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Rna decay

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https://www.readbyqxmd.com/read/29334551/rapid-decline-of-hiv-1-dna-and-rna-in-infants-starting-very-early-art-may-pose-a-diagnostic-challenge
#1
Kirsten A Veldsman, Jean Maritz, Shahieda Isaacs, Mary Grace Katusiime, Anita Janse Van Rensburg, Barbara Laughton, John W Mellors, Mark F Cotton, Gert U van Zyl
OBJECTIVE: Birth diagnosis of HIV-1 infection offers an ideal opportunity for early antiretroviral treatment (ART) to limit HIV-1 reservoir size and limit disease progression. Although data on cellular HIV-1 DNA decay exist for children commencing treatment from 2-3 months of age, data is lacking for starting shortly after birth. DESIGN: We studied infants who initiated ART within 8 days after birth to assess HIV-1 DNA levels longitudinally. METHODS: Children were recruited from public health clinics in Cape Town where birth diagnosis of HIV-1 coupled with early ART initiation occurred...
January 13, 2018: AIDS
https://www.readbyqxmd.com/read/29322237/genome-wide-association-study-of-cold-tolerance-of-chinese-indica-rice-varieties-at-the-bud-burst-stage
#2
Mengchen Zhang, Jing Ye, Qun Xu, Yue Feng, Xiaoping Yuan, Hanyong Yu, Yiping Wang, Xinghua Wei, Yaolong Yang
A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China...
January 10, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29314657/molecular-and-genetic-interactions-of-the-rna-degradation-machineries-in-firmicute-bacteria
#3
REVIEW
Peter Redder
Correct balance between bacterial RNA degradation and synthesis is essential for controlling expression level of all RNAs. The RNA polymerase, which performs the RNA synthesis, is highly conserved across the bacterial domain. However, this is surprisingly not the case for the RNA degradation machinery, which is composed of different subunits and performs different enzymatic reactions, depending on the organism. In Escherichia coli, the RNA decay is performed by the degradosome complex, which forms around the membrane-associated endoribonuclease RNase E, and is stable enough to be purified without falling apart...
January 5, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29311343/the-interplay-between-the-rna-decay-and-translation-machinery-in-eukaryotes
#4
Adam M Heck, Jeffrey Wilusz
RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology...
January 8, 2018: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/29311133/dual-ire1-rnase-functions-dictate-glioblastoma-development
#5
Stéphanie Lhomond, Tony Avril, Nicolas Dejeans, Konstantinos Voutetakis, Dimitrios Doultsinos, Mari McMahon, Raphaël Pineau, Joanna Obacz, Olga Papadodima, Florence Jouan, Heloise Bourien, Marianthi Logotheti, Gwénaële Jégou, Néstor Pallares-Lupon, Kathleen Schmit, Pierre-Jean Le Reste, Amandine Etcheverry, Jean Mosser, Kim Barroso, Elodie Vauléon, Marion Maurel, Afshin Samali, John B Patterson, Olivier Pluquet, Claudio Hetz, Véronique Quillien, Aristotelis Chatziioannou, Eric Chevet
Proteostasis imbalance is emerging as a major hallmark of cancer, driving tumor aggressiveness. Evidence suggests that the endoplasmic reticulum (ER), a major site for protein folding and quality control, plays a critical role in cancer development. This concept is valid in glioblastoma multiform (GBM), the most lethal primary brain cancer with no effective treatment. We previously demonstrated that the ER stress sensor IRE1α (referred to as IRE1) contributes to GBM progression, through XBP1 mRNA splicing and regulated IRE1-dependent decay (RIDD) of RNA Here, we first demonstrated IRE1 signaling significance to human GBM and defined specific IRE1-dependent gene expression signatures that were confronted to human GBM transcriptomes...
January 8, 2018: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/29309033/nonsense-mrna-suppression-via-nonstop-decay
#6
Joshua A Arribere, Andrew Z Fire
Nonsense-mediated mRNA decay is the process by which mRNAs bearing premature stop codons are recognized and cleared from the cell. While considerable information has accumulated regarding recognition of the premature stop codon, less is known about the ensuing mRNA suppression. During the characterization of a second, distinct translational surveillance pathway (nonstop mRNA decay), we trapped intermediates in nonsense mRNA degradation. We present data in support of a model wherein nonsense-mediated decay funnels into the nonstop decay pathway in C...
January 8, 2018: ELife
https://www.readbyqxmd.com/read/29298683/global-accumulation-of-circrnas-during-aging-in-caenorhabditis-elegans
#7
Mariela Cortés-López, Matthew R Gruner, Daphne A Cooper, Hannah N Gruner, Alexandru-Ioan Voda, Alexander M van der Linden, Pedro Miura
BACKGROUND: Circular RNAs (CircRNAs) are a newly appreciated class of RNAs that lack free 5' and 3' ends, are expressed by the thousands in diverse forms of life, and are mostly of enigmatic function. Ostensibly due to their resistance to exonucleases, circRNAs are known to be exceptionally stable. Previous work in Drosophila and mice have shown that circRNAs increase during aging in neural tissues. RESULTS: Here, we examined the global profile of circRNAs in C...
January 3, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29298432/characterizing-zc3h18-a-multi-domain-protein-at-the-interface-of-rna-production-and-destruction-decisions
#8
Kinga Winczura, Manfred Schmid, Claudia Iasillo, Kelly R Molloy, Lea Mørch Harder, Jens S Andersen, John LaCava, Torben Heick Jensen
Nuclear RNA metabolism is influenced by protein complexes connecting to both RNA-productive and -destructive pathways. The ZC3H18 protein binds the cap-binding complex (CBC), universally present on capped RNAs, while also associating with the nuclear exosome targeting (NEXT) complex, linking to RNA decay. To dissect ZC3H18 function, we conducted interaction screening and mutagenesis of the protein, which revealed a phosphorylation-dependent isoform. Surprisingly, the modified region of ZC3H18 associates with core histone proteins...
January 2, 2018: Cell Reports
https://www.readbyqxmd.com/read/29297464/context-dependent-deposition-and-regulation-of-mrnas-in-p-bodies
#9
Congwei Wang, Fabian Schmich, Sumana Srivatsa, Julie Weidner, Niko Beerenwinkel, Anne Spang
Cells respond to stress by remodeling their transcriptome through transcription and degradation. Xrn1p-dependent degradation in P-bodies is the most prevalent decay pathway, yet, P-bodies may facilitate not only decay, but also act as a storage compartment. However, which and how mRNAs are selected into different degradation pathways and what determines the fate of any given mRNA in P-bodies remain largely unknown. We devised a new method to identify both common and stress-specific mRNA subsets associated with P-bodies...
January 3, 2018: ELife
https://www.readbyqxmd.com/read/29247756/determining-mrna-half-lives-on-a-transcriptome-wide-scale
#10
Andrew Lugowski, Beth Nicholson, Olivia S Rissland
Every step in the life cycle of an RNA transcript provides opportunity for regulation. One important aspect of post-transcriptional control is the regulation of RNA stability. Of the many strategies for determining mRNA stability, transcription inhibition and metabolic labeling have proved the most amenable to high-throughput analysis and have opened the door to dissecting mRNA decay transcriptome-wide. Here, we describe experimental and computational methods to determine transcriptome-wide RNA stabilities using both pharmacological inhibition of transcription and metabolic labeling...
December 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29244767/regulatory-elements-located-in-the-upstream-region-of-the-rhizobium-leguminosarum-rosr-global-regulator-are-essential-for-its-transcription-and-mrna-stability
#11
Kamila Rachwał, Paulina Lipa, Iwona Wojda, José-María Vinardell, Monika Janczarek
Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing a symbiotic relationship with clover (Trifolium spp.). Previously, the rosR gene, encoding a global regulatory protein involved in motility, synthesis of cell-surface components, and other cellular processes was identified and characterized in this bacterium. This gene possesses a long upstream region that contains several regulatory motifs, including inverted repeats (IRs) of different lengths. So far, the role of these motifs in the regulation of rosR transcription has not been elucidated in detail...
December 15, 2017: Genes
https://www.readbyqxmd.com/read/29244194/arid5a-stabilizes-ox40-mrna-in-murine-cd4-t-cells-by-recognizing-a-stem-loop-structure-in-its-3-utr
#12
Hamza Hanieh, Kazuya Masuda, Hozaifa Metwally, Jaya P Chalise, Maged Mohamed, Kishan K Nyati, Daron M Standley, Songling Li, Mitsuru Higa, Mohammad M Zaman, Tadamitsu Kishimoto
AT-rich interactive domain-containing protein 5a (Arid5a) is an RNA-binding protein (RBP) required for autoimmunity via stabilization of interleukin-6 (Il6) and signal transducer and activator of transcription 3 (STAT3) mRNAs. However, the roles of Arid5a in Th17 cells and its association with autoimmunity remains unknown. Here, we show that the levels of Arid5a and OX40 are correlated in CD4+ T cells under Th17 conditions in an IL-6-dependent manner. Lack of Arid5a in T cells reduced OX40 expression levels and repressed IL-17 production in response to OX40 ligation...
December 15, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/29237832/the-partitivirus-hetpv13-an1-mediates-severe-growth-debilitation-and-major-alterations-in-the-gene-expression-of-a-fungal-forest-pathogen
#13
Eeva J Vainio, Jaana Jurvansuu, Rafiqul Hyder, Muhammad Kashif, Tuula Piri, Tero Tuomivirta, Anna Poimala, Ping Xu, Salla Mäkelä, Dina Nitisa, Jarkko Hantula
The fungal genus Heterobasidion includes some of the most devastating conifer pathogens in the Boreal forest region. In this study we showed that the alphapartitivirus Heterobasidion partitivirus 13 from H. annosum (HetPV13-an1) is the main causal agent of severe phenotypic debilitation in the host fungus. Based on RNA sequencing using isogenic virus-infected and cured fungal strains, HetPV13-an1 affected the transcription of 683 genes, from which 60% were downregulated and 40% upregulated. Alterations observed in carbohydrate and amino acid metabolism suggest that the virus causes a state of starvation, which is compensated for by alternative synthesis routes...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29236296/rna-decay-factor-upf1-promotes-protein-decay-a-hidden-talent
#14
REVIEW
Terra-Dawn M Plank, Miles F Wilkinson
The RNA-binding protein, UPF1, is best known for its central role in the nonsense-mediated RNA decay (NMD) pathway. Feng et al. now report a new function for UPF1-it is an E3 ubiquitin ligase that specifically promotes the decay of a key pro-muscle transcription factor: MYOD. UPF1 achieves this through its RING-like domain, which confers ubiquitin E3 ligase activity. Feng et al. provide evidence that the ability of UPF1 to destabilize MYOD represses myogenesis. In the future, it will be important to define other protein substrates of UPF1-driven ubiquitination and to determine whether this biochemical activity is responsible for some of UPF1's previously defined biological functions, including in development and stress responses...
December 13, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29236259/identifying-cellular-nonsense-mediated-mrna-decay-nmd-targets-immunoprecipitation-of-phosphorylated-upf1-followed-by-rna-sequencing-p-upf1-rip-seq
#15
Tatsuaki Kurosaki, Mainul Hoque, Lynne E Maquat
Recent progress in the technology of transcriptome-wide high-throughput sequencing has revealed that nonsense-mediated mRNA decay (NMD) targets ~10% of physiologic transcripts for the purpose of tuning gene expression in response to various environmental conditions. Regardless of the eukaryote studied, NMD requires the ATP-dependent RNA helicase upframeshift 1 (UPF1). It was initially thought that cellular NMD targets could be defined by their binding to steady-state UPF1, which is largely hypophosphorylated...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236258/using-tet-off-cells-and-rnai-knockdown-to-assay-mrna-decay
#16
Thomas D Baird, J Robert Hogg
Cellular mRNA levels are determined by the competing forces of transcription and decay. A wide array of cellular mRNA decay pathways carry out RNA turnover either on a constitutive basis or in response to changing cellular conditions. Here, we outline a method to investigate mRNA decay that employs RNAi knockdown of known or putative decay factors in commercially available Tet-off cell systems. Reporter mRNAs of interest are expressed under the control of a tetracycline-regulated promoter, allowing pulse-chase mRNA decay assays to be conducted...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236257/identifying-risc-components-using-ago2-immunoprecipitation-and-mass-spectrometry
#17
Tingfang Yi
Complex immunoprecipitation (Co-IP) is a powerful technique for precipitating an intact protein complex out of solution and cell lysates using an antibody that specifically binds to a particular protein in a large complex of proteins. Mass spectrometry (MS) is used to identify, sequence, and quantify proteins. RNA-induced silencing complexes (RISCs), Ago2 centered protein assemblies, are essential for miRNA mediated RNA decay and gene expression regulation; however, the complete list of RISCs is unknown. Here we describe methods used to combine IP and MS to identify new components of RISCs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236249/metabolic-labeling-of-newly-synthesized-rna-with-4su-to-in-parallel-assess-rna-transcription-and-decay
#18
Wei Sun, Wei Chen
The development of genome-wide RNA profiling technologies greatly facilitates the global analysis of gene expression. However, such technologies alone could not distinguish the contribution to cellular RNA abundance by transcription versus decay. To overcome such limitation, metabolic labeling of newly synthesized RNA with 4-thiouridine (4sU) combined with genome-wide RNA profiling was used to in parallel measure RNA transcription and decay. Here, we describe the detailed protocol for using metabolic labeling with 4sU to separate newly synthesized RNA from the preexisting RNA in mammalian cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236248/determining-mrna-decay-rates-using-rna-approach-to-equilibrium-sequencing-rate-seq
#19
Farah Abdul-Rahman, David Gresham
RATE-seq is a 4-thiouracil (4-tU)-based method that enables the in vivo measurement of transcriptome-wide RNA degradation rates. 4-tU is an analog of uracil that is rapidly incorporated into newly synthesized RNA and facilitates the conjugation of a biotinylated molecule containing a reactive thiol group. The biotinylated RNA can then be fractionated from the unlabeled RNA with streptavidin magnetic beads. By adding 4-tU to a culture of cells growing in steady-state conditions, fractionating the labeled population of RNA at multiple time points following 4-tU addition, and quantifying the abundance of newly transcribed RNAs using RNAseq, it is possible to estimate the degradation rates of all transcripts in a single experiment...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29225039/a-massively-parallel-reporter-assay-of-3-utr-sequences-identifies-in%C3%A2-vivo-rules-for-mrna-degradation
#20
Michal Rabani, Lindsey Pieper, Guo-Liang Chew, Alexander F Schier
The stability of mRNAs is regulated by signals within their sequences, but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR-seq, a combination of massively parallel reporter assays and regression models, to survey the dynamics of tens of thousands of 3' UTR sequences during early zebrafish embryogenesis. UTR-seq revealed two temporal degradation programs: a maternally encoded early-onset program and a late-onset program that accelerated degradation after zygotic genome activation...
November 30, 2017: Molecular Cell
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