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Subcellular RNA

Pu Liu, Chao Zhang, Jin-Qi Ma, Li-Yuan Zhang, Bo Yang, Xin-Yu Tang, Ling Huang, Xin-Tong Zhou, Kun Lu, Jia-Na Li
Cytokinin oxidase/dehydrogenases (CKXs) play a critical role in the irreversible degradation of cytokinins, thereby regulating plant growth and development. Brassica napus is one of the most widely cultivated oilseed crops worldwide. With the completion of whole-genome sequencing of B. napus , genome-wide identification and expression analysis of the BnCKX gene family has become technically feasible. In this study, we identified 23 BnCKX genes and analyzed their phylogenetic relationships, gene structures, conserved motifs, protein subcellular localizations, and other properties...
March 16, 2018: Genes
Shannon N Rhoads, Zachary T Monahan, Debra S Yee, Frank P Shewmaker
Subcellular mislocalization and aggregation of the human FUS protein occurs in neurons of patients with subtypes of amyotrophic lateral sclerosis and frontotemporal dementia. FUS is one of several RNA-binding proteins that can functionally self-associate into distinct liquid-phase droplet structures. It is postulated that aberrant interactions within the dense phase-separated state can potentiate FUS's transition into solid prion-like aggregates that cause disease. FUS is post-translationally modified at numerous positions, which affect both its localization and aggregation propensity...
March 16, 2018: International Journal of Molecular Sciences
Olivier Poupel, Caroline Proux, Bernd Jagla, Tarek Msadek, Sarah Dubrac
The success of Staphylococcus aureus, as both a human and animal pathogen, stems from its ability to rapidly adapt to a wide spectrum of environmental conditions. Two-component systems (TCSs) play a crucial role in this process. Here, we describe a novel staphylococcal virulence factor, SpdC, an Abi-domain protein, involved in signal sensing and/or transduction. We have uncovered a functional link between the WalKR essential TCS and the SpdC Abi membrane protein. Expression of spdC is positively regulated by the WalKR system and, in turn, SpdC negatively controls WalKR regulon genes, effectively constituting a negative feedback loop...
March 2018: PLoS Pathogens
Yunyun Liang, Shengli Zhang
The apoptosis protein has a central role in the development and the homeostasis of an organism. Obtaining information about the subcellular localization of apoptosis protein is very helpful to understand the apoptosis mechanism and the function of this protein. Prediction of apoptosis protein's subcellular localization is a challenging task, and currently the existing feature extraction methods mainly rely on the protein's primary sequence. In this paper we develop a feature extraction model based on two different descriptors of evolutionary information, which contains the 192 frequencies of triplet codons (FTC) in the RNA sequence derived from the protein's primary sequence and the 190 features from a detrended forward moving-average cross-correlation analysis (DFMCA) based on a position-specific scoring matrix (PSSM) generated by the PSI-BLAST program...
March 12, 2018: Acta Biotheoretica
Zongyou Lv, Lei Zhang, Lingxian Chen, Fangyuan Zhang, Kexuan Tang
Artemisia annua is a typical short-day photoperiod (SD) and belongs to Asteraceae family. FLOWERING LOCUS T Homolog genes play important roles in regulation of flowering time. Two FT-like genes AaFT1 and AaFT2 were isolated from cDNA libraries constructed from leaves of A. annua. The gene expression analysis revealed that AaFT1 and AaFT2 mRNAs were expressed predominantly in leaves and could be induced by GA3. Subcellular localization results indicated that AaFT1 and AaFT2 proteins were both localized to the nuclei and cytoplasm...
March 5, 2018: Plant Physiology and Biochemistry: PPB
Ke Chen, Yuxuan Wang, Jie Sun
The Alu-element plays important roles in mediating alternative splicing, RNA editing and translation regulation. However, the distribution and function of the Alu-element are never analysed at the transcriptome level. This study presents a statistical analysis of the Alu-element on human transcriptome. We found that mRNAs and lncRNAs share the same sequence form for the Alu-element. The Alu-element covers 5.8% of the coding transcripts and 17.1% of the coding genes for mRNAs, and covers 9.3% of the transcripts and 13...
March 7, 2018: Biochemical and Biophysical Research Communications
Minlan Yang, Hairi Li, Yanru Li, Yang Ruan, Chengshi Quan
Multidrug resistance (MDR) is a major problem in the treatment of breast cancer. In the present study, next-generation sequencing technology was employed to identify differentially expressed genes in MCF‑7/MDR cells and MCF‑7 cells, and aimed to investigate the underlying molecular mechanisms of MDR in breast cancer. Differentially expressed genes between MCF‑7/MDR and MCF‑7 cells were selected using software; a total of 2085 genes were screened as differentially expressed in MCF‑7/MDR cells. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the DAVID database...
March 7, 2018: Molecular Medicine Reports
Natsumi Takei, Takuma Nakamura, Shohei Kawamura, Yuki Takada, Yui Satoh, Atsushi P Kimura, Tomoya Kotani
Background: Subcellular localization of coding and non-coding RNAs has emerged as major regulatory mechanisms of gene expression in various cell types and many organisms. However, techniques that enable detection of the subcellular distribution of these RNAs with high sensitivity and high resolution remain limited, particularly in vertebrate adult tissues and organs. In this study, we examined the expression and localization of mRNAs encoding Pou5f1/Oct4, Mos, Cyclin B1 and Deleted in Azoospermia-like (Dazl) in zebrafish and mouse ovaries by combining tyramide signal amplification (TSA)-based in situ hybridization with paraffin sections which can preserve cell morphology of tissues and organs at subcellular levels...
2018: Biological Procedures Online
Gyosuke Sakashita, Hitoshi Kiyoi, Tomoki Naoe, Takeshi Urano
Nucleophosmin (NPM1) is a multifunctional phosphoprotein which plays important roles in diverse biological processes. NPM1 can form homo- or hetero-oligomers through its N-terminal region, and bind DNA and RNA through its C-terminal region. However, the monomer-oligomer distribution of NPM1, and the extent of NPM1 binding and unbinding to RNA in living cells, are not fully understood. In this work, we analysed molecular complexes of NPM1 using size exclusion chromatography. We found that a substantial fraction of NPM1 behaves as an oligomer in HeLa cells...
March 5, 2018: Scientific Reports
Michael Briese, Lena Saal-Bauernschubert, Changhe Ji, Mehri Moradi, Hanaa Ghanawi, Michael Uhl, Silke Appenzeller, Rolf Backofen, Michael Sendtner
Disturbed RNA processing and subcellular transport contribute to the pathomechanisms of motoneuron diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy. RNA-binding proteins are involved in these processes, but the mechanisms by which they regulate the subcellular diversity of transcriptomes, particularly in axons, are not understood. Heterogeneous nuclear ribonucleoprotein R (hnRNP R) interacts with several proteins involved in motoneuron diseases. It is located in axons of developing motoneurons, and its depletion causes defects in axon growth...
March 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
Lisa Hartmann, Theresa Wießner, Andreas Wachter
Alternative splicing (AS) is prevalent in higher eukaryotes, and generation of different AS variants is tightly regulated. Widespread AS occurs in response to altered light conditions and plays a critical role in seedling photomorphogenesis, but despite its frequency and effect on plant development, the functional role of AS remains unknown for most splicing variants. Here, we characterized the light-dependent AS variants of the gene encoding the splicing regulator Serine/Arginine-rich protein SR30 in Arabidopsis (Arabidopsis thaliana)...
March 1, 2018: Plant Physiology
Zvonimir Marelja, Silke Leimkühler, Fanis Missirlis
Iron sulfur (Fe-S) clusters and the molybdenum cofactor (Moco) are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism...
2018: Frontiers in Physiology
Fumiaki Ito, Hanjing Yang, Xiao Xiao, Shu-Xing Li, Aaron Wolfe, Brett Zirkle, Vagan Arutiunian, Xiaojiang S Chen
APOBEC3H (A3H) is a member of the APOBEC3 subfamily of DNA cytosine deaminases that are important for innate immune defense and have been implicated in cancer biogenesis. To understand the structural basis for A3H biochemical function, we determined a high-resolution structure of human A3H and performed extensive biochemical analysis. The 2.49 Å crystal structure reveals a uniquely long C-terminal helix 6 (h6), a disrupted β5 strand of the canonical five-stranded β-sheet core, and a long loop 1 around the Zn-active center...
February 28, 2018: Scientific Reports
Li Li, Pieter C van Breugel, Fabricio Loayza-Puch, Alejandro Pineiro Ugalde, Gozde Korkmaz, Naama Messika-Gold, Ruiqi Han, Rui Lopes, Eric P Barbera, Hans Teunissen, Elzo de Wit, Ricardo J Soares, Boye S Nielsen, Kim Holmstrøm, Dannys J Martínez-Herrera, Maite Huarte, Annita Louloupi, Jarno Drost, Ran Elkon, Reuven Agami
Oncogene-induced senescence (OIS), provoked in response to oncogenic activation, is considered an important tumor suppressor mechanism. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nt without a protein-coding capacity. Functional studies showed that deregulated lncRNA expression promote tumorigenesis and metastasis and that lncRNAs may exhibit tumor-suppressive and oncogenic function. Here, we first identified lncRNAs that were differentially expressed between senescent and non-senescent human fibroblast cells...
February 22, 2018: Nucleic Acids Research
Ying Zhang, Lei Jiao, Li-Hua Sun, Yanru Li, Yuqiu Gao, Chaoqian Xu, Yingchun Shao, Mengmeng Li, Chunyan Li, Yanjie Lu, Zhenwei Pan, Li-Na Xuan, Yiyuan Zhang, Qingqi Li, Rui Yang, Yuting Zhuang, Yong Zhang, Baofeng Yang
<u>Rationale:</u> Ca2+ homeostasis, a critical determinant of cardiac contractile function, is critically regulated by sarcoplasmic reticulum Ca2+ -ATPase 2a (SERCA2a). Our previous study has identified ZFAS1 as a new long non-coding RNA (lncRNA) biomarker of acute myocardial infarction (MI). <u>Objective:</u> To evaluate the effects of ZFAS1 on SERCA2a and the associated Ca2+ homeostasis and cardiac contractile function in the setting of MI. <u>Methods and Results:</u> ZFAS1 expression was robustly increased in cytoplasm and sarcoplasmic reticulum in a mouse model of MI and a cellular model of hypoxia...
February 23, 2018: Circulation Research
Meijun Yuan, Mingxiao Ning, Panpan Wei, Wenjing Hao, Yunting Jing, Wei Gu, Wen Wang, Qingguo Meng
Serpin families classified serine protease inhibitors regulate various physiological processes. However, there is not study on the role of serpin in immune responses against Spiroplasma eriocheiris as a novel causative pathogen in the Chinese mitten crab, Eriocheir sinensis. In our study, quantitative real-time PCR (qRT-PCR) revealed that the mRNA transcripts of Esserpin-2 were ubiquitous in every tissue, relative higher expression in hepatopancreas, gill and hemocytes, while the intestine, muscle, heart and nerve showed relative lower expression...
February 20, 2018: Fish & Shellfish Immunology
Ying Li, Mahima Aggarwal, Ke Ke, Kim Nguyen, Robert C Spitale
Recent analysis of transcriptomes has revealed that RNAs perform a myriad of functions beyond coding for proteins. Critical to RNA function is its transport to unique subcellular locations. Despite the importance of RNA localization it is still very challenging to study in an unbiased manner. We recently described the ability to tag RNA molecules within subcellular locations through spatially-restricted nucleobase oxidation. Herein we describe a dramatic improvement of this protocol through the localized oxidation and tagging of proteins...
February 23, 2018: Biochemistry
Anastasia V Balakireva, Andrey A Zamyatnin
Plant defense is achieved mainly through the induction of microbe-associated molecular patterns (MAMP)-triggered immunity (MTI), effector-triggered immunity (ETI), systemic acquired resistance (SAR), induced systemic resistance (ISR), and RNA silencing. Plant immunity is a highly complex phenomenon with its own unique features that have emerged as a result of the arms race between plants and pathogens. However, the regulation of these processes is the same for all living organisms, including plants, and is controlled by proteases...
February 23, 2018: International Journal of Molecular Sciences
Muwan Chen, Sofie H Laursen, Mette Habekost, Camilla H Knudsen, Susanne H Buchholdt, Jinrong Huang, Fengping Xu, Xin Liu, Lars Bolund, Yonglun Luo, Poul Nissen, Fabia Febbraro, Mark Denham
The P-type ATPases family consists of ion and lipid transporters. Their unique diversity in function and expression is critical for normal development. In this study we investigated human pluripotent stem cells (hPSC) and different neural progenitor states to characterize the expression of the plasma membrane calcium ATPases (PMCAs) during human neural development and in mature mesencephalic dopaminergic (mesDA) neurons. Our RNA sequencing data identified a dynamic change in ATPase expression correlating with the differentiation time of the neural progenitors, which was independent of the neuronal progenitor type...
2018: Frontiers in Cell and Developmental Biology
Tapiwa Lundu, Yoshimi Tsuda, Ryo Ito, Kenta Shimizu, Shintaro Kobayashi, Kentaro Yoshii, Kumiko Yoshimatsu, Jiro Arikawa, Hiroaki Kariwa
Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV) is a newly emerged phlebovirus identified in China, Japan, and South Korea. Phlebovirus glycoproteins (GP) play a key role in targeting viral structural components to the budding compartments in the ER-Golgi intermediate compartment (ERGIC) and Golgi complex. However, the role of SFTSV GP in targeting structural proteins to the ERGIC and Golgi complex remains unresolved. In this study, we show that SFTSV GP plays a significant role in targeting RNA-dependent RNA polymerase (L) and nucleocapsid protein (NP) to the budding sites...
2018: Biomedical Research
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