunits in the regulation of polyadenylation in plants. To gain further insight into this, we conducted a survey of variability in the plant PAC. For this, we drew upon a database of naturally-occurring variation in numerous geographic isolates of . For a subset of genes encoding PAC subunits, the patterns of variability included the occurrence of premature stop codons in some accessions. These and other observations lead us to conclude that some genes purported to encode PAC subunits in are actually pseudogenes, and that others may encode proteins with dispensable functions in the plant. Many subunits of the PAC showed patterns of variability that were consistent with their roles as essential proteins in the cell. Several other PAC subunits exhibit patterns of variability consistent with selection for new or altered function. We propose that these latter subunits participate in regulatory interactions important for differential usage of poly(A) sites.
PubMed: 38317838
DOI: 10.3389/fpls.2023.1303398 -
Advanced Science (Weinheim,... Apr 2024During maternal-to-zygotic transition (MZT) in the embryo, mRNA undergoes complex post-transcriptional regulatory processes. However, it is unclear whether and how...
During maternal-to-zygotic transition (MZT) in the embryo, mRNA undergoes complex post-transcriptional regulatory processes. However, it is unclear whether and how alternative splicing plays a functional role in MZT. By analyzing transcriptome changes in mouse and human early embryos, dynamic changes in alternative splicing during MZT are observed and a previously unnoticed process of zygotic splicing activation (ZSA) following embryonic transcriptional activation is described. As the underlying mechanism of RNA splicing, splicing factors undergo dramatic maternal-to-zygotic conversion. This conversion relies on the key maternal factors BTG4 and PABPN1L and is zygotic-transcription-dependent. CDK11-dependent phosphorylation of the key splicing factor, SF3B1, and its aggregation with SRSF2 in the subnuclear domains of 2-cell embryos are prerequisites for ZSA. Isoforms generated by erroneous splicing, such as full-length Dppa4, hinder normal embryonic development. Moreover, alternative splicing regulates the conversion of early embryonic blastomeres from totipotency to pluripotency, thereby affecting embryonic lineage differentiation. ZSA is an essential post-transcriptional process of MZT and has physiological significance in generating new life. In addition to transcriptional activation, appropriate expression of transcript isoforms is also necessary for preimplantation embryonic development.
Topics: Humans; Animals; Mice; Transcriptome; Zygote; Embryonic Development; RNA Splicing; Protein Isoforms; Poly(A)-Binding Proteins; Nuclear Proteins
PubMed: 38308190
DOI: 10.1002/advs.202308496 -
Cell Reports Feb 2024Without new transcription, gene expression across the oocyte-to-embryo transition (OET) relies instead on regulation of mRNA poly(A) tails to control translation....
Without new transcription, gene expression across the oocyte-to-embryo transition (OET) relies instead on regulation of mRNA poly(A) tails to control translation. However, how tail dynamics shape translation across the OET in mammals remains unclear. We perform long-read RNA sequencing to uncover poly(A) tail lengths across the mouse OET and, incorporating published ribosome profiling data, provide an integrated, transcriptome-wide analysis of poly(A) tails and translation across the entire transition. We uncover an extended wave of global deadenylation during fertilization in which short-tailed, oocyte-deposited mRNAs are translationally activated without polyadenylation through resistance to deadenylation. Subsequently, in the embryo, mRNAs are readenylated and translated in a surge of global polyadenylation. We further identify regulation of poly(A) tail length at the isoform level and stage-specific enrichment of mRNA sequence motifs among regulated transcripts. These data provide insight into the stage-specific mechanisms of poly(A) tail regulation that orchestrate gene expression from oocyte to embryo in mammals.
Topics: Animals; Mice; Embryo, Mammalian; Gene Expression Profiling; Oocytes; RNA, Messenger; Mammals
PubMed: 38306272
DOI: 10.1016/j.celrep.2024.113710 -
RNA (New York, N.Y.) Mar 20243' untranslated regions (3' UTRs) are critical elements of messenger RNAs, as they contain binding sites for RNA-binding proteins (RBPs) and microRNAs that affect...
3' untranslated regions (3' UTRs) are critical elements of messenger RNAs, as they contain binding sites for RNA-binding proteins (RBPs) and microRNAs that affect various aspects of the RNA life cycle including transcript stability and cellular localization. In response to T cell receptor activation, T cells undergo massive expansion during the effector phase of the immune response and dynamically modify their 3' UTRs. Whether this serves to directly regulate the abundance of specific mRNAs or is a secondary effect of proliferation remains unclear. To study 3'-UTR dynamics in T helper cells, we investigated division-dependent alternative polyadenylation (APA). In addition, we generated 3' end UTR sequencing data from naive, activated, memory, and regulatory CD4 T cells. 3'-UTR length changes were estimated using a nonnegative matrix factorization approach and were compared with those inferred from long-read PacBio sequencing. We found that APA events were transient and reverted after effector phase expansion. Using an orthogonal bulk RNA-seq data set, we did not find evidence of APA association with differential gene expression or transcript usage, indicating that APA has only a marginal effect on transcript abundance. 3'-UTR sequence analysis revealed conserved binding sites for T cell-relevant microRNAs and RBPs in the alternative 3' UTRs. These results indicate that poly(A) site usage could play an important role in the control of cell fate decisions and homeostasis.
Topics: 3' Untranslated Regions; Polyadenylation; MicroRNAs; RNA-Seq; RNA, Messenger; T-Lymphocytes, Helper-Inducer; RNA-Binding Proteins
PubMed: 38302256
DOI: 10.1261/rna.079897.123 -
Pain Jul 2024Metabolism is inextricably linked to every aspect of cellular function. In addition to energy production and biosynthesis, metabolism plays a crucial role in regulating...
Metabolism is inextricably linked to every aspect of cellular function. In addition to energy production and biosynthesis, metabolism plays a crucial role in regulating signal transduction and gene expression. Altered metabolic states have been shown to maintain aberrant signaling and transcription, contributing to diseases like cancer, cardiovascular disease, and neurodegeneration. Metabolic gene polymorphisms and defects are also associated with chronic pain conditions, as are increased levels of nerve growth factor (NGF). However, the mechanisms by which NGF may modulate sensory neuron metabolism remain unclear. This study demonstrated that intraplantar NGF injection reprograms sensory neuron metabolism. Nerve growth factor suppressed mitochondrial pyruvate oxidation and enhanced lactate extrusion, requiring 24 hours to increase lactate dehydrogenase A and pyruvate dehydrogenase kinase 1 (PDHK1) expression. Inhibiting these metabolic enzymes reversed NGF-mediated effects. Remarkably, directly disrupting mitochondrial pyruvate oxidation induced severe, persistent allodynia, implicating this metabolic dysfunction in chronic pain. Nanopore long-read sequencing of poly(A) mRNA uncovered extensive transcriptomic changes upon metabolic disruption, including altered gene expression, splicing, and poly(A) tail lengths. By linking metabolic disturbance of dorsal root ganglia to transcriptome reprogramming, this study enhances our understanding of the mechanisms underlying persistent nociceptive sensitization. These findings imply that impaired mitochondrial pyruvate oxidation may drive chronic pain, possibly by impacting transcriptomic regulation. Exploring these metabolite-driven mechanisms further might reveal novel therapeutic targets for intractable pain.
Topics: Animals; Ganglia, Spinal; Mitochondria; Transcriptome; Pyruvic Acid; Male; Oxidation-Reduction; Nerve Growth Factor; Hyperalgesia; Mice; Sensory Receptor Cells
PubMed: 38285538
DOI: 10.1097/j.pain.0000000000003158 -
Journal of Visualized Experiments : JoVE Jan 2024Polyadenylation is a crucial posttranscriptional modification that adds poly(A) tails to the 3' end of mRNA molecules. The length of the poly(A) tail is tightly...
Polyadenylation is a crucial posttranscriptional modification that adds poly(A) tails to the 3' end of mRNA molecules. The length of the poly(A) tail is tightly regulated by cellular processes. Dysregulation of mRNA polyadenylation has been associated with abnormal gene expression and various diseases, including cancer, neurological disorders, and developmental abnormalities. Therefore, comprehending the dynamics of polyadenylation is vital for unraveling the complexities of mRNA processing and posttranscriptional gene regulation. This paper presents a method for measuring poly(A) tail lengths in RNA samples isolated from Drosophila larval brains and Drosophila Schneider S2 cells. We employed the guanosine/inosine (G/I) tailing approach, which involves the enzymatic addition of G/I residues at the 3' end of mRNA using yeast poly(A) polymerase. This modification protects the RNA's 3' end from enzymatic degradation. The protected full-length poly(A) tails are then reverse-transcribed using a universal antisense primer. Subsequently, PCR amplification is performed using a gene-specific oligo that targets the gene of interest, along with a universal sequence oligo used for reverse transcription. This generates PCR products encompassing the poly(A) tails of the gene of interest. Since polyadenylation is not a uniform modification and results in tails of varying lengths, the PCR products display a range of sizes, leading to a smear pattern on agarose gel. Finally, the PCR products are subjected to high-resolution capillary gel electrophoresis, followed by quantification using the sizes of the poly(A) PCR products and the gene-specific PCR product. This technique offers a straightforward and reliable tool for analyzing poly(A) tail lengths, enabling us to gain deeper insights into the intricate mechanisms governing mRNA regulation.
Topics: Animals; Drosophila; Cell Line; Polyadenylation; RNA, Messenger; Brain; Poly A
PubMed: 38284531
DOI: 10.3791/66116 -
Molecules (Basel, Switzerland) Jan 2024The textile industry produces high volumes of colored effluents that require multiple treatments to remove non-adsorbed dyes, which could be recalcitrant due to their...
The textile industry produces high volumes of colored effluents that require multiple treatments to remove non-adsorbed dyes, which could be recalcitrant due to their complex chemical structure. Most of the studies have dealt with the biodegradation of mono or diazo dyes but rarely with poly-azo dyes. Therefore, the aim of this paper was to study the biodegradation of a four azo-bond dye (Sirius grey) and to optimize its decolorization conditions. Laccase-containing cell-free supernatant from the culture of a newly isolated fungal strain, strain BS9 was used in the presence of 1-hydroxybenzotriazol (HBT) to optimize the dye decolorization conditions. A Box-Benken design with four factors, namely pH, enzyme concentration, HBT concentration, and dye concentration, was performed to determine optimal conditions for the decolorization of Sirius grey. The optimal conditions were pH 5, 1 U/mL of laccase, 1 mM of HBT, and 50 mg/L of initial dye concentration, ensuring a decolorization yield and rate of 87.56% and 2.95%/min, respectively. The decolorized dye solution showed a decrease in its phytotoxicity (Germination index GI = 80%) compared to the non-treated solution (GI = 29%). This study suggests that the laccase-mediator system could be a promising alternative for dye removal from textile wastewater.
Topics: Laccase; Azo Compounds; Biodegradation, Environmental; Coloring Agents; Poly A; Polyporaceae
PubMed: 38257390
DOI: 10.3390/molecules29020477 -
International Journal of Molecular... Jan 2024The cationic platinum(II) organometallic complex [Pt(terpy)Me] (terpy = 2,2':6',2″-terpyridine) at mild acidic pH interacts with poly(L-glutamic acid) (L-PGA) in its...
A Kinetic Investigation of the Supramolecular Chiral Self-Assembling Process of Cationic Organometallic (2,2':6',2″-terpyridine)methylplatinum(II) Complexes with Poly(L-glutamic Acid).
The cationic platinum(II) organometallic complex [Pt(terpy)Me] (terpy = 2,2':6',2″-terpyridine) at mild acidic pH interacts with poly(L-glutamic acid) (L-PGA) in its α-helix conformation, affording chiral supramolecular adducts. Their kinetics of formation have been investigated in detail as a function of the concentrations of both reagents and changing pH, ionic strength, the length of the polymeric scaffold and temperature. After a very fast early stage, the kinetic traces have been analyzed as three consecutive steps, suggesting a mechanism based on the electrostatic fast formation of a not-organized aggregate that subsequently evolves through different rearrangements to form the eventual supramolecular adduct. A model for this species has been proposed based on (i) the attractive electrostatic interaction of the cationic platinum(II) complexes and the polyelectrolyte and (ii) the π-stacking interactions acting among the [Pt(terpy)Me] units.
Topics: Glutamic Acid; Platinum; Poly A; Cations; Kinetics
PubMed: 38256248
DOI: 10.3390/ijms25021176 -
International Journal of Molecular... Jan 2024Polymer nanocomposites filled with carbon nanoparticles (CNPs) are a hot topic in materials science. This article discusses the current research on the use of these...
Polymer nanocomposites filled with carbon nanoparticles (CNPs) are a hot topic in materials science. This article discusses the current research on the use of these materials as interfacial electron transfer films for solid contact potentiometric membrane sensors (SC-PMSs). The results of a comparative study of plasticized poly (vinyl chloride) (pPVC) matrices modified with single-walled carbon nanotubes (SWCNTs), fullerenes-C60, and their hybrid ensemble (SWCNTs-C60) are reported. The morphological characteristics and electrical conductivity of the prepared nanostructured composite films are reported. It was found that the specific electrical conductivity of the pPVC/SWCNTs-C60 polymer film was higher than that of pPVC filled with individual nanocomponents. The effectiveness of this composite material as an electron transfer film in a new potentiometric membrane sensor for detecting phenylpyruvic acid (in anionic form) was demonstrated. Screening for this metabolic product of phenylalanine in body fluids is of significant diagnostic interest in phenylketonuria (dementia), viral hepatitis, and alcoholism. The developed sensor showed a stable and fast Nernstian response for phenylpyruvate ions in aqueous solutions over the wide linear concentration range of 5 × 10-1 × 10 M, with a detection limit of 10 M.
Topics: Nanotubes, Carbon; Vinyl Chloride; Membranes; Nanocomposites; Poly A; Polymers; Phenylpyruvic Acids
PubMed: 38256194
DOI: 10.3390/ijms25021124 -
International Journal of Molecular... Jan 2024In this study, a novel film of poly(vinyl alcohol) (PVA)/pullulan (PULL) with improved surface characteristics was prepared from poly(vinyl acetate) (PVAc)/PULL blend...
In this study, a novel film of poly(vinyl alcohol) (PVA)/pullulan (PULL) with improved surface characteristics was prepared from poly(vinyl acetate) (PVAc)/PULL blend films with various mass ratios after the saponification treatment in a heterogeneous medium. According to proton nuclear magnetic resonance (H-NMR), Fourier transform infrared, and X-ray diffraction results, it was established that the successful fabrication of saponified PVA/PULL (100/0, 90/10, and 80/20) films could be obtained from PVAc/PULL (100/0, 90/10, and 80/20) films, respectively, after 72 h saponification at 50 °C. The degree of saponification calculated from H-NMR analysis results showed that fully saponified PVA was obtained from all studied films. Improved hydrophilic characteristics of the saponified films were revealed by a water contact angle test. Moreover, the saponified films showed improved mechanical behavior, and the micrographs of saponified films showed higher surface roughness than the unsaponified films. This kind of saponified film can be widely used for biomedical applications. Moreover, the reported saponified film dressing extended the lifespan of dressing as determined by its self-healing capacity and considerably advanced in vivo wound-healing development, which was attributed to its multifunctional characteristics, meaning that saponified film dressings are promising candidates for full-thickness skin wound healing.
Topics: Polyvinyl Alcohol; Ethanol; Glucans; Bandages; Poly A; Polyvinyl Chloride
PubMed: 38256100
DOI: 10.3390/ijms25021026