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https://www.readbyqxmd.com/read/28637691/settling-the-m-6-a-debate-methylation-of-mature-mrna-is-not-dynamic-but-accelerates-turnover
#1
REVIEW
Nicolle A Rosa-Mercado, Johanna B Withers, Joan A Steitz
Post-transcriptional modification of RNA nucleosides has been implicated as a pivotal regulator of mRNA biology. In this issue of Genes & Development, Ke and colleagues (pp. 990-1006) provide insights into the temporal and spatial distribution of N(6)-methyladenosine (m(6)A) in RNA transcripts by analyzing different subcellular fractions. Using a recently developed biochemical approach for detecting m(6)A, the researchers show that m(6)A methylations are enriched in exons and are added to transcripts prior to splicing...
May 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28635588/genome-sequence-variation-in-the-constricta-strain-dramatically-alters-the-protein-interaction-and-localization-map-of-potato-yellow-dwarf-virus
#2
Chanyong Jang, Renyuan Wang, Joseph Wells, Fabian Leon, Mark Farman, John Hammond, Michael M Goodin
The genome sequence of the constricta strain of Potato yellow dwarf virus (CYDV) was determined to be 12 792 nt long and organized into seven ORFs with the gene order 3'-N-X-P-Y-M-G-L-5', which encodes the nucleocapsid, phospho, movement, matrix, glyco, and RNA-dependent RNA polymerase proteins, respectively, except for X, which is of unknown function. Cloned ORFs for each gene, except L, were used to construct a protein interaction and localization map (PILM) for this virus, which shares greater than 80 % amino acid similarity in all ORFs except X and P with the sanguinolenta strain of this species (SYDV)...
June 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28634384/alternative-splicing-regulates-distinct-subcellular-localization-of-epithelial-splicing-regulatory-protein-1-esrp1-isoforms
#3
Yueqin Yang, Russ P Carstens
Epithelial-Splicing-Regulatory-Protein 1 (Esrp1) is a cell-type specific RNA-binding protein (RBP) that is essential for mammalian development through maintenance of epithelial cell properties including barrier function. Esrp1 also regulates splicing during the epithelial to mesenchymal transition (EMT). It contains three highly conserved RNA recognition motifs (RRMs) in the absence of other clearly defined protein domains. Esrp1 itself is also alternatively spliced to produce multiple protein isoforms. Here we determined that two competing alternative 5' splice sites in exon 12 yield Esrp1 isoforms with differential nucleocytoplasmic localization...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630007/rna-localization-making-its-way-to-the-center-stage
#4
REVIEW
Ashley Chin, Eric Lécuyer
Cells are highly organized entities that rely on intricate addressing mechanisms to sort their constituent molecules to precise subcellular locations. These processes are crucial for cells to maintain their proper organization and carry out specialized functions in the body, while genetic perturbations that clog up these addressing systems can contribute to disease aetiology. The trafficking of RNA molecules represents an important layer in the control of cellular organization, a process that is both highly prevalent and for which features of the regulatory machineries have been deeply conserved evolutionarily...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28624537/visualizing-rna-granule-transport-and-translation-in-living-neurons
#5
REVIEW
Karl E Bauer, Michael A Kiebler, Inmaculada Segura
In polarized cells, such as neurons, the synthesis of an mRNA does not ensure its proper cellular expression. Most mature transcripts require the association with RNA-binding proteins, resulting in the formation of RNA granules, which are then transported within the cytoplasm along the cytoskeleton and delivered to their proper subcellular locations, where they can be locally translated. Here we review current microscopy methods that have been developed to visualize RNA granule formation, transport and translation at the single cell level with a special emphasis on the MS2 and SunTag systems...
June 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28623268/ascorbate-induces-apoptosis-in-melanoma-cells-by-suppressing-clusterin-expression
#6
Sushmita Mustafi, David W Sant, Zhao-Jun Liu, Gaofeng Wang
Pharmacological levels of ascorbate have long been suggested as a potential treatment of cancer. However, we observed that EC50 of ascorbate was at a similar level for cultured healthy melanocytes and melanoma cells, suggesting a limit of pharmacological ascorbate in treating cancer. Loss of 5-hydroxymethylcytosine (5 hmC) is an epigenetic hallmark of cancer and ascorbate promotes 5 hmC generation by serving as a cofactor for TET methylcytosine dioxygenases. Our previous work demonstrated that ascorbate treatment at physiological level (100 μM) increased 5 hmC content in melanoma cells toward the level of healthy melanocytes...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28621225/decreased-expression-of-mgmt-in-correlation-with-aberrant-dna-methylation-in-esophageal-cancer-patients-from-north-india
#7
Asad Ur Rehman, Snigdha Saikia, Mohammad Askandar Iqbal, Istaq Ahmad, Sadaf, Afzal Anees, P S Aravinda, Pramod Kumar Mishra, Suresh Hedau, Sundeep Singh Saluja, Subhash Medhi, Syed Akhtar Husain
O-6-methylguanine-DNA methyltransferase, DNA repair gene, has been found to be involved with the pathogenesis of the esophageal cancer. DNA hypermethylation and other factors have been suggested to downregulate O-6-methylguanine-DNA methyltransferase. In this communication, the methylation status of O-6-methylguanine-DNA methyltransferase gene and the corresponding O-6-methylguanine-DNA methyltransferase protein expression in esophageal cancer from North India has been studied. In all, 80 samples of tumor tissue along with adjacent normal tissue as controls were analyzed for messenger RNA level of O-6-methylguanine-DNA methyltransferase gene, protein expression, and subcellular localization...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28611388/aberrant-plasticity-of-peripheral-sensory-axons-in-a-painful-neuropathy
#8
Takashi Hirai, Yatendra Mulpuri, Yanbing Cheng, Zheng Xia, Wei Li, Supanigar Ruangsri, Igor Spigelman, Ichiro Nishimura
Neuronal cells express considerable plasticity responding to environmental cues, in part, through subcellular mRNA regulation. Here we report on the extensive changes in distribution of mRNAs in the cell body and axon compartments of peripheral sensory neurons and the 3' untranslated region (3'UTR) landscapes after unilateral sciatic nerve entrapment (SNE) injury in rats. Neuronal cells dissociated from SNE-injured and contralateral L4 and L5 dorsal root ganglia were cultured in a compartmentalized system. Axonal and cell body RNA samples were separately subjected to high throughput RNA sequencing (RNA-Seq)...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28591567/a-role-for-dystroglycan-in-the-pathophysiology-of-acute-leukemic-cells
#9
Lea Alonso-Rangel, Tizziani Benítez-Guerrero, Ivette Martínez-Vieyra, Bulmaro Cisneros, Adolfo Martínez-Tovar, Steve J Winder, Doris Cerecedo
AIMS: Previous reports have demonstrated that alterations or reduced expression of Dystroglycan (Dg) complex (αDg and βDg subunits) are related to progression and severity of neoplastic solid tissues. Therefore we determined the expression pattern and subcellular distribution of Dg complex in Acute Myeloid Leukemia (AML) primary blasts (M1, M2, and M3 phenotypes), as well as HL-60 and Kasumi-1 leukemia cell lines. Additionally, we evaluated the relative expression of the main enzymes controlling α-Dg glycosylation to ascertain the post-translational modifications in the leukemia cell phenotype...
June 4, 2017: Life Sciences
https://www.readbyqxmd.com/read/28589356/characterization-of-the-b-cell-transcriptome-bound-by-rna-binding-proteins-with-iclip
#10
Manuel D Díaz-Muñoz, Elisa Monzón-Casanova, Martin Turner
Posttranscriptional regulation of gene expression shapes the B cell transcriptome and controls messenger RNA (mRNA) translation into protein. Recent reports have highlighted the importance of RNA binding proteins (RBPs) for mRNA splicing, subcellular location, stability, and translation during B lymphocyte development, activation, and differentiation. Here we describe individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) in primary lymphocytes, a method that maps RNA-protein interactions in a genome-wide scale allowing mechanistic analysis of RBP function...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28586434/the-arabidopsis-cys2-his2-zinc-finger-transcription-factor-zat18-is-a-positive-regulator-of-plant-tolerance-to-drought-stress
#11
Mingzhu Yin, Yanping Wang, Lihua Zhang, Jinzhu Li, Wenli Quan, Li Yang, Qingfeng Wang, Zhulong Chan
Environmental stress poses a global threat to plant growth and reproduction, especially drought stress. Zinc finger proteins comprise a family of transcription factors that play essential roles in response to various abiotic stresses. Here, we found that ZAT18 (At3g53600), a nuclear C2H2 zinc finger protein, was transcriptionally induced by dehydration stress. Overexpression (OE) of ZAT18 in Arabidopsis improved drought tolerance while mutation of ZAT18 resulted in decreased plant tolerance to drought stress...
June 6, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28579748/functional-characterization-of-rs2229094-t-c-polymorphism-in-the-tumor-necrosis-factor-locus-and-lymphotoxin-alpha-expression-in-human-retina-the-retina-4-project
#12
Salvador Pastor-Idoate, Irene Rodríguez-Hernández, Jimena Rojas, Lucia Gonzalez-Buendia, Santiago Delgado-Tirado, Jose Carlos López, Rogelio González-Sarmiento, Jose C Pastor
PURPOSE: The objective of this study is to determine the expression and localization of lymphotoxin alpha (LTA) in human retinas and the functionality of one of its polymorphisms rs2229094 (C13R) (T>C), previously associated with proliferative vitreoretinopathy (PVR) development. MATERIALS AND METHODS: Total RNA from three healthy human retinas were extracted and subjected to reverse transcription-polymerase chain reaction (RT-PCR) analysis, using flanking primers of LTA cDNA...
2017: Clinical Ophthalmology
https://www.readbyqxmd.com/read/28579403/cefra-seq-systematic-mapping-of-rna-subcellular-distribution-properties-through-cell-fractionation-coupled-to-deep-sequencing
#13
Fabio Alexis Lefebvre, Neal Cody, Louis Philip Benoit Bouvrette, Julie Bergalet, Xiaofeng Wang, Eric Lécuyer
The subcellular trafficking of RNA molecules is a conserved feature of eukaryotic cells and plays key functions in diverse processes implicating polarised cellular activities. Large-scale imaging and subcellular transcriptomic studies suggest that regulated RNA localization is a highly prevalent process that appears to be disrupted in several neuromuscular disorders. These features underline the importance and usefulness of implementing procedures to assess global transcriptome subcellular distribution properties...
June 1, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28562030/switching-protein-localization-by-site-directed-rna-editing-under-control-of-light
#14
Paul Vogel, Alfred Hanswillemenke, Thorsten Stafforst
Site directed RNA editing is an engineered tool for the posttranscriptional manipulation of RNA and proteins. Here, we demonstrate the inclusion of additional N- and C-terminal protein domains in an RNA editing-dependent manner to switch between protein isoforms in mammalian cell culture. By inclusion of localization signals, a switch of the subcellular protein localization was achieved. This included the shift from the cytoplasm to the outer-membrane, which typically is inaccessible at the protein-level. Furthermore, the strategy allows to implement photocaging to achieve spatiotemporal control of isoform switching...
June 15, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28559798/in-situ-rt-pcr-optimized-for-electron-microscopy-allows-description-of-subcellular-morphology-of-target-mrna-expressing-cells-in-the-brain
#15
Laura Cubas-Nuñez, María Duran-Moreno, Jessica Castillo-Villalba, Jorge Fuentes-Maestre, Bonaventura Casanova, José M García-Verdugo, Sara Gil-Perotín
In situ RT-PCR detects and amplifies mRNA (cDNA) while obtaining spatial information of gene expression. When the intended use is an ultrastructural analysis of morphology, the procedure may be technically challenging and quality of tissue dramatically altered by proteolytic digestion and extreme astringency and temperature conditions. We describe a low-damaging protocol of in situ RT-PCR combined to conventional electron microscopy that preserves fine morphology, increases sensitivity, and decreases costs and complexity associated to RNA probes...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28539450/mimic-phosphorylation-of-a-%C3%AE-c1-encoded-by-tylccnb-impairs-its-functions-as-a-viral-suppressor-of-rna-silencing-and-a-symptom-determinant
#16
Xueting Zhong, Zhan Qi Wang, Ruyuan Xiao, Linge Cao, Yaqin Wang, Yan Xie, Xueping Zhou
Phosphorylation of the βC1 protein encoded by the betasatellite of tomato yellow leaf curl China virus (TYLCCNB-βC1) by SNF1-related protein kinase 1 (SnRK1) plays a critical role in defense of host plants against geminivirus infection in Nicotiana benthamiana However, how phosphorylation of TYLCCNB-βC1 impacts its pathogenic functions during viral infection remains elusive. In this study, we identified two additional tyrosine residues in TYLCCNB-βC1 that are phosphorylated by SnRK1. The effects of TYLCCNB-βC1 phosphorylation on its functions as a viral suppressor of RNA silencing (VSR) and a symptom determinant were investigated via phosphorylation- mimic mutants in N...
May 24, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28538188/identification-and-characterization-of-a-class-of-malat1-like-genomic-loci
#17
Bin Zhang, Yuntao S Mao, Sarah D Diermeier, Irina V Novikova, Eric P Nawrocki, Tom A Jones, Zsolt Lazar, Chang-Shung Tung, Weijun Luo, Sean R Eddy, Karissa Y Sanbonmatsu, David L Spector
The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a noncoding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using an RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3' end triple-helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a co-occurrence of components of the 3' end module...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28520934/the-smap1-2-proteins-of-the-crenarchaeon-sulfolobus-solfataricus-interact-with-the-exosome-and-stimulate-a-rich-tailing-of-transcripts
#18
Birgit Märtens, Linlin Hou, Fabian Amman, Michael T Wolfinger, Elena Evguenieva-Hackenberg, Udo Bläsi
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28500073/fc%C3%AE-riiia-signaling-modulates-endosomal-tlr-responses-in-human-cd4-t-cells
#19
Anil K Chauhan
Recognition of Ab-opsonized pathogens by immune cells triggers both TLR and Fc receptor signaling. Fc receptors endocytose modified nucleic acids bound to Abs and deliver them to endosomes, where they are recognized by nucleic acid-sensing TLRs (NA-TLRs). We show that in CD4(+) T cells, NA-TLRs, TLR3, TLR8, and TLR9 are upregulated by FcγRIIIa-pSyk cosignaling and localize with FcγRIIIa on the cell surface. TLR9 accumulates on the cell surface, where it recognizes CpG oligonucleotide 2006. Subcellular location of NA-TLRs is a key determinant in discriminating self versus viral nucleic acid...
June 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28498920/copy-number-variation-of-functional-rbmy1-is-associated-with-sperm-motility-an-azoospermia-factor-linked-candidate-for-asthenozoospermia
#20
Yuanlong Yan, Xiling Yang, Yunqiang Liu, Ying Shen, Wenling Tu, Qiang Dong, Dong Yang, Yongyi Ma, Yuan Yang
STUDY QUESTION: What is the influence of copy number variation (CNV) in functional RNA binding motif protein Y-linked family 1 (RBMY1) on spermatogenic phenotypes? SUMMARY ANSWER: The RBMY1 functional copy dosage is positively correlated with sperm motility, and dosage insufficiency is an independent risk factor for asthenozoospermia. WHAT IS KNOWN ALREADY: RBMY1, a multi-copy gene expressed exclusively in the adult testis, is one of the most important candidates for male infertility in the azoospermia factor (AZF) region of the Y-chromosome...
May 12, 2017: Human Reproduction
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