6,330 results match your criteria transcriptional termination


sRNA-mediated RNA processing regulates bacterial cell division.

Nucleic Acids Res 2021 Jun 14. Epub 2021 Jun 14.

Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.

Tight control of cell division is essential for survival of most organisms. For prokaryotes, the regulatory mechanisms involved in the control of cell division are mostly unknown. We show that the small non-coding sRNA StsR has an important role in controlling cell division and growth in the alpha-proteobacterium Rhodobacter sphaeroides. Read More

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Post-diapause transcriptomic restarts: insight from a high-latitude copepod.

BMC Genomics 2021 Jun 3;22(1):409. Epub 2021 Jun 3.

Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd, Honolulu, HI, 96822, USA.

Background: Diapause is a seasonal dormancy that allows organisms to survive unfavorable conditions and optimizes the timing of reproduction and growth. Emergence from diapause reverses the state of arrested development and metabolic suppression returning the organism to an active state. The physiological mechanisms that regulate the transition from diapause to post-diapause are still unknown. Read More

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Iron in Translation: From the Beginning to the End.

Microorganisms 2021 May 13;9(5). Epub 2021 May 13.

Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino 7, Paterna, 46980 Valencia, Spain.

Iron is an essential element for all eukaryotes, since it acts as a cofactor for many enzymes involved in basic cellular functions, including translation. While the mammalian iron-regulatory protein/iron-responsive element (IRP/IRE) system arose as one of the first examples of translational regulation in higher eukaryotes, little is known about the contribution of iron itself to the different stages of eukaryotic translation. In the yeast , iron deficiency provokes a global impairment of translation at the initiation step, which is mediated by the Gcn2-eIF2α pathway, while the post-transcriptional regulator Cth2 specifically represses the translation of a subgroup of iron-related transcripts. Read More

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DNA polymerase III protein, HolC, helps resolve replication/transcription conflicts.

Authors:
Susan T Lovett

Microb Cell 2021 May 6;8(6):143-145. Epub 2021 May 6.

Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA.

In DNA replication is catalyzed by an assembly of proteins, the DNA polymerase III holoenzyme. This complex includes the polymerase and proofreading subunits, the processivity clamp and clamp loader complex. The gene encodes an accessory protein (known as χ) to the core clamp loader complex and is the only protein of the holoenzyme that binds to single-strand DNA binding protein, SSB. Read More

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Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses.

Front Immunol 2021 11;12:662565. Epub 2021 May 11.

Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.

Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Read More

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The transcriptional landscape of a rewritten bacterial genome reveals control elements and genome design principles.

Nat Commun 2021 05 24;12(1):3053. Epub 2021 May 24.

Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.

Sequence rewriting enables low-cost genome synthesis and the design of biological systems with orthogonal genetic codes. The error-free, robust rewriting of nucleotide sequences can be achieved with a complete annotation of gene regulatory elements. Here, we compare transcription in Caulobacter crescentus to transcription from plasmid-borne segments of the synthesized genome of C. Read More

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NF-κB and Its Regulators During Pregnancy.

Front Immunol 2021 5;12:679106. Epub 2021 May 5.

Laboratorio de Inmunidad Innata, Departamento de Inmunología, ENCB-Instituto Politécnico Nacional, Mexico City, Mexico.

The transcriptional factor NF-κB is a nuclear factor involved in both physiological and pathological processes. This factor can control the transcription of more than 400 genes, including cytokines, chemokines, and their modulators, immune and non-immune receptors, proteins involved in antigen presentation and cell adhesion, acute phase and stress response proteins, regulators of apoptosis, growth factors, other transcription factors and their regulators, as well as different enzymes; all these molecules control several biological processes. NF-κB is a tightly regulated molecule that has also been related to apoptosis, cell proliferation, inflammation, and the control of innate and adaptive immune responses during onset of labor, in which it has a crucial role; thus, early activation of this factor may have an adverse effect, by inducing premature termination of pregnancy, with bad outcomes for the mother and the fetus, including product loss. Read More

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Critical Involvement of TFIIB in Viral Pathogenesis.

Front Mol Biosci 2021 30;8:669044. Epub 2021 Apr 30.

Department of Biological Science, Wayne State University, Detroit, MI, United States.

Viral infections and the harm they cause to their host are a perpetual threat to living organisms. Pathogenesis and subsequent spread of infection requires replication of the viral genome and expression of structural and non-structural proteins of the virus. Generally, viruses use transcription and translation machinery of the host cell to achieve this objective. Read More

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Activation of GSK3 Prevents Termination of TNF-Induced Signaling.

J Inflamm Res 2021 6;14:1717-1730. Epub 2021 May 6.

Institute of Clinical Chemistry, Hannover Medical School, Hannover, 30625, Germany.

Background: Termination of TNF-induced signaling plays a key role in the resolution of inflammation with dysregulations leading to severe pathophysiological conditions (sepsis, chronic inflammatory disease, cancer). Since a recent phospho-proteome analysis in human monocytes suggested GSK3 as a relevant kinase during signal termination, we aimed at further elucidating its role in this context.

Materials And Methods: For the analyses, THP-1 monocytic cells and primary human monocytes were used. Read More

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RNA polymerase I subunit 12 plays opposite roles in cell proliferation and migration.

Biochem Biophys Res Commun 2021 Jun 10;560:112-118. Epub 2021 May 10.

College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China. Electronic address:

RNA polymerase I (Pol I) is responsible for the synthesis of the majority of ribosomal RNA molecules in eukaryotes. Pol I subunit 12 (RPA12) is involved in the transcriptional termination and lipid metabolism in yeast. However, its role in human cells hasn't been investigated so far. Read More

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The potential role of m6A RNA methylation in diabetic retinopathy.

Exp Eye Res 2021 May 9;208:108616. Epub 2021 May 9.

Department of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; CSIR-IICB Translational Research Unit of Excellence (TRUE), Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India. Electronic address:

Diabetic retinopathy (DR), a major microvascular complication of diabetes, affects most diabetic individuals and has become the leading cause of vision loss. Metabolic memory associated with diabetes retains the risk of disease occurrence even after the termination of glycemic insult. Further, various limitations associated with its current diagnostic and treatment strategies like unavailability of early diagnostic and treatment methods, variation in treatment response from patient to patient, and cost-effectiveness have driven the need to find alternative solutions. Read More

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Gene Architecture Facilitates Intron-Mediated Enhancement of Transcription.

Front Mol Biosci 2021 21;8:669004. Epub 2021 Apr 21.

Department of Biological Science, Wayne State University, Detroit, MI, United States.

Introns impact several vital aspects of eukaryotic organisms like proteomic plasticity, genomic stability, stress response and gene expression. A role for introns in the regulation of gene expression at the level of transcription has been known for more than thirty years. The molecular basis underlying the phenomenon, however, is still not entirely clear. Read More

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Mastering the control of the Rho transcription factor for biotechnological applications.

Appl Microbiol Biotechnol 2021 May 8;105(10):4053-4071. Epub 2021 May 8.

Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia.

The present review represents an update on the fundamental role played by the Rho factor, which facilitates the process of Rho-dependent transcription termination in the prokaryotic world; it also provides a summary of relevant mutations in the Rho factor and the insights they provide into the functions carried out by this protein. Furthermore, a section is dedicated to the putative future use of Rho (the 'taming' of Rho) to facilitate biotechnological processes and adapt them to different technological contexts. Novel bacterial strains can be designed, containing mutations in the rho gene, that are better suited for different biotechnological applications. Read More

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A novel computational framework for genome-scale alternative transcription units prediction.

Brief Bioinform 2021 May 6. Epub 2021 May 6.

School of Mathematics, Shandong University, Jinan 250200, China.

Alternative transcription units (ATUs) are dynamically encoded under different conditions and display overlapping patterns (sharing one or more genes) under a specific condition in bacterial genomes. Genome-scale identification of ATUs is essential for studying the emergence of human diseases caused by bacterial organisms. However, it is unrealistic to identify all ATUs using experimental techniques because of the complexity and dynamic nature of ATUs. Read More

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Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome.

mSystems 2021 May 4;6(3). Epub 2021 May 4.

Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea

Identification of transcriptional regulatory elements in the GC-rich genome is essential for the production of novel biochemicals from secondary metabolite biosynthetic gene clusters (smBGCs). Despite many efforts to understand the regulation of transcription initiation in smBGCs, information on the regulation of transcription termination and posttranscriptional processing remains scarce. In this study, we identified the transcriptional regulatory elements in β-lactam antibiotic-producing ATCC 27064 by determining a total of 1,427 transcript 3'-end positions (TEPs) using the term-seq method. Read More

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Nucleoside Analogue Reverse Transcriptase Inhibitors Improve Clinical Outcome in Transcriptional Active Human Parvovirus B19-Positive Patients.

J Clin Med 2021 Apr 29;10(9). Epub 2021 Apr 29.

Institute of Cardiac Diagnostics and Therapy, 12203 Berlin, Germany.

Human parvovirus B19 (B19V) is the predominant cardiotropic virus associated with dilated inflammatory cardiomyopathy (DCMi). Transcriptionally active cardiotropic B19V infection is clinically relevant and triggers adverse long-term mortality. During the study; we evaluated whether antiviral treatment with the nucleoside analogue telbivudine (LTD) is effective in suppressing transcriptional active B19V in endomyocardial biopsies (EMBs) of B19V positive patients and improving clinical outcomes. Read More

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Read between the lines: Diversity of non-translational selection pressures on local codon usage.

Genome Biol Evol 2021 May 4. Epub 2021 May 4.

Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France.

Protein coding genes can contain specific motifs within their nucleotide sequence that function as a signal for various biological pathways. The presence of such sequence motifs within a gene can have beneficial or detrimental effects on the phenotype and fitness of an organism, and this can lead to the enrichment or avoidance of this sequence motif. The degeneracy of the genetic code allows for the existence of alternative synonymous sequences that exclude or include these motifs, while keeping the encoded amino acid sequence intact. Read More

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Mitochondrial Aminoacyl-tRNA Synthetase and Disease: The Yeast Contribution for Functional Analysis of Novel Variants.

Int J Mol Sci 2021 Apr 26;22(9). Epub 2021 Apr 26.

Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy.

In most eukaryotes, mitochondrial protein synthesis is essential for oxidative phosphorylation (OXPHOS) as some subunits of the respiratory chain complexes are encoded by the mitochondrial DNA (mtDNA). Mutations affecting the mitochondrial translation apparatus have been identified as a major cause of mitochondrial diseases. These mutations include either heteroplasmic mtDNA mutations in genes encoding for the mitochondrial rRNA (mtrRNA) and tRNAs (mttRNAs) or mutations in nuclear genes encoding ribosomal proteins, initiation, elongation and termination factors, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases (mtARSs). Read More

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Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice ( L.).

Plants (Basel) 2021 Apr 7;10(4). Epub 2021 Apr 7.

Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, University Kebangsaan Malaysia, Bangi 43000 UKM, Malaysia.

Rice is an important grain that is the staple food for most of the world's population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Read More

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ZC3H4 restricts non-coding transcription in human cells.

Elife 2021 Apr 29;10. Epub 2021 Apr 29.

The Living Systems Institute, University of Exeter, Exeter, United Kingdom.

The human genome encodes thousands of non-coding RNAs. Many of these terminate early and are then rapidly degraded, but how their transcription is restricted is poorly understood. In a screen for protein-coding gene transcriptional termination factors, we identified ZC3H4. Read More

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Widespread premature transcription termination of NLR genes by the spen protein FPA.

Elife 2021 Apr 27;10. Epub 2021 Apr 27.

School of Life Sciences, University of Dundee, Dundee, United Kingdom.

Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. Read More

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Protein phosphatases in the RNAPII transcription cycle: erasers, sculptors, gatekeepers, and potential drug targets.

Genes Dev 2021 May 22;35(9-10):658-676. Epub 2021 Apr 22.

Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.

The transcription cycle of RNA polymerase II (RNAPII) is governed at multiple points by opposing actions of cyclin-dependent kinases (CDKs) and protein phosphatases, in a process with similarities to the cell division cycle. While important roles of the kinases have been established, phosphatases have emerged more slowly as key players in transcription, and large gaps remain in understanding of their precise functions and targets. Much of the earlier work focused on the roles and regulation of sui generis and often atypical phosphatases-FCP1, Rtr1/RPAP2, and SSU72-with seemingly dedicated functions in RNAPII transcription. Read More

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Use of circular RNAs as markers of readthrough transcription to identify factors regulating cleavage/polyadenylation events.

Methods 2021 Apr 18. Epub 2021 Apr 18.

Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. Electronic address:

Circular RNAs with covalently linked ends are generated from many eukaryotic protein-coding genes when the pre-mRNA splicing machinery backsplices. These mature transcripts are resistant to digestion by exonucleases and typically have much longer half-lives than their associated linear mRNAs. Circular RNAs thus have great promise as sensitive biomarkers, including for detection of transcriptional activity. Read More

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Exploring the Roles of HERC2 and the NEDD4L HECT E3 Ubiquitin Ligase Subfamily in p53 Signaling and the DNA Damage Response.

Front Oncol 2021 31;11:659049. Epub 2021 Mar 31.

Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA, United States.

Cellular homeostasis is governed by the precise expression of genes that control the translation, localization, and termination of proteins. Oftentimes, environmental and biological factors can introduce mutations into the genetic framework of cells during their growth and division, and these genetic abnormalities can result in malignant transformations caused by protein malfunction. For example, p53 is a prominent tumor suppressor protein that is capable of undergoing more than 300 posttranslational modifications (PTMs) and is involved with controlling apoptotic signaling, transcription, and the DNA damage response (DDR). Read More

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Meet the authors: Anniina Vihervaara and Lea Sistonen.

Authors:

Mol Cell 2021 04;81(8):1588-1590

Anniina Vihervaara and Lea Sistonen share with us some of their experiences, including the paths to setting up their own labs and some behind-the-scenes details about their paper, "Stress-induced transcriptional memory accelerates promoter-proximal pause-release and decelerates termination over mitotic divisions." Read More

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Design of novel peptide-inhibitors against the conserved bacterial transcription terminator, Rho.

J Biol Chem 2021 Apr 9:100653. Epub 2021 Apr 9.

Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Inner Ring Road, Uppal, Hyderabad-39, India. Electronic address:

The transcription terminator Rho regulates many physiological processes in bacteria, such as antibiotic sensitivity, DNA repair, RNA-remodeling, etc, and hence, is a potential antimicrobial target, which is unexplored. The bacteriophage P4 capsid protein, Psu, moonlights as a natural Rho antagonist. Here, we report the design of novel peptides based on the C-terminal region of Psu using phenotypic screening methods. Read More

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Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy.

Data Brief 2021 Apr 15;35:106951. Epub 2021 Mar 15.

Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.

Pervasive transcription originating from the ubiquitous activity of RNA Polymerase II (RNAPII) generates a vast mass of non-coding RNAs (ncRNAs) that represent a potential harm to gene expression. In the compact genome of the yeast , the main genomewide safeguard against pervasive ncRNAs is the Nrd1-Nab3-Sen1 (NNS) complex, composed of two RNA-binding proteins (Nrd1 and Nab3) and the helicase Sen1. The NNS complex directs transcription termination of ncRNA genes and promotes the rapid degradation of pervasive transcripts from yeast nuclei through its physical and functional coupling to the nuclear RNA exosome. Read More

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DNA molecular combing-based replication fork directionality profiling.

Nucleic Acids Res 2021 Apr 9. Epub 2021 Apr 9.

Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, F-75005 Paris, France.

The replication strategy of metazoan genomes is still unclear, mainly because definitive maps of replication origins are missing. High-throughput methods are based on population average and thus may exclusively identify efficient initiation sites, whereas inefficient origins go undetected. Single-molecule analyses of specific loci can detect both common and rare initiation events along the targeted regions. Read More

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Is a Direct Target of AGAMOUS and WUSCHEL and Is Specifically Expressed in the Floral Meristematic Cells.

Front Plant Sci 2021 18;12:642879. Epub 2021 Mar 18.

Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.

The specified floral meristem will develop a pre-established number of floral organs and, thus, terminate the floral meristematic cells. The floral meristematic pool of cells is controlled, among some others, by WUSCHEL (WUS) and AGAMOUS (AG) transcription factors (TFs). Here, we demonstrate that the () gene, a cell proliferation regulator, starts to be expressed since the floral meristem specification of and is expressed in all floral meristematic cells. Read More

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RNA Sequence and Structure Determinants of Pol III Transcriptional Termination in Human Cells.

J Mol Biol 2021 Jun 1;433(13):166978. Epub 2021 Apr 1.

Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, USA. Electronic address:

The precise mechanism of transcription termination of the eukaryotic RNA polymerase III (Pol III) has been a subject of considerable debate. Although previous studies have clearly shown that multiple uracils at the end of RNA transcripts are required for Pol III termination, the effects of upstream RNA secondary structure in the nascent transcript on transcriptional termination is still unclear. To address this, we developed an in cellulo Pol III transcription termination assay using the recently developed Tornado-Corn RNA aptamer system to create a Pol III-transcribed RNA that produces a detectable fluorescent signal when transcribed in human cells. Read More

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