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Subcellular RNA

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https://www.readbyqxmd.com/read/29781763/new-insights-into-the-nucleolar-localization-of-a-plant-rna-virus-encoded-protein-that-acts-in-both-rna-packaging-and-rna-silencing-suppression-involvement-of-importins-alpha-and-relevance-for-viral-infection
#1
Miryam Pérez-Cañamás, Carmen Hernández
Despite replication of plus strand RNA viruses takes place in the cytoplasm of host cells, different proteins encoded by these infectious agents have been shown to localize in the nucleus, with high accumulation at the nucleolus. In most cases, the molecular determinants and/or biological significance of such subcellular localization remain elusive. Recently, we reported that protein p37 encoded by Pelargonium line pattern virus (family Tombusviridae) acts in both RNA packaging and RNA silencing suppression...
May 21, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29769273/genome-wide-posttranscriptional-dysregulation-by-micrornas-in-human-asthma-as-revealed-by-frac-seq
#2
Rocio T Martinez-Nunez, Hitasha Rupani, Manuela Platé, Mahesan Niranjan, Rachel C Chambers, Peter H Howarth, Tilman Sanchez-Elsner
MicroRNAs are small noncoding RNAs that inhibit gene expression posttranscriptionally, implicated in virtually all biological processes. Although the effect of individual microRNAs is generally studied, the genome-wide role of multiple microRNAs is less investigated. We assessed paired genome-wide expression of microRNAs with total (cytoplasmic) and translational (polyribosome-bound) mRNA levels employing subcellular fractionation and RNA sequencing (Frac-seq) in human primary bronchoepithelium from healthy controls and severe asthmatics...
May 16, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29765511/immunohistochemical-analysis-of-rhamm-expression-in-normal-and-neoplastic-human-tissues-a-cell-cycle-protein-with-distinctive-expression-in-mitotic-cells-and-testicular-germ-cells
#3
Yao-Tseng Chen, Zhengming Chen, Yi-Chieh Nancy Du
Expression of Receptor for Hyaluronic Acid Mediated Motility (RHAMM) increases cellular motility and RHAMM overexpression promotes invasive phenotype and metastasis of cancer cells. RHAMM has been suggested as a biomarker for poor prognosis in several tumor types, including lung, breast, colorectal, gastric, pancreatic ductal, and ovarian cancers. RNA studies showed restricted RHAMM expression in normal tissues, but its protein expression data in tissues were limited. In light of its potential as a prognostic marker and a therapeutic target, we performed immunohistochemical analysis to systematically characterize RHAMM expression in normal and neoplastic human tissues...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29762913/an-online-compendium-of-cho-rna-seq-data-allows-identification-of-cho-cell-line-specific-transcriptomic-signatures
#4
Ankita Singh, Helene F Kildegaard, Mikael R Andersen
Chinese hamster ovary (CHO) cell lines can fold, assemble and modify proteins post-translationally to produce human-like proteins; as a consequence, it is the single most common expression systems for industrial production of recombinant therapeutic proteins. A thorough knowledge of cultivation conditions of different CHO cell lines has been developed over the last decade, but comprehending gene or pathway-specific distinctions between CHO cell lines at transcriptome level remains a challenge. To address these challenges, we compiled a compendium of 23 RNA-Seq studies from public and in-house data on CHO cell lines, i...
May 15, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29759990/epigenetic-targeting-of-adipocytes-inhibits-high-grade-serous-ovarian-cancer-cell-migration-and-invasion
#5
Jessica Tang, Nicholas Pulliam, Ali Ozes, Aaron Buechlein, Ning Ding, Doug Rusch, Harold Keer, Heather O'Hagan, M Sharon Stack, Kenneth P Nephew
Ovarian cancer (OC) cells frequently metastasize to the omentum and adipocytes play a significant role in ovarian tumor progression. Therapeutic interventions targeting aberrant DNA methylation in ovarian tumors have shown promise in the clinic but the effects of epigenetic therapy on the tumor microenvironment are understudied. Here, we examined the effect of adipocytes on OC cell behavior in culture and impact of targeting DNA methylation in adipocytes on OC metastasis. The presence of adipocytes increased OC cell migration and invasion and proximal and direct co-culture of adipocytes increased OC proliferation alone or after treatment with carboplatin...
May 14, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29758473/genome-wide-analysis-of-poplar-saur-gene-family-and-expression-profiles-under-cold-polyethylene-glycol-and-indole-3-acetic-acid-treatments
#6
Wenfang Hu, Hanwei Yan, Shuangshuang Luo, Feng Pan, Yue Wang, Yan Xiang
Small auxin-up RNA (SAUR) proteins play an important role in the regulation of plant growth and development. Here, we identified 105 SAUR genes and comprehensively analyzed them in Populus trichocarpa. Based on the phylogenetic relationships, the PtSAURs were classified into ten subfamilies. Of the 105 PtSAURs, 100 were randomly distributed along the nineteen chromosomes, while the remaining genes were located along unassigned scafoolds. These genes mainly evolved through segmental duplications. In total, 94 PtSAURs contained no introns, and each group had a similar conserved motif structure...
May 8, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29756767/spatially-restricting-bioorthogonal-nucleoside-biosynthesis-enables-selective-metabolic-labeling-of-the-mitochondrial-transcriptome
#7
Kim Nguyen, Mahima B Aggarwal, Chao Feng, Gabriela Balderrama, Michael Fazio, Ali Mortazavi, Robert C Spitale
The cellular RNA pool in animals arises from two separate genomes stored in the nucleus and multiple mitochondria. Chemical methods to track nascent RNA syntheses are unable to distinguish between these two with stringency. Herein we report that spatially restricting bioorthogonal nucleoside biosynthesis enables, for the first time, selective metabolic labeling of the RNA transcribed in the mitochondria. We envision this approach could open the door for heretofore-impossible analyses of mitochondrial RNA. Beyond our results revealed herein, our approach provides a roadmap for researchers to begin to design strategies to examine biomolecules within subcellular compartments...
May 14, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29746582/assembly-hub-function-of-er-localized-snare-proteins-in-biogenesis-of-tombusvirus-replication-compartment
#8
Zsuzsanna Sasvari, Nikolay Kovalev, Paulina Alatriste Gonzalez, Kai Xu, Peter D Nagy
Positive-strand RNA viruses assemble numerous membrane-bound viral replicase complexes within large replication compartments to support their replication in infected cells. Yet the detailed mechanism of how given subcellular compartments are subverted by viruses is incompletely understood. Although, Tomato bushy stunt virus (TBSV) uses peroxisomal membranes for replication, in this paper, we show evidence that the ER-resident SNARE (soluble NSF attachment protein receptor) proteins play critical roles in the formation of active replicase complexes in yeast model host and in plants...
May 10, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29743377/equine-myxovirus-resistance-protein-2-restricts-lentiviral-replication-by-blocking-nuclear-uptake-of-capsid-protein
#9
Shuang Ji, Lei Na, Huiling Ren, Yujie Wang, Xiaojun Wang
Human Myxovirus resistance 2 (huMxB) has been shown to be a determinant type I interferon-induced host factor involved in the inhibition of HIV-1 as well as many other primate lentiviruses. This blocking occurs after the reverse transcription of viral RNA and ahead of the integration into the host DNA, which is closely connected to the ability of the protein to bind the viral capsid. To date, Mx2s derived from non-primate animals have shown no capacity for HIV-1 suppression. In this study, we examined the restrictive effect of equine Mx2 (eqMx2) on both the equine infectious anemia virus (EIAV) and HIV-1 and investigated possible mechanisms for its specific function...
May 9, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29738614/proteomic-and-cellular-localisation-studies-suggest-non-tight-junction-cytoplasmic-and-nuclear-roles-for-occludin-in-astrocytes
#10
S V Morgan, C J Garwood, L Jennings, J E Simpson, L M Castelli, P R Heath, S R Mihaylov, I Vazquez Villasenor, T C Minshull, P G Ince, M J Dickman, G M Hautbergue, S B Wharton
Occludin is a component of tight junctions, which are essential structural components of the blood brain barrier. However, occludin is expressed in cells without tight junctions, implying additional functions. We determined the expression and localisation of occludin in astrocytes in cell culture and in human brain tissue, and sought novel binding partners using a proteomic approach. Expression was investigated by immunocytochemistry and immunoblotting in the 1321N1 astrocytoma cell line and ScienCell human primary astrocytes, and by immunohistochemistry in human autopsy brain tissue...
May 8, 2018: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29735682/laboratory-evolution-of-virus-like-nucleocapsids-from-nonviral-protein-cages
#11
Naohiro Terasaka, Yusuke Azuma, Donald Hilvert
Viruses are remarkable nanomachines that efficiently hijack cellular functions to replicate and self-assemble their components within a complex biological environment. As all steps of the viral life cycle depend on formation of a protective proteinaceous shell that packages the DNA or RNA genome, bottom-up construction of virus-like nucleocapsids from nonviral materials could provide valuable insights into virion assembly and evolution. Such constructs could also serve as safe alternatives to natural viruses for diverse nano- and biotechnological applications...
May 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29734178/long-non-coding-rna-sh3pxd2a-as1-promotes-cell-progression-partly-through-epigenetic-silencing-p57-and-klf2-in-colorectal-cancer
#12
Zhonghua Ma, Peng Peng, Jing Zhou, Bingqing Hui, Hao Ji, Juan Wang, Keming Wang
BACKGROUND/AIMS: Colorectal cancer (CRC) is one of the most commonly diagnosed malignancies worldwide. Current evidence has revealed the key roles of long non-coding RNAs (IncRNAs) in multiple cancers, including CRC. In this study we identified the lncRNA SH3PXD2A-AS1 as a novel molecule associated with CRC progression by analyzing the publicly available data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. METHODS: Quantitative real-time polymerase chain reaction (qRT-PCR) assays were performed to examine the expression levels of SH3PXD2A-AS1 in CRC tissue samples and CRC cell lines...
May 3, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29724793/rna-editing-in-nascent-rna-affects-pre-mrna-splicing
#13
Yun-Hua Esther Hsiao, Jae Hoon Bahn, Yun Yang, Xianzhi Lin, Stephen Tran, Ei-Wen Yang, Giovanni Quinones-Valdez, Xinshu Xiao
In eukaryotes, nascent RNA transcripts undergo an intricate series of RNA processing steps to achieve mRNA maturation. RNA editing and alternative splicing are two major RNA processing steps that can introduce significant modifications to the final gene products. By tackling these processes in isolation, recent studies have enabled substantial progress in understanding their global RNA targets and regulatory pathways. However, the interplay between individual steps of RNA processing, an essential aspect of gene regulation, remains poorly understood...
May 3, 2018: Genome Research
https://www.readbyqxmd.com/read/29720995/transcriptome-wide-annotation-of-m-5-c-rna-modifications-using-machine-learning
#14
Jie Song, Jingjing Zhai, Enze Bian, Yujia Song, Jiantao Yu, Chuang Ma
The emergence of epitranscriptome opened a new chapter in gene regulation. 5-methylcytosine (m5 C), as an important post-transcriptional modification, has been identified to be involved in a variety of biological processes such as subcellular localization and translational fidelity. Though high-throughput experimental technologies have been developed and applied to profile m5 C modifications under certain conditions, transcriptome-wide studies of m5 C modifications are still hindered by the dynamic and reversible nature of m5 C and the lack of computational prediction methods...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29710510/long-non-coding-rna-nnt-as1-affects-progression-of-breast-cancer-through-mir-142-3p-zeb1-axis
#15
Yan Li, Min Lv, Ziyan Song, Zhi Lou, Ran Wang, Min Zhuang
Some evidences have been provided to verify the effects of lncRNA NNT-AS1 on cancer progression. However, the crucial impacts of NNT-AS1 on the malignancy of breast cancer have not been elaborated. This study aims to detect the expression pattern and functional effects of NNT-AS1 in breast cancer. qRT-PCR analysis was applied to detect the expression of NNT-AS1 in both BC tissues and matched normal tissues. Loss of function assay was carried out to detect the effects of silenced NNT-AS1 on proliferation, metastasis and EMT process of BC cells...
April 24, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29710428/horizons-of-systems-biocatalysis-and-renaissance-of-metabolite-synthesis
#16
REVIEW
Roland Wohlgemuth
The small molecule domain of biological cellular systems is closely related to the synthesis and breakdown of larger molecules such as DNA, RNA, proteins or polysaccharides. Although the analysis, identification, characterization and synthesis of metabolites has a long history of milestone discoveries, it continues to be of great interest in the search for novel biological activities, metabolic pathways, diagnostic and therapeutic applications. Biologically active metabolites benefit from advantages in diffusion and transport for various interactions with proteins and nucleic acids and regulatory events...
April 30, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29709775/characterization-of-cathepsin-d-from-eriocheir-sinensis-involved-in-spiroplasma-eriocheiris-infection
#17
Mingxiao Ning, Meijun Yuan, Min Liu, Qi Gao, Panpan Wei, Wei Gu, Wen Wang, Qingguo Meng
Cathepsin D (catD) belongs to a lysosomal aspartic protease superfamily. The full-length catD cDNA from the Chinese mitten crab Eriocheir sinensis (EscatD) was 2748 bp and contained a 1158-bp ORF encoding a protein of 385 amino acids, including a signal peptide and two N-glycosylation sites. Phylogenetic analysis showed that EscatD was clustered into a single group, together with other catD for crustaceans. Quantitative real-time PCR revealed that EscatD was expressed mainly in the eyes, hemocytes, intestine and nerve and was expressed weakly in heart, muscle and gills...
April 23, 2018: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29709018/phospholipase-a2-activity-during-the-replication-cycle-of-the-flavivirus-west-nile-virus
#18
Susann Liebscher, Rebecca L Ambrose, Turgut E Aktepe, Andrea Mikulasova, Julia E Prier, Leah K Gillespie, Adam J Lopez-Denman, Thusitha W T Rupasinghe, Dedreia Tull, Malcolm J McConville, Jason M Mackenzie
Positive-sense RNA virus intracellular replication is intimately associated with membrane platforms that are derived from host organelles and comprised of distinct lipid composition. For flaviviruses, such as West Nile virus strain Kunjin virus (WNVKUN) we have observed that these membrane platforms are derived from the endoplasmic reticulum and are rich in (at least) cholesterol. To extend these studies and identify the cellular lipids critical for WNVKUN replication we utilized a whole cell lipidomics approach and revealed an elevation in phospholipase A2 (PLA2) activity to produce lyso-phosphatidylcholine (lyso-PChol)...
April 30, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29709000/control-of-pem-protein-level-by-localized-maternal-factors-for-transcriptional-regulation-in-the-germline-of-the-ascidian-halocynthia-roretzi
#19
Kaori Miyaoku, Ayaki Nakamoto, Hiroki Nishida, Gaku Kumano
Localized maternal mRNAs play important roles in embryogenesis, e.g. the establishment of embryonic axes and the developmental cell fate specification, in various animal species. In ascidians, a group of maternal mRNAs, called postplasmic/PEM RNAs, is localized to a subcellular structure, called the Centrosome-Attracting Body (CAB), which contains the ascidian germ plasm, and is inherited by the germline cells during embryogenesis. Posterior end mark (Pem), a postplasmic/PEM RNAs member, represses somatic gene expression in the germline during cleavage stages by inhibition of RNA polymerase II activity...
2018: PloS One
https://www.readbyqxmd.com/read/29704630/knockdown-of-nup160-inhibits-cell-proliferation-induces-apoptosis-autophagy-and-cell-migration-and-alters-the-expression-and-localization-of-podocyte-associated-molecules-in-mouse-podocytes
#20
Ping Wang, Feng Zhao, Xiaojing Nie, Jiewei Liu, Zihua Yu
Genetic mutations in dozens of monogenic genes can lead to serious podocyte dysfunction, which is a major cause of steroid-resistant nephrotic syndrome (SRNS). The NUP160 gene is expressed in both human kidney and mouse kidney. However, whether knockdown of NUP160 impairs podocytes has not yet been established. Therefore, we knocked down NUP160 by targeted short hairpin RNA (shRNA) in conditionally immortalized mouse podocytes and observed the effect of NUP160 knockdown on the proliferation, apoptosis, autophagy and cell migration of podocytes...
April 25, 2018: Gene
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