71,243 results match your criteria dna polymerases

Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far.

Noncoding RNA 2021 Jul 14;7(3). Epub 2021 Jul 14.

Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ), University Hospital Würzburg, Josef-Schneider Str. 2, 97080 Würzburg, Germany.

Gene expression is an essential process for cellular growth, proliferation, and differentiation. The transcription of protein-coding genes and non-coding loci depends on RNA polymerases. Interestingly, numerous loci encode long non-coding (lnc)RNA transcripts that are transcribed by RNA polymerase II (RNAPII) and fine-tune the RNA metabolism. Read More

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Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting .

J Virol 2021 Jul 21:JVI0239120. Epub 2021 Jul 21.

Department of Animal Science, Texas A&M University, Kleberg Center, Suite 133 2471, 474 Olsen Blvd, College Station, TX 77843, USA.

The majority of previously described bacteriophages belong to three major groups: P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. Here we present three novel "jumbo" phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of myophage. Read More

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Nonspecific Synthesis in the Reactions of Isothermal Nucleic Acid Amplification.

Biochemistry (Mosc) 2021 Jul;86(7):887-897

Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.

The review focuses on the main factors involved in the formation of nonspecific products in isothermal nucleic acid amplification, such as mispriming, ab initio DNA synthesis, and additional activities of DNA polymerases, and discusses approaches to prevent formation of such nonspecific products in LAMP, RPA, NASBA, RCA, SDA, LSDA, NDA, and EXPAR. Read More

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Structural basis for template switching by a group II intron-encoded non-LTR-retroelement reverse transcriptase.

J Biol Chem 2021 Jul 16:100971. Epub 2021 Jul 16.

Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712. Electronic address:

Reverse transcriptases (RTs) can switch template strands during cDNA synthesis, enabling them to join discontinuous nucleic acid sequences. Template switching plays crucial roles in retroviral replication and recombination, is used for adapter addition in RNA-seq, and may contribute to retroelement fitness by increasing evolutionary diversity and enabling continuous cDNA synthesis on damaged templates. Here, we determined an X-ray crystal structure of a template-switching complex of a group II intron RT bound simultaneously to an acceptor RNA and donor RNA template/DNA heteroduplex with a 1-nt 3'-DNA overhang. Read More

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DeepEMhancer: a deep learning solution for cryo-EM volume post-processing.

Commun Biol 2021 07 15;4(1):874. Epub 2021 Jul 15.

Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada.

Cryo-EM maps are valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed to improve their interpretability. Most popular approaches, based on global B-factor correction, suffer from limitations. Read More

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Transcriptional Run-on: Measuring Nascent Transcription at Specific Genomic Sites in Yeast.

Bio Protoc 2021 Jun 20;11(12):e4064. Epub 2021 Jun 20.

Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, 41012, Spain.

DNA transcription by RNA polymerases has always interested the scientific community as it is one of the most important processes involved in genome expression. This has led scientists to come up with different protocols allowing analysis of this process in specific locations across the genome by quantitating the amount of RNA polymerases transcribing that genomic site in a cell population. This can be achieved by either detecting the total number of polymerases in contact with that region (, by chromatin immunoprecipitation (ChIP) with anti-RNA polymerase antibodies) or by measuring the number of polymerases that are effectively engaged in transcription in that position. Read More

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Coordinated Cut and Bypass: Replication of Interstrand Crosslink-Containing DNA.

Front Cell Dev Biol 2021 28;9:699966. Epub 2021 Jun 28.

HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Hungary.

DNA interstrand crosslinks (ICLs) are covalently bound DNA lesions, which are commonly induced by chemotherapeutic drugs, such as cisplatin and mitomycin C or endogenous byproducts of metabolic processes. This type of DNA lesion can block ongoing RNA transcription and DNA replication and thus cause genome instability and cancer. Several cellular defense mechanism, such as the Fanconi anemia pathway have developed to ensure accurate repair and DNA replication when ICLs are present. Read More

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An uncommon [K+(Mg2+)2] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch.

RNA 2021 Jul 13. Epub 2021 Jul 13.

National Heart, Lung, and Blood Institute.

The widespread ykkC-I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the X-ray crystal structure of the Burkholderia sp. TJI49 ykkC-I subtype-1 (Guanidine-I) riboswitch aptamer domain. Read More

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Effects of Chemopreventive Natural Compounds on the Accuracy of 8-oxo-7,8-dihydro-2'-deoxyguanosine Translesion Synthesis.

Planta Med 2021 Jul 8. Epub 2021 Jul 8.

Unit of Therapeutic Chemistry and Pharmacognosy, Research Institute for Health Sciences and Technology, University of Mons (UMONS), Mons, Belgium.

Translesion synthesis is a DNA damage tolerance mechanism that relies on a series of specialized DNA polymerases able to bypass a lesion on a DNA template strand during replication or post-repair synthesis. Specialized translesion synthesis DNA polymerases pursue replication by inserting a base opposite to this lesion, correctly or incorrectly depending on the lesion nature, involved DNA polymerase(s), sequence context, and still unknown factors. To measure the correct or mutagenic outcome of 8-oxo-7,8-dihydro-2'-deoxyguanosine bypass by translesion synthesis, a primer-extension assay was performed on a template DNA bearing this lesion in the presence of nuclear proteins extracted from human intestinal epithelial cells (FHs 74 Int cell line); the reaction products were analyzed by both denaturing capillary electrophoresis (to measure the yield of translesion elongation) and pyrosequencing (to determine the identity of the nucleotide inserted in front of the lesion). Read More

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Single molecule analysis indicates stimulation of MUTYH by UV-DDB through enzyme turnover.

Nucleic Acids Res 2021 Jul 7. Epub 2021 Jul 7.

UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA.

The oxidative base damage, 8-oxo-7,8-dihydroguanine (8-oxoG) is a highly mutagenic lesion because replicative DNA polymerases insert adenine (A) opposite 8-oxoG. In mammalian cells, the removal of A incorporated across from 8-oxoG is mediated by the glycosylase MUTYH during base excision repair (BER). After A excision, MUTYH binds avidly to the abasic site and is thus product inhibited. Read More

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Transcription, Reverse Transcription, and Amplification of Backbone-Modified Nucleic Acids with Laboratory-Evolved Thermophilic DNA Polymerases.

Curr Protoc 2021 Jul;1(7):e188

MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China.

Backbone-modified nucleic acids are usually more stable enzymatically than their natural counterparts, enabling their broad application as potential diagnostic or therapeutic agents. Moreover, the development of nucleic acids with unnatural backbones has expanded the pool of genetic information carriers and paved the way toward synthetic xenobiology. However, synthesizing these molecules remains very challenging due to the requirement for harsh reaction conditions and the low coupling efficiency during their traditional solid-phase synthesis. Read More

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Expression of the cancer-associated DNA polymerase ε P286R in fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication.

PLoS Genet 2021 Jul 6;17(7):e1009526. Epub 2021 Jul 6.

ZRAB, University of Oxford, Oxford, United Kingdom.

Somatic and germline mutations in the proofreading domain of the replicative DNA polymerase ε (POLE-exonuclease domain mutations, POLE-EDMs) are frequently found in colorectal and endometrial cancers and, occasionally, in other tumours. POLE-associated cancers typically display hypermutation, and a unique mutational signature, with a predominance of C > A transversions in the context TCT and C > T transitions in the context TCG. To understand better the contribution of hypermutagenesis to tumour development, we have modelled the most recurrent POLE-EDM (POLE-P286R) in Schizosaccharomyces pombe. Read More

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Development of DNA Biosensors Based on DNAzymes and Nucleases.

Crit Rev Anal Chem 2021 Jul 6:1-16. Epub 2021 Jul 6.

College of Life Science, Yangtze University, Jingzhou, Hubei, China.

DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. Read More

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A structural framework for DNA replication and transcription through chromatin.

Curr Opin Struct Biol 2021 Jul 1;71:51-58. Epub 2021 Jul 1.

Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK. Electronic address:

In eukaryotic cells, DNA replication and transcription machineries uncoil nucleosomes along the double helix, to achieve the exposure of the single-stranded DNA template for nucleic acid synthesis. The replisome and RNA polymerases then redeposit histones onto DNA behind the advancing molecular motor, in a process that is crucial for epigenetic inheritance and homeostasis, respectively. Here, we compare and contrast the mechanisms by which these molecular machines advance through nucleosome arrays and discuss how chromatin remodellers can facilitate DNA replication and transcription. Read More

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Towards the enzymatic synthesis of phosphorothioate containing LNA oligonucleotides.

Bioorg Med Chem Lett 2021 Jul 1;48:128242. Epub 2021 Jul 1.

Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France. Electronic address:

Therapeutic oligonucleotides require the addition of multiple chemical modifications to the nucleosidic scaffold in order to improve their drug delivery efficiency, cell penetration capacity, biological stability, and pharmacokinetic properties. This chemical modification pattern is often accompanied by a synthetic burden and by limitations in sequence length. Here, we have synthesized a nucleoside triphosphate analog bearing two simultaneous modifications at the level of the sugar (LNA) and the backbone (thiophosphate) and have tested its compatibility with enzymatic DNA synthesis which could abrogate some of these synthetic limitations. Read More

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Protein Domain Specific Covalent Inhibition of Human DNA Polymerase β.

Chembiochem 2021 Jul 2. Epub 2021 Jul 2.

Department of Chemistry, Johns Hopkins University, 3400N. Charles St., Baltimore, MD 21218, USA.

DNA polymerase β (Pol β) is a frequently overexpressed and/or mutated bifunctional repair enzyme. Pol β possesses polymerase and lyase active sites, that are employed in two steps of base excision repair. Pol β is an attractive therapeutic target for which there is a need for inhibitors. Read More

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Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases.

Int J Mol Sci 2021 Jun 16;22(12). Epub 2021 Jun 16.

Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.

The vast majority of the genetic variants (mainly SNPs) associated with various human traits and diseases map to a noncoding part of the genome and are enriched in its regulatory compartment, suggesting that many causal variants may affect gene expression. The leading mechanism of action of these SNPs consists in the alterations in the transcription factor binding via creation or disruption of transcription factor binding sites (TFBSs) or some change in the affinity of these regulatory proteins to their cognate sites. In this review, we first focus on the history of the discovery of regulatory SNPs (rSNPs) and systematized description of the existing methodical approaches to their study. Read More

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Targeting Telomere Biology in Acute Lymphoblastic Leukemia.

Int J Mol Sci 2021 Jun 22;22(13). Epub 2021 Jun 22.

Laboratory for Hematopoiesis and Molecular Genetics, Experimental Hematology, Department of BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.

Increased cell proliferation is a hallmark of acute lymphoblastic leukemia (ALL), and genetic alterations driving clonal proliferation have been identified as prognostic factors. To evaluate replicative history and its potential prognostic value, we determined telomere length (TL) in lymphoblasts, B-, and T-lymphocytes, and measured telomerase activity (TA) in leukocytes of patients with ALL. In addition, we evaluated the potential to suppress the in vitro growth of B-ALL cells by the telomerase inhibitor imetelstat. Read More

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Potential of Naturally Derived Compounds in Telomerase and Telomere Modulation in Skin Senescence and Aging.

Int J Mol Sci 2021 Jun 15;22(12). Epub 2021 Jun 15.

Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, 49 Przybyszewskiego St., 60-355 Poznań, Poland.

Proper functioning of cells-their ability to divide, differentiate, and regenerate-is dictated by genomic stability. The main factors contributing to this stability are the telomeric ends that cap chromosomes. Telomere biology and telomerase activity have been of interest to scientists in various medical science fields for years, including the study of both cancer and of senescence and aging. Read More

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TENT4A Non-Canonical Poly(A) Polymerase Regulates DNA-Damage Tolerance via Multiple Pathways That Are Mutated in Endometrial Cancer.

Int J Mol Sci 2021 Jun 28;22(13). Epub 2021 Jun 28.

Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.

TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here, we show that TENT4A regulates multiple biological pathways and focuses on its multilayer regulation of translesion DNA synthesis (TLS), in which error-prone DNA polymerases bypass unrepaired DNA lesions. We show that TENT4A regulates mRNA stability and/or translation of DNA polymerase η and RAD18 E3 ligase, which guides the polymerase to replication stalling sites and monoubiquitinates PCNA, thereby enabling recruitment of error-prone DNA polymerases to damaged DNA sites. Read More

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Exploring New Scaffolds for the Dual Inhibition of HIV-1 RT Polymerase and Ribonuclease Associated Functions.

Molecules 2021 Jun 23;26(13). Epub 2021 Jun 23.

Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy.

Current therapeutic protocols for the treatment of HIV infection consist of the combination of diverse anti-retroviral drugs in order to reduce the selection of resistant mutants and to allow for the use of lower doses of each single agent to reduce toxicity. However, avoiding drugs interactions and patient compliance are issues not fully accomplished so far. Pursuing on our investigation on potential anti HIV multi-target agents we have designed and synthesized a small library of biphenylhydrazo 4-arylthiazoles derivatives and evaluated to investigate the ability of the new derivatives to simultaneously inhibit both associated functions of HIV reverse transcriptase. Read More

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The Ultimate (Mis)match: When DNA Meets RNA.

Cells 2021 Jun 8;10(6). Epub 2021 Jun 8.

Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA.

RNA-containing structures, including ribonucleotide insertions, DNA:RNA hybrids and R-loops, have recently emerged as critical players in the maintenance of genome integrity. Strikingly, different enzymatic activities classically involved in genome maintenance contribute to their generation, their processing into genotoxic or repair intermediates, or their removal. Here we review how this substrate promiscuity can account for the detrimental and beneficial impacts of RNA insertions during genome metabolism. Read More

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3' Endonuclease Cleavage Polymerase Chain Reaction (3TEC-PCR) Technology for Single-Base-Specific Multiplex Pathogen Detection using a Two-Oligonucleotide System.

Int J Mol Sci 2021 Jun 4;22(11). Epub 2021 Jun 4.

Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland.

Polymerase chain reaction (PCR) is the standard in nucleic acid amplification technology for infectious disease pathogen detection and has been the primary diagnostic tool employed during the global COVID-19 pandemic. Various PCR technology adaptations, typically using two-oligonucleotide dye-binding methods or three-oligonucleotide hydrolysis probe systems, enable real-time multiplex target detection or single-base specificity for the identification of single-nucleotide polymorphisms (SNPs). A small number of two-oligonucleotide PCR systems facilitating both multiplex detection and SNP identification have been reported; however, these methods often have limitations in terms of target specificity, production of variable or false-positive results, and the requirement for extensive optimisation or post-amplification analysis. Read More

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Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase.

Nat Commun 2021 06 29;12(1):4020. Epub 2021 Jun 29.

Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

PrimPol is a human DNA polymerase-primase that localizes to mitochondria and nucleus and bypasses the major oxidative lesion 7,8-dihydro-8-oxoguanine (oxoG) via translesion synthesis, in mostly error-free manner. We present structures of PrimPol insertion complexes with a DNA template-primer and correct dCTP or erroneous dATP opposite the lesion, as well as extension complexes with C or A as a 3'-terminal primer base. We show that during the insertion of C and extension from it, the active site is unperturbed, reflecting the readiness of PrimPol to accommodate oxoG(anti). Read More

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Daughter-strand gaps in DNA replication - substrates of lesion processing and initiators of distress signalling.

DNA Repair (Amst) 2021 Jun 23;105:103163. Epub 2021 Jun 23.

Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany. Electronic address:

Dealing with DNA lesions during genome replication is particularly challenging because damaged replication templates interfere with the progression of the replicative DNA polymerases and thereby endanger the stability of the replisome. A variety of mechanisms for the recovery of replication forks exist, but both bacteria and eukaryotic cells also have the option of continuing replication downstream of the lesion, leaving behind a daughter-strand gap in the newly synthesized DNA. In this review, we address the significance of these single-stranded DNA structures as sites of DNA damage sensing and processing at a distance from ongoing genome replication. Read More

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Novel Escherichia coli active site dnaE alleles with altered base and sugar selectivity.

Mol Microbiol 2021 Jun 28. Epub 2021 Jun 28.

Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892-3371, USA.

The Escherichia coli dnaE gene encodes the α-catalytic subunit (pol IIIα) of DNA polymerase III, the cell's main replicase. Like all high-fidelity DNA polymerases, pol III possesses stringent base and sugar discrimination. The latter is mediated by a so-called "steric gate" residue in the active site of the polymerase that physically clashes with the 2'-OH of an incoming ribonucleotide. Read More

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Structure of the bacteriophage PhiKZ non-virion RNA polymerase.

Nucleic Acids Res 2021 Jul;49(13):7732-7739

Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.

Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, intrinsically antibiotic resistant, pathogen that kills tens of thousands worldwide each year. ΦKZ is an incredibly interesting virus, expressing many systems that the host already possesses. Read More

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Adaptive resistance mutations at supra-inhibitory concentrations independent of SOS mutagenesis.

Mol Biol Evol 2021 Jun 27. Epub 2021 Jun 27.

The Koret School of Veterinary Medicine, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel.

Emergence of resistant bacteria during antimicrobial treatment is one of the most critical and universal health threats. It is known that several stress-induced mutagenesis and heteroresistance mechanisms can enhance microbial adaptation to antibiotics. Here, we demonstrate that the pathogen Bartonella, can undergo stress-induced mutagenesis despite the fact it lacks error-prone polymerases, the rpoS gene and functional UV-induced mutagenesis. Read More

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Cryo-EM reveals conformational flexibility in apo DNA polymerase ζ.

J Biol Chem 2021 Jun 24;297(2):100912. Epub 2021 Jun 24.

Nephrology and Hypertension Research, Division of Hypertension and Nephrology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA. Electronic address:

The translesion synthesis (TLS) DNA polymerases Rev1 and Polζ function together in DNA lesion bypass during DNA replication, acting as nucleotide inserter and extender polymerases, respectively. While the structural characterization of the Saccharomyces cerevisiae Polζ in its DNA-bound state has illuminated how this enzyme synthesizes DNA, a mechanistic understanding of TLS also requires probing conformational changes associated with DNA- and Rev1 binding. Here, we used single-particle cryo-electron microscopy to determine the structure of the apo Polζ holoenzyme. Read More

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SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity.

Nat Commun 2021 06 25;12(1):3965. Epub 2021 Jun 25.

Institute for Genetics, University of Cologne, Cologne, Germany.

Eukaryotic gene expression is constantly controlled by the translation-coupled nonsense-mediated mRNA decay (NMD) pathway. Aberrant translation termination leads to NMD activation, resulting in phosphorylation of the central NMD factor UPF1 and robust clearance of NMD targets via two seemingly independent and redundant mRNA degradation branches. Here, we uncover that the loss of the first SMG5-SMG7-dependent pathway also inactivates the second SMG6-dependent branch, indicating an unexpected functional connection between the final NMD steps. Read More

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