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Subcellular RNA

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https://www.readbyqxmd.com/read/29335528/exd2-governs-germ-stem-cell-homeostasis-and-lifespan-by-promoting-mitoribosome-integrity-and-translation
#1
Joana Silva, Suvi Aivio, Philip A Knobel, Laura J Bailey, Andreu Casali, Maria Vinaixa, Isabel Garcia-Cao, Étienne Coyaud, Alexis A Jourdain, Pablo Pérez-Ferreros, Ana M Rojas, Albert Antolin-Fontes, Sara Samino-Gené, Brian Raught, Acaimo González-Reyes, Lluís Ribas de Pouplana, Aidan J Doherty, Oscar Yanes, Travis H Stracker
Mitochondria are subcellular organelles that are critical for meeting the bioenergetic and biosynthetic needs of the cell. Mitochondrial function relies on genes and RNA species encoded both in the nucleus and mitochondria, and on their coordinated translation, import and respiratory complex assembly. Here, we characterize EXD2 (exonuclease 3'-5' domain-containing 2), a nuclear-encoded gene, and show that it is targeted to the mitochondria and prevents the aberrant association of messenger RNAs with the mitochondrial ribosome...
January 15, 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29322631/cold-inducible-rna-binding-protein-in-cancer-and-inflammation
#2
REVIEW
Daniel A Lujan, Joey L Ochoa, Rebecca S Hartley
RNA binding proteins (RBPs) play key roles in RNA dynamics, including subcellular localization, translational efficiency and metabolism. Cold-inducible RNA binding protein (CIRP) is a stress-induced protein that was initially described as a DNA damage-induced transcript (A18 hnRNP), as well as a cold-shock domain containing cold-stress response protein (CIRBP) that alters the translational efficiency of its target messenger RNAs (mRNAs). This review summarizes recent work on the roles of CIRP in the context of inflammation and cancer...
January 11, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29322442/single-molecule-fluorescence-in-situ-hybridization-fish-of-circular-rna-cdr1as
#3
Christine Kocks, Anastasiya Boltengagen, Monika Piwecka, Agnieszka Rybak-Wolf, Nikolaus Rajewsky
Individual mRNA molecules can be imaged in fixed cells by hybridization with multiple, singly labeled oligonucleotide probes, followed by computational identification of fluorescent signals. This approach, called single-molecule RNA fluorescence in situ hybridization (smRNA FISH), allows subcellular localization and absolute quantification of RNA molecules in individual cells. Here, we describe a simple smRNA FISH protocol for two-color imaging of a circular RNA, CDR1as, simultaneously with an unrelated messenger RNA...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29322441/detecting-circular-rnas-by-rna-fluorescence-in-situ-hybridization
#4
Anne Zirkel, Argyris Papantonis
Fluorescence in situ hybridization (FISH) coupled to high-resolution microscopy is a powerful method for analyzing the subcellular localization of RNA. However, the detection of circular RNAs (circRNAs) using microscopy is challenging because the only feature of a circRNA that can be used for the probe design is its junction. Circular RNAs are expressed at varying levels, and for their efficient monitoring by FISH, background fluorescence levels need to be kept low. Here, we describe a FISH protocol coupled to high-precision localizations using a single fluorescently labeled probe spanning the circRNA junction; this allows circRNA detection in mammalian cells with high signal-to-noise ratios...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321322/dengue-virus-selectively-annexes-endoplasmic-reticulum-associated-translation-machinery-as-a-strategy-for-co-opting-host-cell-protein-synthesis
#5
David W Reid, Rafael K Campos, Jessica R Child, Tianli Zheng, Kitti Wing Ki Chan, Shelton S Bradrick, Subhash G Vasudevan, Mariano A Garcia-Blanco, Christopher V Nicchitta
A primary question in Dengue virus (DENV) biology is the molecular strategy for recruitment of host cell protein synthesis machinery. Here we combined cell fractionation, ribosome profiling, and RNA-seq to investigate the subcellular organization of viral genome translation and replication as well as host cell translation and its response to DENV infection. We report that throughout the viral life cycle, DENV (+) and (-) strand RNAs were highly partitioned to the endoplasmic reticulum (ER), identifying the ER as the primary site of DENV translation...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29321003/a-prototypical-non-malignant-epithelial-model-to-study-genome-dynamics-and-concurrently-monitor-micro-rnas-and-proteins-in-situ-during-oncogene-induced-senescence
#6
Eirini-Stavroula Komseli, Ioannis S Pateras, Thorbjørn Krejsgaard, Konrad Stawiski, Sophia V Rizou, Alexander Polyzos, Fani-Marlen Roumelioti, Maria Chiourea, Ioanna Mourkioti, Eleni Paparouna, Christos P Zampetidis, Sentiljana Gumeni, Ioannis P Trougakos, Dafni-Eleftheria Pefani, Eric O'Neill, Sarantis Gagos, Aristides G Eliopoulos, Wojciech Fendler, Dipanjan Chowdhury, Jiri Bartek, Vassilis G Gorgoulis
BACKGROUND: Senescence is a fundamental biological process implicated in various pathologies, including cancer. Regarding carcinogenesis, senescence signifies, at least in its initial phases, an anti-tumor response that needs to be circumvented for cancer to progress. Micro-RNAs, a subclass of regulatory, non-coding RNAs, participate in senescence regulation. At the subcellular level micro-RNAs, similar to proteins, have been shown to traffic between organelles influencing cellular behavior...
January 10, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29305335/identification-and-functional-characterization-of-toll-like-receptor-13-from-orange-spotted-grouper-epinephelus-coioides
#7
Yaosi Liang, Xu Ding, Xue Yu, Yu Wang, Ying Zhou, Jianan He, Yu Shi, Yong Zhang, Haoran Lin, Danqi Lu
Toll-like receptors (TLRs) are one of the most important innate immune receptors, which recognize various pathogen-associated molecular patterns from different pathogens and activate the downstream immune response. Mouse TLR13 has been found to recognize a highly conserved sequence from bacterial or viral RNA and activate the myeloid differentiation primary response gene 88-dependent signaling response. The function of teleost tlr13 is still not fully understood, especially its relationship with bacterial RNA...
January 2, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29295891/a-peptidylic-inhibitor-for-neutralizing-expanded-cag-rna-induced-nucleolar-stress-in-polyglutamine-diseases
#8
Qian Zhang, Zhefan Stephen Chen, Ying An, Haizhen Liu, Yonghui Hou, Wen Li, Kwok-Fai Lau, Alex Koon, Jacky Ngo, Edwin Chan
Polyglutamine (polyQ) diseases are a set of progressive neurodegenerative disorders ascribed by the expression of both expanded CAG RNA and misfolded polyQ protein. We previously reported that the direct interaction between expanded CAG RNA and nucleolar protein nucleolin (NCL) leads to impediment of pre-ribosomal RNA (pre-rRNA) transcription, and eventually triggers nucleolar stress-induced apoptosis in polyQ diseases. Here, we report a 21-amino acid peptide, named beta-structured inhibitor for neurodegenerative disease (BIND), effectively suppresses expanded CAG RNA toxicity...
January 2, 2018: RNA
https://www.readbyqxmd.com/read/29288326/fverga1-encoding-a-della-protein-negatively-regulates-runner-production-in-fragaria-vesca
#9
Weijia Li, Junxiang Zhang, Hongying Sun, Shouming Wang, Keqin Chen, Yuexue Liu, He Li, Yue Ma, Zhihong Zhang
FveRGA1 was highly expressed in tender tissues such as young leaves and stem apices and was localized in the nucleus. RNAi silencing of FveRGA1 in non-runnering woodland strawberry produced many runners. FveRGA1 is thus a key gene controlling strawberry runner formation. The propagation of strawberry is mainly based on runners, while the genes controlling runner production have not been well characterized. Exogenous applications of optimum concentration gibberellins (GAs) promote runner formation in strawberry cultivation and GA can accelerate the degradation of DELLA proteins...
December 29, 2017: Planta
https://www.readbyqxmd.com/read/29286479/method-for-labeling-transcripts-in-individual-escherichia-coli-cells-for-single-molecule-fluorescence-in-situ-hybridization-experiments
#10
Rinat Arbel-Goren, Yonatan Shapira, Joel Stavans
A method is described for labeling individual messenger RNA (mRNA) transcripts in fixed bacteria for use in single-molecule fluorescence in situ hybridization (smFISH) experiments in E. coli. smFISH allows the measurement of cell-to-cell variability in mRNA copy number of genes of interest, as well as the subcellular location of the transcripts. The main steps involved are fixation of the bacterial cell culture, permeabilization of cell membranes, and hybridization of the target transcripts with sets of commercially available short fluorescently-labeled oligonucleotide probes...
December 21, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29286307/signaling-pathways-driving-aberrant-splicing-in-cancer-cells
#11
REVIEW
Vânia Gonçalves, Joana F S Pereira, Peter Jordan
Aberrant profiles of pre-mRNA splicing are frequently observed in cancer. At the molecular level, an altered profile results from a complex interplay between chromatin modifications, the transcriptional elongation rate of RNA polymerase, and effective binding of the spliceosome to the generated transcripts. Key players in this interplay are regulatory splicing factors (SFs) that bind to gene-specific splice-regulatory sequence elements. Although mutations in genes of some SFs were described, a major driver of aberrant splicing profiles is oncogenic signal transduction pathways...
December 29, 2017: Genes
https://www.readbyqxmd.com/read/29278708/genome-wide-identification-of-chromatin-enriched-rna-reveals-that-unspliced-dentin-matrix-protein-1-mrna-regulates-cell-proliferation-in-squamous-cell-carcinoma
#12
Shigeki Suzuki, Hiroaki Hoshino, Kazuma Yoshida, Jun Nakanishi, Shizu Tsuchiya-Hirata, Seiji Kobuke, Naoto Haruyama, Fusanori Nishimura, Hideki Shiba
Chromatin-enriched noncoding RNAs (ncRNAs) have emerged as key molecules in epigenetic processes by interacting with chromatin-associated proteins. Recently, protein-coding mRNA genes have been reported to be chromatin-tethered, similar with ncRNA. However, very little is known about whether chromatin-enriched mRNA is involved in the chromatin modification process. Here, we comprehensively examined chromatin-enriched RNA in squamous cell carcinoma (SQCC) cells by RNA subcellular localization analysis, which was a combination of RNA fractionation and RNA-seq...
December 23, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29275436/transcriptomic-profiles-of-the-bovine-mammary-gland-during-lactation-and-the-dry-period
#13
Wen-Ting Dai, Yi-Xuan Zou, Robin R White, Jian-Xin Liu, Hong-Yun Liu
The initiation and maintenance of lactation are complex phenomena governed by biochemical and endocrine processes in the mammary gland (MG). Although DNA-based approaches have been used to study the onset of lactation, more comprehensive RNA-based techniques may be critical in furthering our understanding of gene alterations that occur to support lactation in the bovine MG. To further determine how gene profiles vary during lactation compared with the dry period, RNA-seq transcriptomic analysis was used to identify differentially expressed genes (DEG) in bovine MG tissues from animals that were lactating and not lactating...
December 23, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29241568/the-atmc4-regulates-the-stem-cell-homeostasis-in-arabidopsis-by-catalyzing-the-cleavage-of-atla1-protein-in-response-to-environmental-hazards
#14
Yifeng Huang, Yuchao Cui, Xueliang Hou, Tao Huang
The AtLa1 protein is an RNA binding factor that initiates the translation of WUSCHEL (WUS) mRNA in Arabidopsis. The AtLa1 protein can regulate the stem cell homeostasis via the nuclear-to-cytoplasmic translocation in response to environmental hazards. However, the translocation mechanism of AtLa1 protein remains to be elucidated. In the present study, we have explored the role of AtMC4 protein in the subcellular translocation of AtLa1 protein. Our results showed that the AtLa1 protein is a substrate of AtMC4 protein...
January 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29239719/live-cell-mapping-of-organelle-associated-rnas-via-proximity-biotinylation-combined-with-protein-rna-crosslinking
#15
Pornchai Kaewsapsak, David Michael Shechner, William Mallard, John L Rinn, Alice Y Ting
The spatial organization of RNA within cells is a crucial factor influencing a wide range of biological functions throughout all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we develop such a method, termed APEX-RIP, which combines peroxidase-catalyzed, spatially restricted in situ protein biotinylation with RNA-protein chemical crosslinking. We demonstrate that, using a single protocol, APEX-RIP can isolate RNAs from a variety of subcellular compartments, including the mitochondrial matrix, nucleus, cytosol, and endoplasmic reticulum (ER), with specificity and sensitivity that rival or exceed those of conventional approaches...
December 14, 2017: ELife
https://www.readbyqxmd.com/read/29237839/upon-infection-the-cellular-wd-repeat-containing-protein-5-wdr5-localizes-to-cytoplasmic-inclusion-bodies-and-enhances-measles-virus-replication
#16
Dzwokai Ma, Cyril X George, Jason Nomburg, Christian K Pfaller, Roberto Cattaneo, Charles E Samuel
Replication of negative-strand RNA viruses occurs in association with discrete cytoplasmic foci called inclusion bodies. Whereas inclusion bodies represent a prominent subcellular structure induced by viral infection, our knowledge of the cellular protein components involved in inclusion body formation and function is limited. Using measles virus-infected HeLa cells, we found that the WD repeat-containing protein 5 (WDR5), a subunit of histone H3 lysine 4 methyltransferases, was selectively recruited to virus-induced inclusion bodies...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29222062/evolutionary-history-of-the-cobalamin-independent-methionine-synthase-gene-family-across-the-land-plants
#17
Hugo Vianna Silva Rody, Luiz Orlando de Oliveira
Plants are successful paleopolyploids. The wide diversity of land plants is driven strongly by their gene duplicates undergoing distinct evolutionary fates after duplication. We used genomic resources from 35 model plant species to unravel the evolutionary fate of gene copies (paralogs) of the cobalamin-independent methionine synthase (metE) gene family across the land plants. To explore genealogical relationships and characterize positive selection as a driving force in the evolution of metE paralogs within a single species, we carried out complementary analyses on genomic data of 32 genotypes of soybean...
December 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29219966/gigadalton-scale-shape-programmable-dna-assemblies
#18
Klaus F Wagenbauer, Christian Sigl, Hendrik Dietz
Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29218056/respiratory-burst-oxidase-homolog-gene-a-is-crucial-for-rhizobium-infection-and-nodule-maturation-and-function-in-common-bean
#19
Manoj-Kumar Arthikala, Jesús Montiel, Rosana Sánchez-López, Noreide Nava, Luis Cárdenas, Carmen Quinto
Reactive oxygen species (ROS) produced by respiratory burst oxidase homologs (RBOHs) regulate numerous plant cell processes, including the symbiosis between legumes and nitrogen-fixing bacteria. Rapid and transient ROS production was reported after Phaseolus vulgaris root hairs were treated with Nod factors, indicating the presence of a ROS-associated molecular signature in the symbiosis signaling pathway. Rboh is a multigene family containing nine members (RbohA-I) in P. vulgaris. RNA interference of RbohB suppresses ROS production and attenuates rhizobial infection thread (IT) progression in P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29206227/slam-protein-dictates-subcellular-localization-and-translation-of-its-own-mrna
#20
Shuling Yan, Sreemukta Acharya, Stephanie Gröning, Jörg Großhans
Many mRNAs specifically localize within the cytoplasm and are present in RNA-protein complexes. It is generally assumed that localization and complex formation of these RNAs are controlled by trans-acting proteins encoded by genes different than the RNAs themselves. Here, we analyze slow as molasses (slam) mRNA that prominently colocalizes with its encoded protein at the basal cortical compartment during cellularization. The functional implications of this striking colocalization have been unknown. Here, we show that slam mRNA translation is spatiotemporally controlled...
December 2017: PLoS Biology
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