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Journal articles on the topic 'Messenger RNA couple'

Author: Grafiati

Published: 30 November 2024

Last updated: 31 July 2025

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1

Al Fayez, Nojoud, Majed S. Nassar, Abdullah A. Alshehri, et al. "Recent Advancement in mRNA Vaccine Development and Applications." Pharmaceutics 15, no. 7 (2023): 1972. http://dx.doi.org/10.3390/pharmaceutics15071972.

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Messenger RNA (mRNA) vaccine development for preventive and therapeutic applications has evolved rapidly over the last decade. The mRVNA vaccine has proven therapeutic efficacy in various applications, including infectious disease, immunotherapy, genetic disorders, regenerative medicine, and cancer. Many mRNA vaccines have made it to clinical trials, and a couple have obtained FDA approval. This emerging therapeutic approach has several advantages over conventional methods: safety; efficacy; adaptability; bulk production; and cost-effectiveness. However, it is worth mentioning that the deliver

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2

Oohayyed, N. A., M. M. Mohammed, A. M. Al-Rahim, R. N. Al Chalabi, S. A. Shaban, and A. A. J. Suleiman. "Identification of key miRNAs as regulatory biomarkers of gonadotropins leading to infertility in males." Obstetrics, Gynecology and Reproduction 17, no. 5 (2023): 607–24. http://dx.doi.org/10.17749/2313-7347/ob.gyn.rep.2023.398.

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Introduction. Infertility is a highly fatal reproductive system disorder that affects the ability of a couple to reproduce. Over the past decades, a drastic uplift has been recorded in infertility cases among males ranging from 20 to 70 % indicating spermatogenesis impairment.Aim: to identify key microRNAs (miRNAs) as regulatory biomarkers of gonadotropins involved in dysregulation of fertility-related genes to propose potential therapeutic strategies that would combat the action of oncogenic miRNAs (oncomiRs).Materials and Methods. Interaction analysis was performed between miRNAs and fertili

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3

Gong, Congcong, Yang Hu, Mao Zhou, et al. "Identification of specific modules and hub genes associated with the progression of gastric cancer." Carcinogenesis 40, no. 10 (2019): 1269–77. http://dx.doi.org/10.1093/carcin/bgz040.

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Abstract Gastric cancer (GC) has high morbidity and mortality rates worldwide. Abundant literature has reported several individual genes and their related pathways intimately involved in tumor progression. However, little is known about GC progression at the gene network level. Therefore, understanding the underlying mechanisms of pathological transition from early stage to late stage is urgently needed. This study aims to identify potential vital genes and modules involved in the progression of GC. To understand the gene regulatory network of GC progression, we analyzed micro RNAs and messeng

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Weber, Ramona, Min-Yi Chung, Csilla Keskeny, et al. "4EHP and GIGYF1/2 Mediate Translation-Coupled Messenger RNA Decay." Cell Reports 33, no. 2 (2020): 108262. http://dx.doi.org/10.1016/j.celrep.2020.108262.

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Hanjin, Cui, Liu Tao, Li Pengfei, et al. "Altered Long Noncoding RNA and Messenger RNA Expression in Experimental Intracerebral Hemorrhage - a Preliminary Study." Cellular Physiology and Biochemistry 45, no. 3 (2018): 1284–301. http://dx.doi.org/10.1159/000487464.

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Background/Aims: Functional recovery in the chronic phase is a difficult problem in intracerebral hemorrhage (ICH) treatment. Long noncoding RNAs (lncRNAs) are demonstrated to be involved in central nervous system (CNS) disorders. However, the roles of lncRNAs in post-ICH injury and repair are poorly understood, especially those that may be attributed to long-term neurological deficit. The present study depicted the lncRNA and messenger RNA (mRNA) profile by microarray at late stage after an experimental ICH. Methods: LncRNA and mRNA microarray was used to first identify differentially express

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Estevez, Mariana, Rui Li, Biplab Paul, et al. "Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells." RNA 28, no. 5 (2022): 697–710. http://dx.doi.org/10.1261/rna.079043.121.

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The human immunodeficiency virus type 1 (HIV-1) encodes multiple RNA molecules. Transcripts that originate from the proviral 5′ long terminal repeat (LTR) function as messenger RNAs for the expression of 16 different mature viral proteins. In addition, HIV-1 expresses an antisense transcript (Ast) from the 3′LTR, which has both protein-coding and noncoding properties. While the mechanisms that regulate the coding and noncoding activities of Ast remain unknown, post-transcriptional modifications are known to influence RNA stability, interaction with protein partners, and translation capacity. H

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Yang, Jing, Ying Cao, and Ligeng Ma. "Co-Transcriptional RNA Processing in Plants: Exploring from the Perspective of Polyadenylation." International Journal of Molecular Sciences 22, no. 7 (2021): 3300. http://dx.doi.org/10.3390/ijms22073300.

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Most protein-coding genes in eukaryotes possess at least two poly(A) sites, and alternative polyadenylation is considered a contributing factor to transcriptomic and proteomic diversity. Following transcription, a nascent RNA usually undergoes capping, splicing, cleavage, and polyadenylation, resulting in a mature messenger RNA (mRNA); however, increasing evidence suggests that transcription and RNA processing are coupled. Plants, which must produce rapid responses to environmental changes because of their limited mobility, exhibit such coupling. In this review, we summarize recent advances in

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8

Liu, Yaojuan, Yesenia Rodriguez, Robert L. Ross, et al. "RNA abasic sites in yeast and human cells." Proceedings of the National Academy of Sciences 117, no. 34 (2020): 20689–95. http://dx.doi.org/10.1073/pnas.2011511117.

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RNA abasic sites and the mechanisms involved in their regulation are mostly unknown; in contrast, DNA abasic sites are well-studied. We found surprisingly that, in yeast and human cells, RNA abasic sites are prevalent. When a base is lost from RNA, the remaining ribose is found as a closed-ring or an open-ring sugar with a reactive C1′ aldehyde group. Using primary amine-based reagents that react with the aldehyde group, we uncovered evidence for abasic sites in nascent RNA, messenger RNA, and ribosomal RNA from yeast and human cells. Mass spectroscopic analysis confirmed the presence of RNA a

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Grüschow, Sabine, Catherine S. Adamson, and Malcolm F. White. "Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector." Nucleic Acids Research 49, no. 22 (2021): 13122–34. http://dx.doi.org/10.1093/nar/gkab1190.

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Abstract Type III CRISPR systems detect invading RNA, resulting in the activation of the enzymatic Cas10 subunit. The Cas10 cyclase domain generates cyclic oligoadenylate (cOA) second messenger molecules, activating a variety of effector nucleases that degrade nucleic acids to provide immunity. The prophage-encoded Vibrio metoecus type III-B (VmeCmr) locus is uncharacterised, lacks the HD nuclease domain in Cas10 and encodes a NucC DNA nuclease effector that is also found associated with Cyclic-oligonucleotide-based anti-phage signalling systems (CBASS). Here we demonstrate that VmeCmr is acti

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Stephan, W., and D. A. Kirby. "RNA folding in Drosophila shows a distance effect for compensatory fitness interactions." Genetics 135, no. 1 (1993): 97–103. http://dx.doi.org/10.1093/genetics/135.1.97.

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Abstract Phylogenetic-comparative analysis was used to construct a secondary structure of Adh precursor messenger RNA (pre-mRNA) in Drosophila. The analysis revealed that the rate of coevolution of base-pairing residues decreases with their physical distance. This result is in qualitative agreement with a model of compensatory fitness interactions which assumes that mutations are individually deleterious but become harmless (neutral) in appropriate combinations. This model predicts that coupled mutations can become fixed in a population under mutation pressure and random genetic drift, when th

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Hurt, Jessica A., Robert A. Obar, Bo Zhai, Natalie G. Farny, Steven P. Gygi, and Pamela A. Silver. "A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export." Journal of Cell Biology 185, no. 2 (2009): 265–77. http://dx.doi.org/10.1083/jcb.200811072.

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Coupling of messenger RNA (mRNA) nuclear export with prior processing steps aids in the fidelity and efficiency of mRNA transport to the cytoplasm. In this study, we show that the processes of export and polyadenylation are coupled via the Drosophila melanogaster CCCH-type zinc finger protein CG6694/dZC3H3 through both physical and functional interactions. We show that depletion of dZC3H3 from S2R+ cells results in transcript hyperadenylation. Using targeted coimmunoprecipitation and liquid chromatography mass spectrometry (MS)/MS techniques, we characterize interactions of known components of

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12

Ryabova, L., E. Volianik, O. Kurnasov, A. Spirin, Y. Wu, and F. R. Kramer. "Coupled replication-translation of amplifiable messenger RNA. A cell-free protein synthesis system that mimics viral infection." Journal of Biological Chemistry 269, no. 2 (1994): 1501–5. http://dx.doi.org/10.1016/s0021-9258(17)42284-8.

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13

Faza, Marius Boulos, Stefan Kemmler, Sonia Jimeno, et al. "Sem1 is a functional component of the nuclear pore complex–associated messenger RNA export machinery." Journal of Cell Biology 184, no. 6 (2009): 833–46. http://dx.doi.org/10.1083/jcb.200810059.

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The evolutionarily conserved protein Sem1/Dss1 is a subunit of the regulatory particle (RP) of the proteasome, and, in mammalian cells, binds the tumor suppressor protein BRCA2. Here, we describe a new function for yeast Sem1. We show that sem1 mutants are impaired in messenger RNA (mRNA) export and transcription elongation, and induce strong transcription-associated hyper-recombination phenotypes. Importantly, Sem1, independent of the RP, is functionally linked to the mRNA export pathway. Biochemical analyses revealed that, in addition to the RP, Sem1 coenriches with components of two other m

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14

Wang, Chengyuan, Vadim Molodtsov, Emre Firlar, et al. "Structural basis of transcription-translation coupling." Science 369, no. 6509 (2020): 1359–65. http://dx.doi.org/10.1126/science.abb5317.

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In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)–synthesizing messenger RNA (mRNA) is coordinated with the movement of the first ribosome-translating mRNA. Coupling is modulated by the transcription factors NusG (which is thought to bridge RNAP and the ribosome) and NusA. Here, we report cryo–electron microscopy structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P site. Structures of TTCs containing short spacers show a state

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15

B. Malas, Tareq, and Timothy Ravasi. "Computational Tools for Genome-Wide miRNA Prediction and Study." Open Biology Journal 5, no. 1 (2012): 23–30. http://dx.doi.org/10.2174/1874196701205010023.

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MicroRNAs (miRNAs) are single-stranded non-coding RNA susually of 22 nucleotidesin length that play an important post-transcriptional regulation role in many organisms. MicroRNAs bind a seed sequence to the 3'-untranslated region (UTR) region of the target messenger RNA (mRNA), inducing degradation or inhibition of translation and resulting in a reduction in the protein level. This regulatory mechanism is central to many biological processes and perturbation could lead to diseases such as cancer. Given the biological importance, of miRNAs, there is a great need to identify and study their targ

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Aitken, Stuart, Ross D. Alexander, and Jean D. Beggs. "A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation." Journal of The Royal Society Interface 10, no. 86 (2013): 20130438. http://dx.doi.org/10.1098/rsif.2013.0438.

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The complexity of many RNA processing pathways is such that a conventional systems modelling approach is inadequate to represent all the molecular species involved. We demonstrate that rule-based modelling permits a detailed model of a complex RNA signalling pathway to be defined. Phosphorylation of the RNA polymerase II (RNAPII) C-terminal domain (CTD; a flexible tail-like extension of the largest subunit) couples pre-messenger RNA capping, splicing and 3′ end maturation to transcriptional elongation and termination, and plays a central role in integrating these processes. The phosphorylation

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Adams, Grace. "A beginner’s guide to RT-PCR, qPCR and RT-qPCR." Biochemist 42, no. 3 (2020): 48–53. http://dx.doi.org/10.1042/bio20200034.

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The development of the polymerase chain reaction (PCR), for which Kary Mullis received the 1992 Novel Prize in Chemistry, revolutionized molecular biology. At around the time that prize was awarded, research was being carried out by Russel Higuchi which led to the discovery that PCR can be monitored using fluorescent probes, facilitating quantitative real-time PCR (qPCR). In addition, the earlier discovery of reverse transcriptase (in 1970) laid the groundwork for the development of RT-PCR (used in molecular cloning). The latter can be coupled to qPCR, termed RT-qPCR, allowing analysis of gene

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18

Schuwirth, Barbara S., Maria A. Borovinskaya, Cathy W. Hau, et al. "Structures of the Bacterial Ribosome at 3.5 Å Resolution." Science 310, no. 5749 (2005): 827–34. http://dx.doi.org/10.1126/science.1117230.

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We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the t

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Chatterjee, Surajit, Adrien Chauvier, Shiba S. Dandpat, Irina Artsimovitch, and Nils G. Walter. "A translational riboswitch coordinates nascent transcription–translation coupling." Proceedings of the National Academy of Sciences 118, no. 16 (2021): e2023426118. http://dx.doi.org/10.1073/pnas.2023426118.

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Bacterial messenger RNA (mRNA) synthesis by RNA polymerase (RNAP) and first-round translation by the ribosome are often coupled to regulate gene expression, yet how coupling is established and maintained is ill understood. Here, we develop biochemical and single-molecule fluorescence approaches to probe the dynamics of RNAP–ribosome interactions on an mRNA with a translational preQ1-sensing riboswitch in its 5′ untranslated region. Binding of preQ1 leads to the occlusion of the ribosome binding site (RBS), inhibiting translation initiation. We demonstrate that RNAP poised within the mRNA leade

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Carter, T. D., X. Y. Chen, G. Carlile, E. Kalapothakis, D. Ogden, and W. H. Evans. "Porcine aortic endothelial gap junctions: identification and permeation by caged InsP3." Journal of Cell Science 109, no. 7 (1996): 1765–73. http://dx.doi.org/10.1242/jcs.109.7.1765.

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Gap junction channels permit the direct intercellular transfer of ions and small molecules and allow electrotonic coupling within tissues. Porcine aortic endothelial cells were extensively coupled, as assessed by gap junctional transfer of Lucifer yellow and the fluorescent calcium indicators fluo-3 and furaptra, but were not permeable to rhodamine B isothiocyanate-dextran 10S. The subunit composition of gap junction channels of porcine aortic endothelial cells was characterised using both northern blot analysis and RT-PCR techniques. Messenger RNA encoding connexins 37 and 43, but not 26, 32

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Li, Zhouhua, Liwei Wang, Thomas S. Hays, and Yu Cai. "Dynein-mediated apical localization of crumbs transcripts is required for Crumbs activity in epithelial polarity." Journal of Cell Biology 180, no. 1 (2008): 31–38. http://dx.doi.org/10.1083/jcb.200707007.

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Asymmetrical localization of transcripts coupled with localized translation constitutes an important mechanism widely deployed to regulate gene activity in a spatial manner. The conserved transmembrane protein Crumbs (Crb) is an important regulator of epithelial polarity. However, it remains unclear how Crb is targeted to the apical domain. Here, we show that the cytoplasmic dynein complex transports both Crb protein and transcripts to the apical domain of Drosophila melanogaster follicular cells (FCs). The crb 3′ untranslated region (UTR) is necessary and sufficient for the apical localizatio

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Divorty, Nina, Graeme Milligan, Delyth Graham, and Stuart A. Nicklin. "The Orphan Receptor GPR35 Contributes to Angiotensin II–Induced Hypertension and Cardiac Dysfunction in Mice." American Journal of Hypertension 31, no. 9 (2018): 1049–58. http://dx.doi.org/10.1093/ajh/hpy073.

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Abstract BACKGROUND The orphan receptor G protein–coupled receptor 35 (GPR35) has been associated with a range of diseases, including cancer, inflammatory bowel disease, diabetes, hypertension, and heart failure. To assess the potential for GPR35 as a therapeutic target in cardiovascular disease, this study investigated the cardiovascular phenotype of a GPR35 knockout mouse under both basal conditions and following pathophysiological stimulation. METHODS Blood pressure was monitored in male wild-type and GPR35 knockout mice over 7–14 days using implantable telemetry. Cardiac function and dimen

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Stoll, S., G. Müller, M. Kurimoto, et al. "Production of IL-18 (IFN-gamma-inducing factor) messenger RNA and functional protein by murine keratinocytes." Journal of Immunology 159, no. 1 (1997): 298–302. http://dx.doi.org/10.4049/jimmunol.159.1.298.

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Abstract Recently, the novel cytokine IL-18 (IFN-gamma-inducing factor) has been described as a growth and differentiation factor for Th1 cells. Epidermal keratinocytes (KC) are known to direct T cell education by production of cytokines. Therefore, expression of IL-18 was sought in KC. Epidermal RNA was analyzed following stimulation with contact sensitizers or controls for IL-18 mRNA expression by semiquantitative reverse transcription-PCR. Constitutive expression of IL-18 mRNA was low in untreated epidermal cells (EC), but early up-regulation of IL-18 mRNA signals was detected following app

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Calero, Guillermo, Guowu Lin, Ulises Santiago, Sandra Vergara, Silvia Russi, and Aina Cohen. "Optochemistry and Transcription at 160 Kelvin." Structural Dynamics 12, no. 2_Supplement (2025): A252. https://doi.org/10.1063/4.0000558.

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DNA-directed RNA Polymerase II (Pol II) is one of the most important molecules in biology. Pol II is highly-conserved among eukaryotic organisms and plays a fundamental role in cellular life, the transcription of genes into messenger RNA. Through technology development and innovation in structural biology approaches we have uncovered the time evolution of the molecular events during Pol II transcription elongation using optochemical approaches. In order to perform real time studies of transcription, we demonstrate that 1) a photoactive caged ATP can bind to Pol II; and 2) that shinning a UV li

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Webster, Michael William, Maria Takacs, Chengjin Zhu, et al. "Structural basis of transcription-translation coupling and collision in bacteria." Science 369, no. 6509 (2020): 1355–59. http://dx.doi.org/10.1126/science.abb5036.

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Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo–electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface.

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Feng, Mengdie, Xueqin Xie, Guoqiang Han, et al. "YBX1 is required for maintaining myeloid leukemia cell survival by regulating BCL2 stability in an m6A-dependent manner." Blood 138, no. 1 (2021): 71–85. http://dx.doi.org/10.1182/blood.2020009676.

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Abstract RNA-binding proteins (RBPs) are critical regulators of transcription and translation that are often dysregulated in cancer. Although RBPs are increasingly recognized as being important for normal hematopoiesis and for hematologic malignancies as oncogenes or tumor suppressors, RBPs that are essential for the maintenance and survival of leukemia remain elusive. Here we show that YBX1 is specifically required for maintaining myeloid leukemia cell survival in an N6-methyladenosine (m6A)-dependent manner. We found that expression of YBX1 is significantly upregulated in myeloid leukemia ce

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Schultz, P., P. Stannek, M. Voigt, K. H. Jakobs, and P. Gierschik. "Complementation of formyl peptide receptor-mediated signal transduction in Xenopus laevis oocytes." Biochemical Journal 284, no. 1 (1992): 207–12. http://dx.doi.org/10.1042/bj2840207.

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Formyl-methionine-containing peptides (e.g. fMet-Leu-Phe) stimulate a variety of neutrophil functions by interacting with specific cell surface receptors which are coupled via G-proteins to stimulation of phospholipase C. Two markedly distinct cDNAs coding for formyl peptide receptors have recently been isolated from a rabbit and a human cDNA library respectively. To examine the hitherto unknown signal transduction properties of the formyl peptide receptor encoded by the human cDNA, we have used the PCR to clone this cDNA from poly(A)+ RNA of myeloid differentiated human leukaemia (HL-60) cell

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Tikhonov, M. V., P. G. Georgiev, and O. G. Maksimenko. "Competition within Introns: Splicing Wins over Polyadenylation via a General Mechanism." Acta Naturae 5, no. 4 (2013): 52–61. http://dx.doi.org/10.32607/20758251-2013-5-4-52-61.

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Most eukaryotic messenger RNAs are capped, spliced, and polyadenylated via co-transcriptional processes that are coupled to each other and to the transcription machinery. Coordination of these processes ensures correct RNA maturation and provides for the diversity of the transcribed isoforms. Thus, RNA processing is a chain of events in which the completion of one event is coupled to the initiation of the next one. In this context, the relationship between splicing and polyadenylation is an important aspect of gene regulation. We have found that cryptic polyadenylation signals are widely distr

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Kashida, Shunnichi, Dan Ohtan Wang, Hirohide Saito, and Zoher Gueroui. "Nanoparticle-based local translation reveals mRNA as a translation-coupled scaffold with anchoring function." Proceedings of the National Academy of Sciences 116, no. 27 (2019): 13346–51. http://dx.doi.org/10.1073/pnas.1900310116.

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The spatial regulation of messenger RNA (mRNA) translation is central to cellular functions and relies on numerous complex processes. Biomimetic approaches could bypass these endogenous complex processes, improve our comprehension of the regulation, and allow for controlling local translation regulations and functions. However, the causality between local translation and nascent protein function remains elusive. Here, we developed a nanoparticle (NP)-based strategy to magnetically control mRNA spatial patterns in mammalian cell extracts and investigate how local translation impacts nascent pro

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Guo, Caixia, Lisa Savage, Kevin D. Sarge та Ok-Kyong Park-Sarge. "Gonadotropins Decrease Estrogen Receptor-β Messenger Ribonucleic Acid Stability in Rat Granulosa Cells*". Endocrinology 142, № 6 (2001): 2230–37. http://dx.doi.org/10.1210/endo.142.6.8102.

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Abstract We have previously shown that the preovulatory LH surge down-regulates estrogen receptor-β (ERβ) messenger RNA (mRNA) levels selectively in the granulosa cells of preovulatory follicles. To gain insight into the underlying mechanisms, we examined whether the LH-induced loss of ERβ mRNA expression in rat granulosa cells is attributable to the hormone-induced changes at the level of transcription and/or mRNA degradation. When the rate of ERβ gene transcription was assessed in cultured granulosa cells, by nuclear run-off assays, we observed only a marginal effect of hCG on ERβ gene trans

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Albarqi, Mennatallah M. Y., and Sean P. Ryder. "The endogenous mex-3 3´UTR is required for germline repression and contributes to optimal fecundity in C. elegans." PLOS Genetics 17, no. 8 (2021): e1009775. http://dx.doi.org/10.1371/journal.pgen.1009775.

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RNA regulation is essential to successful reproduction. Messenger RNAs delivered from parent to progeny govern early embryonic development. RNA-binding proteins (RBPs) are the key effectors of this process, regulating the translation and stability of parental transcripts to control cell fate specification events prior to zygotic gene activation. The KH-domain RBP MEX-3 is conserved from nematode to human. It was first discovered in Caenorhabditis elegans, where it is essential for anterior cell fate and embryo viability. Here, we show that loss of the endogenous mex-3 3´UTR disrupts its germli

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Fang, Liying, Lina Guo, Min Zhang, Xianchun Li, and Zhongyuan Deng. "Analysis of Polyadenylation Signal Usage with Full-Length Transcriptome in Spodoptera frugiperda (Lepidoptera: Noctuidae)." Insects 13, no. 9 (2022): 803. http://dx.doi.org/10.3390/insects13090803.

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During the messenger RNA (mRNA) maturation process, RNA polyadenylation is a key step, and is coupled to the termination of transcription. Various cis-acting elements near the cleavage site and their binding factors would affect the process of polyadenylation, and AAUAAA, a highly conserved hexamer, was the most important polyadenylation signal (PAS). PAS usage is one of the critical modification determinants targeted at mRNA post-transcription. The full-length transcriptome has recently generated a massive amount of sequencing data, revealing poly(A) variation and alternative polyadenylation

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Carling, Tobias, Jonas Rastad, Eva Szabó, Gunnar Westin, and Göran Åkerström. "Reduced Parathyroid Vitamin D Receptor Messenger Ribonucleic Acid Levels in Primary and Secondary Hyperparathyroidism*." Journal of Clinical Endocrinology & Metabolism 85, no. 5 (2000): 2000–2003. http://dx.doi.org/10.1210/jcem.85.5.6607.

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Abstract Vitamin D, via its receptor (VDR), inhibits the hormone secretion and proliferation of parathyroid cells. Vitamin D deficiency and reduced parathyroid VDR expression has been associated with development of hyperparathyroidism (HPT) secondary to uremia. VDR polymorphisms may influence VDR messenger RNA (mRNA) levels and have been coupled to an increased risk of parathyroid adenoma of primary HPT. VDR mRNA relative to glyceraldehyde-3-phosphate dehydrogenase mRNA levels were determined by RNase protection assay in 42 single parathyroid adenomas of patients with primary HPT, 23 hyperplas

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Li, Shanshan, Huoqing Luo, Ronghui Lou, et al. "Multiregional profiling of the brain transmembrane proteome uncovers novel regulators of depression." Science Advances 7, no. 30 (2021): eabf0634. http://dx.doi.org/10.1126/sciadv.abf0634.

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Transmembrane proteins play vital roles in mediating synaptic transmission, plasticity, and homeostasis in the brain. However, these proteins, especially the G protein–coupled receptors (GPCRs), are underrepresented in most large-scale proteomic surveys. Here, we present a new proteomic approach aided by deep learning models for comprehensive profiling of transmembrane protein families in multiple mouse brain regions. Our multiregional proteome profiling highlights the considerable discrepancy between messenger RNA and protein distribution, especially for region-enriched GPCRs, and predicts an

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Oikonomou, Panos, Roberto Salatino, and Saeed Tavazoie. "In vivo mRNA display enables large-scale proteomics by next generation sequencing." Proceedings of the National Academy of Sciences 117, no. 43 (2020): 26710–18. http://dx.doi.org/10.1073/pnas.2002650117.

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Large-scale proteomic methods are essential for the functional characterization of proteins in their native cellular context. However, proteomics has lagged far behind genomic approaches in scalability, standardization, and cost. Here, we introduce in vivo mRNA display, a technology that converts a variety of proteomics applications into a DNA sequencing problem. In vivo-expressed proteins are coupled with their encoding messenger RNAs (mRNAs) via a high-affinity stem-loop RNA binding domain interaction, enabling high-throughput identification of proteins with high sensitivity and specificity

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Li, Li, Xincang Li, Lu Li, Jinxing Wang, and Wenrui Jin. "Ultra-sensitive DNA assay based on single-molecule detection coupled with fluorescent quantum dot-labeling and its application to determination of messenger RNA." Analytica Chimica Acta 685, no. 1 (2011): 52–57. http://dx.doi.org/10.1016/j.aca.2010.11.012.

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Ruan, B., I. Ahel, A. Ambrogelly, et al. "Genomics and the evolution of aminoacyl-tRNA synthesis." Acta Biochimica Polonica 48, no. 2 (2001): 313–21. http://dx.doi.org/10.18388/abp.2001_3917.

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Translation is the process by which ribosomes direct protein synthesis using the genetic information contained in messenger RNA (mRNA). Transfer RNAs (tRNAs) are charged with an amino acid and brought to the ribosome, where they are paired with the corresponding trinucleotide codon in mRNA. The amino acid is attached to the nascent polypeptide and the ribosome moves on to the next codon. Thus, the sequential pairing of codons in mRNA with tRNA anticodons determines the order of amino acids in a protein. It is therefore imperative for accurate translation that tRNAs are only coupled to amino ac

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Pei, Jingjing, Nicole D. Wagner, Angela J. Zou, et al. "Structural basis for IFN antagonism by human respiratory syncytial virus nonstructural protein 2." Proceedings of the National Academy of Sciences 118, no. 10 (2021): e2020587118. http://dx.doi.org/10.1073/pnas.2020587118.

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Human respiratory syncytial virus (RSV) nonstructural protein 2 (NS2) inhibits host interferon (IFN) responses stimulated by RSV infection by targeting early steps in the IFN-signaling pathway. But the molecular mechanisms related to how NS2 regulates these processes remain incompletely understood. To address this gap, here we solved the X-ray crystal structure of NS2. This structure revealed a unique fold that is distinct from other known viral IFN antagonists, including RSV NS1. We also show that NS2 directly interacts with an inactive conformation of the RIG-I–like receptors (RLRs) RIG-I an

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Mick, David U., Milena Vukotic, Heike Piechura, et al. "Coa3 and Cox14 are essential for negative feedback regulation of COX1 translation in mitochondria." Journal of Cell Biology 191, no. 1 (2010): 141–54. http://dx.doi.org/10.1083/jcb.201007026.

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Regulation of eukaryotic cytochrome oxidase assembly occurs at the level of Cox1 translation, its central mitochondria-encoded subunit. Translation of COX1 messenger RNA is coupled to complex assembly in a negative feedback loop: the translational activator Mss51 is thought to be sequestered to assembly intermediates, rendering it incompetent to promote translation. In this study, we identify Coa3 (cytochrome oxidase assembly factor 3; Yjl062w-A), a novel regulator of mitochondrial COX1 translation and cytochrome oxidase assembly. We show that Coa3 and Cox14 form assembly intermediates with ne

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Hu, S.-P., J.-J. Zhao, W.-X. Wang, et al. "Dexmedetomidine increases acetylation level of histone through ERK1/2 pathway in dopamine neuron." Human & Experimental Toxicology 36, no. 5 (2016): 474–82. http://dx.doi.org/10.1177/0960327116652458.

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Dexmedetomidine is a highly selective α2-adrenoceptor agonist with sedation, anesthetic sparing, analgesia, sympatholytic, and neuroprotective properties. This study evaluated neuroprotective effects of dexmedetomidine on dopamine neurons correlated to histone acetylation via extracellular signal-regulated protein kinase 1 and 2 (ERK1/2) pathway. Animals were randomly assigned to four groups and treatments were given as onetime doses: dimethyl sulfoxide (DMSO; n = 6), dexmedetomidine 1 mg/kg ( n = 6), 10 mg/kg ( n = 6), and 100 mg/kg ( n = 6). Acetylation histone protein levels and ERK protein

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Ren, Xianyun, Xueqiong Bian, Huixin Shao, et al. "Regulation Mechanism of Dopamine Receptor 1 in Low Temperature Response of Marsupenaeus japonicus." International Journal of Molecular Sciences 24, no. 20 (2023): 15278. http://dx.doi.org/10.3390/ijms242015278.

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Dopamine receptors (DARs) are important transmembrane receptors responsible for receiving extracellular signals in the DAR-mediated signaling pathway, and are involved in a variety of physiological functions. Herein, the D1 DAR gene from Marsupenaeus japonicus (MjDAD1) was identified and characterized. The protein encoded by MjDAD1 has the typical structure and functional domains of the G-protein coupled receptor family. MjDAD1 expression was significantly upregulated in the gills and hepatopancreas after low temperature stress. Moreover, double-stranded RNA-mediated silencing of MjDAD1 signif

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Crisanti, Patricia, Boubaker Omri, Eleanor J. Hughes, et al. "The Expression of Thyrotropin Receptor in the Brain**This work was supported in part by a grant from the Faculté de Médecine de Bicêtre (Université Paris XI, Orsay, France) and Program Tournesol (Ministère des Affaires Etrangères, Paris, France)." Endocrinology 142, no. 2 (2001): 812–22. http://dx.doi.org/10.1210/endo.142.2.7943.

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Abstract The regulation of the thyroid gland by TSH is mediated by a heterotrimeric G protein-coupled receptor. Nonthyroid effects of TSH have been reported, and expression of its receptor has been described in adipocytes and lymphocytes. We have previously reported the existence of specific and saturable binding sites of TSH and specific TSH effects in primary cultured rat brain astroglial cells. We now report expression of the TSH receptor gene in these cells; the coding sequence of the corresponding complementary DNA is identical to that previously established in thyroid. Using specific ant

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Kong, Ling-Shang, Ran Tao, Yi-Fan Li, Wen-Bin Wang, and Xue Zhao. "METTL5 promotes cell proliferation, invasion, and migration by up-regulating Toll-like receptor 8 expression in colorectal cancer." World Journal of Gastrointestinal Oncology 16, no. 5 (2024): 2006–17. http://dx.doi.org/10.4251/wjgo.v16.i5.2006.

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BACKGROUND N6-methyladenosine (m6A) modification represents the predominant alteration found in eukaryotic messenger RNA and plays a crucial role in the progression of various tumors. However, despite its significance, the comprehensive investigation of METTL5, a key m6A methyltransferase, in colorectal cancer (CRC) remains limited. AIM To investigate the role of METTL5 in CRC. METHODS We assessed METTL5 expression levels in clinical samples obtained from CRC patients as well as in CRC cell lines. To elucidate the downstream targets of METTL5, we performed RNA-sequencing analysis coupled with

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Gobeil, Jr., Fernand, Alejandro Vazquez-Tello, Anne Marilise Marrache, et al. "Nuclear prostaglandin signaling system: biogenesis and actions via heptahelical receptors." Canadian Journal of Physiology and Pharmacology 81, no. 2 (2003): 196–204. http://dx.doi.org/10.1139/y02-163.

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Prostaglandins are ubiquitous lipid mediators that play pivotal roles in cardiovascular homeostasis, reproduction, and inflammation, as well as in many important cellular processes including gene expression and cell proliferation. The mechanism of action of these lipid messengers is thought to be primarily dependent on their interaction with specific cell surface receptors that belong to the heptahelical transmembrane spanning G protein-coupled receptor superfamily. Accumulating evidence suggests that these receptors may co-localize at the cell nucleus where they can modulate gene expression t

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Sanchez-Pernaute, Rosario, and Anna-Liisa Brownell. "Therapeutic Exploration of Metabotropic Glutamate Receptor Antagonists in Parkinson’s Disease by Positron Emission Tomography." US Neurology 05, no. 02 (2010): 21. http://dx.doi.org/10.17925/usn.2010.05.02.21.

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Metabotropic glutamate receptors (mGluR)s are G-protein-coupled receptors that function as modulators of synaptic function and glutamate transmission. Post-synaptically localized subtype 5 mGlu5 receptors are co-localized with adenosine A2a, dopamine, and N-methyl-D-aspartate (NMDA) receptors and regulate local protein synthesis and messenger RNA (mRNA) translation at synapses, and are thus ideally positioned to control synaptic plasticity. Aberrant synaptic plasticity appears to be involved in a number of developmental and degenerative neuropsychiatric disorders, including Parkinsons disease

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Erales, Jenny, Virginie Marchand, Baptiste Panthu, et al. "Evidence for rRNA 2′-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes." Proceedings of the National Academy of Sciences 114, no. 49 (2017): 12934–39. http://dx.doi.org/10.1073/pnas.1707674114.

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Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2′-O-methylation (2′-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2′-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2′-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2′-O-Me globally by inhibiting the rRNA methyl-transferase fibri

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Müller, Berndt, Jane Blackburn, Carmen Feijoo, Xiujie Zhao, and Carl Smythe. "DNA-activated protein kinase functions in a newly observed S phase checkpoint that links histone mRNA abundance with DNA replication." Journal of Cell Biology 179, no. 7 (2007): 1385–98. http://dx.doi.org/10.1083/jcb.200708106.

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DNA and histone synthesis are coupled and ongoing replication is required to maintain histone gene expression. Here, we expose S phase–arrested cells to the kinase inhibitors caffeine and LY294002. This uncouples DNA replication from histone messenger RNA (mRNA) abundance, altering the efficiency of replication stress–induced histone mRNA down-regulation. Interference with caffeine-sensitive checkpoint kinases ataxia telangiectasia and Rad3 related (ATR)/ataxia telangiectasia mutated (ATM) does not affect histone mRNA down- regulation, which indicates that ATR/ATM alone cannot account for such

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KAUNISTO, KARI M., and HANNU J. RAJANIEMI. "Expression and Localization of the Na⁺/H⁺ Exchanger Isoform NHE3 in the Rat Efferent Ducts." Journal of Andrology 23, no. 2 (2002): 237–41. http://dx.doi.org/10.1002/j.1939-4640.2002.tb02620.x.

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ABSTRACT: The efferent ducts reabsorb most of the fluid released with spermatozoa from the testis. This absorptive capacity results in a severalfold increase in sperm concentration in the proximal epididymis and is partly responsible for maintenance of the optimal microenvironment for the sperm maturation. The fluid absorption is coupled to active Na+ transport and is inhibitable by amiloride, both of which suggest a role for a Na+/H+ exchanger (NHE). NHE3 is an apical membrane NHE responsible for sodium absorption in renal proximal tubule and intestinal epithelium. In the present study, we ex

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Roache, Tavia. "Consequences of Genomic DNA Mono-Ribonucleotides for Chromosomal Stability." Innovation in Aging 5, Supplement_1 (2021): 997. http://dx.doi.org/10.1093/geroni/igab046.3579.

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Abstract Mono-ribonucleotides are building blocks for polynucleotide RNA chains (e.g., messenger RNA), but if mis-incorporated into duplex DNA can cause mutagenesis and chromosomal instability. During DNA synthesis by Pol γ, remnants of unremoved RNA primers contribute to elevated mono-ribonucleotide triphosphates resulting in nucleotide pool imbalance, ultimately favoring mis-incorporated ribonucleotides during replication. Moreover, although polymerases generally replicate DNA with high fidelity, the steric gate occasionally allows a mis-incorporated ribonucleotide. Thus, a mono-ribonucleoti

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Wu, Fengxi, Zhongyuan Xiang, Zhenghao He, et al. "Abnormally high expression of D1-like dopamine receptors on lupus CD4⁺T cells promotes Tfh cell differentiation." Lupus Science & Medicine 10, no. 2 (2023): e000943. http://dx.doi.org/10.1136/lupus-2023-000943.

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ObjectiveSLE is a chronic autoimmune disease that places a great burden on human society. T follicular helper (Tfh) cells play a critical role in the pathological process of SLE. Therefore, elucidating the mechanism of Tfh cell differentiation will contribute to SLE treatment. Dopamine receptors (DRDs) are members of the family of G protein-coupled receptors and are primarily divided into D1-like and D2-like receptors. Previous studies have found that DRDs can regulate differentiation of immune cells. However, there is currently a lack of research on DRDs and Tfh cells. We here explore the rel

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