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https://www.readbyqxmd.com/read/27912775/a-novel-long-non-coding-rna-lnc-gnat1-1-is-low-expressed-in-colorectal-cancer-and-acts-as-a-tumor-suppressor-through-regulating-rkip-nf-%C3%AE%C2%BAb-snail-circuit
#1
Chunxiang Ye, Zhanlong Shen, Bo Wang, Yansen Li, Tao Li, Yang Yang, Kewei Jiang, Yingjiang Ye, Shan Wang
BACKGROUND: The role of long non-coding RNAs (lncRNAs) in colorectal cancer (CRC) progression has not fully been elucidated. This study was designed to report the identification of a novel lncRNA, lnc-GNAT1-1, and its functional role in CRC progression. METHODS: lncRNA expression profile microarray was performed in three paired primary and liver metastatic tissues of CRC, and a novel lncRNA, lnc-GNAT1-1, was identified to be a potential functional lncRNA. Quantitative real-time PCR was used to detect its expression in CRC tissues, cell lines, and patients' plasma, cell fractionation was used to evaluate its subcellular location...
December 3, 2016: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/27911723/ribonucleoprotein-bodies-are-phased-in
#2
REVIEW
Aristeidis P Sfakianos, Alan J Whitmarsh, Mark P Ashe
Intracellular compartments are necessary for the regulation of many biochemical processes that ensure cell survival, growth and proliferation. Compartmentalisation is commonly achieved in organelles with defined lipid membranes, such as mitochondria, endoplasmic reticulum or the Golgi apparatus. While these organelles are responsible for many localised biochemical processes, recent evidence points to another class of compartments that lack membrane boundaries. The structure and content of these bodies depend on their function and subcellular localisation, but they mainly incorporate proteins and RNA...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27895152/spatio-temporal-uncoupling-of-mirna-mediated-translational-repression-and-target-rna-degradation-controls-mirnp-recycling-in-mammalian-cells
#3
Mainak Bose, Bahnisikha Barman, Avijit Goswami, Suvendra N Bhattacharyya
miRNA-mediated repression control expression of more than half of protein coding genes in metazoan animals. Translation repression is associated with target mRNA degradation initiated by decapping and deadenylation of the repressed mRNAs. Earlier evidence suggest Endoplasmic Reticulum (ER) as the site where miRNPs interact with their targets before the translation repression sets in but the subcellular location of subsequent degradation of miRNA-repressed messages is largely unidentified. Here, we explore the subcellular distribution of essential components of degradation machineries of miRNA-targeted mRNAs...
November 28, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27871336/zfas1-a-long-noncoding-rna-associated-with-ribosomes-in-breast-cancer-cells
#4
Herah Hansji, Euphemia Y Leung, Bruce C Baguley, Graeme J Finlay, David Cameron-Smith, Vandre C Figueiredo, Marjan E Askarian-Amiri
BACKGROUND: Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts including thousands of lncRNAs that generally lack protein coding potential. However, only a small percentage of these molecules has been functionally characterised, and discoveries of specific functions demonstrate layers of complexity. A large percentage of lncRNAs is located in the cytoplasm, associated with ribosomes but the function of the majority of these transcripts is unclear. The current study analyses putative mechanisms of action of the lncRNA species member ZFAS1 that was initially discovered by microarray analysis of murine tissues undergoing mammary gland development...
November 21, 2016: Biology Direct
https://www.readbyqxmd.com/read/27858503/high-throughput-sequencing-of-two-populations-of-extracellular-vesicles-provides-an-mrna-signature-that-can-be-detected-in-the-circulation-of-breast-cancer-patients
#5
Andrew Conley, Valentina R Minciacchi, Dhong Hyun Lee, Beatrice S Knudsen, Beth Y Karlan, Luigi Citrigno, Giuseppe Viglietto, Muneesh Tewari, Michael R Freeman, Francesca Demichelis, Dolores Di Vizio
Extracellular vesicles (EVs) contain a wide range of RNA types with a reported prevalence of non-coding RNA. To date a comprehensive characterization of the protein coding transcripts in EVs is still lacking. We performed RNA-Sequencing (RNA-Seq) of two EV populations and identified a small fraction of transcripts that were expressed at significantly different levels in large oncosomes and exosomes, suggesting they may mediate specialized functions. However, these two EV populations exhibited a common mRNA signature that, in comparison to their donor cells, was significantly enriched in mRNAs encoding E2F transcriptional targets and histone proteins...
November 18, 2016: RNA Biology
https://www.readbyqxmd.com/read/27858162/downregulated-klk13-expression-in-bladder-cancer-highlights-tumor-aggressiveness-and-unfavorable-patients-prognosis
#6
Theodoros Tokas, Margaritis Avgeris, Christos Alamanis, Andreas Scorilas, Konstantinos G Stravodimos, Constantinos A Constantinides
PURPOSE: Despite recent research advantages on the molecular and subcellular background, bladder cancer (BlCa) remains a clinically neglected malignancy. This is strongly reflected by the generic approach of disease diagnosis and management. Additionally, patients' prognosis became a rather demanding task due to the great disease heterogeneity. Here, we aimed to evaluate, for the first time, the clinical value of KLK13 in BlCa. METHODS: A total of 279 bladder specimens (137 tumors, 107 adjacent normal tissues and 35 healthy samples) were included...
November 17, 2016: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/27852860/nes-masking-regulates-hiv-1-rev-trafficking-and-viral-rna-nuclear-export
#7
Ryan T Behrens, Mounavya Aligeti, Ginger M Pocock, Christina A Higgins, Nathan M Sherer
: HIV-1's Rev protein forms a homooligomeric adaptor complex linking viral RNAs to the cellular CRM1/Ran-GTP nuclear export machinery through the activity of Rev's prototypical leucine-rich nuclear export signal (NES). In this study we used a functional fluorescently-tagged Rev fusion protein as a platform to study the effects of modulating Rev NES identity, number, position, or strength on Rev subcellular trafficking, viral RNA nuclear export, and infectious virion production. We found Rev activity to be remarkably tolerant of diverse NES sequences including supraphysiological NES (SNES) peptides that otherwise arrest CRM1 transport complexes at nuclear pores...
November 16, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27849555/role-of-post-transcriptional-regulation-of-mrna-stability-in-renal-pathophysiology-focus-on-chronic-kidney-disease
#8
REVIEW
Eva Feigerlová, Shyue-Fang Battaglia-Hsu
Chronic kidney disease (CKD) represents an important public health problem. Its progression to end-stage renal disease is associated with increased morbidity and mortality. The determinants of renal function decline are not fully understood. Recent progress in the understanding of post-transcriptional regulation of mRNA stability has helped the identification of both the trans- and cis-acting elements of mRNA as potential markers and therapeutic targets for difficult-to-diagnose and -treat diseases, including CKDs such as diabetic nephropathy...
November 14, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27830677/-the-application-of-yeast-hybrid-systems-in-protein-interaction-analysis
#9
Z-X Zhu, Z-M Yu, J L Taylor, Y-H Wu, J Ni
Yeast hybrid systems have been widely used due to their convenience and low cost. Based on these systems, many methods have been developed to analyze protein-protein, protein-DNA and protein-RNA interactions. In this paper, we are reviewing these different yeast hybrid systems. According to the number of hybrid proteins, yeast hybrid systems can be divided into three categories, yeast one-hybrid, yeast two-hybrid and yeast three-hybrid systems. Alternatively, yeast hybrid systems can be categorized according to the subcellular localization of the protein interaction process in the cell into nuclear protein-protein interactions, cytosol protein-protein interactions and membrane protein-protein interactions...
September 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/27818379/delayed-greening-238-a-nuclear-encoded-chloroplast-nucleoid-protein-is-involved-in-the-regulation-of-early-chloroplast-development-and-plastid-gene-expression-in-arabidopsis-thaliana
#10
Menglong Wang, Lan Jiang, Qingen Da, Jun Liu, Dongru Feng, Jinfa Wang, Hong-Bin Wang, Hong-Lei Jin
Chloroplast development is an essential process for plant growth that is regulated by numerous proteins. Plastid-encoded plastid RNA polymerase (PEP) is a large complex that regulates plastid gene transcription and chloroplast development. However, many proteins in this complex remain to be identified. Here, through large-scale screening of Arabidopsis mutants by Chl fluorescence imaging, we identified a novel protein, DELAYED GREENING 238 (DG238), which is involved in regulating chloroplast development and plastid gene expression...
October 22, 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/27808156/molecular-characterization-of-a-novel-effector-expansin-like-protein-from-heterodera-avenae-that-induces-cell-death-in-nicotiana-benthamiana
#11
Jing Liu, Huan Peng, Jiangkuan Cui, Wenkun Huang, Lingan Kong, Jihong Liu Clarke, Heng Jian, Guo Liang Wang, Deliang Peng
Cereal cyst nematodes are sedentary biotrophic endoparasites that maintain a complex interaction with their host plants. Nematode effector proteins are synthesized in the oesophageal glands and are secreted into plant tissues through the stylet. To understand the function of nematode effectors in parasitic plants, we cloned predicted effectors genes from Heterodera avenae and transiently expressed them in Nicotiana benthamiana. Infiltration assays showed that HaEXPB2, a predicted expansin-like protein, caused cell death in N...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27803124/rice-aleurone-layer-specific-osnf-yb1-regulates-grain-filling-and-endosperm-development-by-interacting-with-an-erf-transcription-factor
#12
Jing-Jing Xu, Xiao-Fan Zhang, Hong-Wei Xue
Grain yield and quality of rice mainly depend on grain filling and endosperm development. Here we report that a rice NUCLEAR FACTOR Y (NF-Y) transcription factor, OsNF-YB1, is specifically expressed in the aleurone layer of developing endosperm and regulates grain filling and endosperm development. Knockdown of OsNF-YB1 expression by RNAi significantly retarded grain filling, leading to small grains with chalky endosperm as well as altered starch quality. Whereas OsNF-YB1 shows subcellular localization in both the cytosol and the nucleus in roots, it was specifically targeted to the nucleus of aleurone layer cells, which was facilitated by interacting with OsNF-YC proteins preferentially expressed in the aleurone layer...
November 1, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/27784754/an-rnai-screen-to-identify-protein-phosphatases-that-function-within-the-drosophila-circadian-clock
#13
Parul Agrawal, Paul E Hardin
Circadian clocks in eukaryotes keep time via cell-autonomous transcriptional feedback loops. A well-characterized example of such a transcriptional feedback loop is in Drosophila, where CLOCK-CYCLE (CLK-CYC) complexes activate transcription of period (per) and timeless (tim) genes, rising levels of PER-TIM complexes feedback to repress CLK-CYC activity, and degradation of PER and TIM permits the next cycle of CLK-CYC transcription. The timing of CLK-CYC activation and PER-TIM repression is regulated post-translationally, in part through rhythmic phosphorylation of CLK, PER and TIM...
October 26, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27765065/extending-gene-ontology-in-the-context-of-extracellular-rna-and-vesicle-communication
#14
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B Gerstein, Andrew F Hill, Robert R Kitchen, Jan Lötvall, Tushar Patel, Dena C Procaccini, Peter Quesenberry, Joel Rozowsky, Robert L Raffai, Aleksandra Shypitsyna, Andrew I Su, Clotilde Théry, Kasey Vickers, Marca H M Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C Laurent
BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. METHODS: By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO...
April 12, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27759007/siks-control-osteocyte-responses-to-parathyroid-hormone
#15
Marc N Wein, Yanke Liang, Olga Goransson, Thomas B Sundberg, Jinhua Wang, Elizabeth A Williams, Maureen J O'Meara, Nicolas Govea, Belinda Beqo, Shigeki Nishimori, Kenichi Nagano, Daniel J Brooks, Janaina S Martins, Braden Corbin, Anthony Anselmo, Ruslan Sadreyev, Joy Y Wu, Kei Sakamoto, Marc Foretz, Ramnik J Xavier, Roland Baron, Mary L Bouxsein, Thomas J Gardella, Paola Divieti-Pajevic, Nathanael S Gray, Henry M Kronenberg
Parathyroid hormone (PTH) activates receptors on osteocytes to orchestrate bone formation and resorption. Here we show that PTH inhibition of SOST (sclerostin), a WNT antagonist, requires HDAC4 and HDAC5, whereas PTH stimulation of RANKL, a stimulator of bone resorption, requires CRTC2. Salt inducible kinases (SIKs) control subcellular localization of HDAC4/5 and CRTC2. PTH regulates both HDAC4/5 and CRTC2 localization via phosphorylation and inhibition of SIK2. Like PTH, new small molecule SIK inhibitors cause decreased phosphorylation and increased nuclear translocation of HDAC4/5 and CRTC2...
October 19, 2016: Nature Communications
https://www.readbyqxmd.com/read/27754875/global-analysis-of-pre-mrna-subcellular-localization-following-splicing-inhibition-by-spliceostatin-a
#16
Rei Yoshimoto, Daisuke Kaida, Masaaki Furuno, A Maxwell Burroughs, Shohei Noma, Harukazu Suzuki, Yumi Kawamura, Yoshihide Hayashizaki, Akila Mayeda, Minoru Yoshida
Spliceostatin A (SSA) is a methyl ketal derivative of FR901464, a potent antitumor compound isolated from a culture broth of Pseudomonas sp. no. 2663. These compounds selectively bind to the essential spliceosome component SF3b, a subcomplex of the U2 snRNP, to inhibit pre-mRNA splicing. However, the mechanism of SSA's antitumor activity is unknown. It is noteworthy that SSA causes accumulation of a truncated form of the CDK inhibitor protein p27 translated from CDKN1B pre-mRNA, which is involved in SSA-induced cell-cycle arrest...
October 17, 2016: RNA
https://www.readbyqxmd.com/read/27741406/bugs-are-not-to-be-silenced-small-rna-pathways-and-antiviral-responses-in-insects
#17
Vanesa Mongelli, Maria-Carla Saleh
Like every other organism on Earth, insects are infected with viruses, and they rely on RNA interference (RNAi) mechanisms to circumvent viral infections. A remarkable characteristic of RNAi is that it is both broadly acting, because it is triggered by double-stranded RNA molecules derived from virtually any virus, and extremely specific, because it targets only the particular viral sequence that initiated the process. Reviews covering the different facets of the RNAi antiviral immune response in insects have been published elsewhere...
September 29, 2016: Annual Review of Virology
https://www.readbyqxmd.com/read/27733621/identification-of-novel-nesprin-1-binding-partners-and-cytoplasmic-matrin-3-in-processing-bodies
#18
Dipen Rajgor, Jonathan G Hanley, Catherine M Shanahan
Nesprins are highly conserved spectrin repeat-containing scaffold proteins predominantly known to function at the nuclear envelope (NE). However, nesprin isoforms are emerging with localizations and scaffolding functions at sites away from the NE, suggesting their functions are more diverse than originally thought. In this study, we combined nesprin-1 coimmunoprecipitations with mass spectrometry to identify novel nesprin-1 binding partners for isoforms that localize to subcellular compartments beyond the NE...
December 1, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27733365/transcriptional-regulation-of-importin-%C3%AE-1-by-jund-modulates-subcellular-localization-of-rna-binding-protein-hur-in-intestinal-epithelial-cells
#19
Yan Xu, Jie Chen, Lan Xiao, Hee Kyoung Chung, Yuan Zhang, Joseph C Robinson, Jaladanki N Rao, Jian-Ying Wang
The RNA-binding protein HuR is crucial for normal intestinal mucosal regeneration by modulating the stability and translation of target mRNAs, but the exact mechanism underlying HuR trafficking between the cytoplasm and nucleus remains largely unknown. Here we report a novel function of transcription factor JunD in the regulation of HuR subcellular localization through the control of importin-α1 expression in intestinal epithelial cells (IECs). Ectopically expressed JunD specifically inhibited importin-α1 at the transcription level, and this repression is mediated via interaction with CREB-binding site that was located at the proximal region of importin-α1 promoter...
December 1, 2016: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/27725644/nop9-is-a-puf-like-protein-that-prevents-premature-cleavage-to-correctly-process-pre-18s-rrna
#20
Jun Zhang, Kathleen L McCann, Chen Qiu, Lauren E Gonzalez, Susan J Baserga, Traci M Tanaka Hall
Numerous factors direct eukaryotic ribosome biogenesis, and defects in a single ribosome assembly factor may be lethal or produce tissue-specific human ribosomopathies. Pre-ribosomal RNAs (pre-rRNAs) must be processed stepwise and at the correct subcellular locations to produce the mature rRNAs. Nop9 is a conserved small ribosomal subunit biogenesis factor, essential in yeast. Here we report a 2.1-Å crystal structure of Nop9 and a small-angle X-ray-scattering model of a Nop9:RNA complex that reveals a 'C'-shaped fold formed from 11 Pumilio repeats...
October 11, 2016: Nature Communications
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