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https://www.readbyqxmd.com/read/28920956/biotin-tagging-of-mecp2-in-mice-reveals-contextual-insights-into-the-rett-syndrome-transcriptome
#1
Brian S Johnson, Ying-Tao Zhao, Maria Fasolino, Janine M Lamonica, Yoon Jung Kim, George Georgakilas, Kathleen H Wood, Daniel Bu, Yue Cui, Darren Goffin, Golnaz Vahedi, Tae Hoon Kim, Zhaolan Zhou
Mutations in MECP2 cause Rett syndrome (RTT), an X-linked neurological disorder characterized by regressive loss of neurodevelopmental milestones and acquired psychomotor deficits. However, the cellular heterogeneity of the brain impedes an understanding of how MECP2 mutations contribute to RTT. Here we developed a Cre-inducible method for cell-type-specific biotin tagging of MeCP2 in mice. Combining this approach with an allelic series of knock-in mice carrying frequent RTT-associated mutations (encoding T158M and R106W) enabled the selective profiling of RTT-associated nuclear transcriptomes in excitatory and inhibitory cortical neurons...
September 18, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28912172/rna-binding-proteins-in-neurodegeneration-mechanisms-in-aggregate
#2
REVIEW
Erin G Conlon, James L Manley
Neurodegeneration is a leading cause of death in the developed world and a natural, albeit unfortunate, consequence of longer-lived populations. Despite great demand for therapeutic intervention, it is often the case that these diseases are insufficiently understood at the basic molecular level. What little is known has prompted much hopeful speculation about a generalized mechanistic thread that ties these disparate conditions together at the subcellular level and can be exploited for broad curative benefit...
August 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28904365/rnai-mediated-silencing-of-a-pyruvate-dehydrogenase-kinase-enhances-triacylglycerol-biosynthesis-in-the-oleaginous-marine-alga-nannochloropsis-salina
#3
Xiaonian Ma, Lina Yao, Bo Yang, Yuan Kun Lee, Feng Chen, Jin Liu
Oleaginous microalgae have been emerging as the third-generation feedstocks for biofuel production. Genetic manipulation for improving triacylglycerol (TAG) accumulation represents a promising approach towards the economics of microalgal biofuels. Acetyl-CoA, the essential carbon precursor for de novo fatty acid biosynthesis, can be derived from pyruvate catalyzed by pyruvate dehydrogenase, which is negatively regulated by pyruvate dehydrogenase kinase (PDK). In the present study, we characterized a PDK gene (NsPDK) from Nannochloropsis salina...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28904350/tia1-dependent-regulation-of-mrna-subcellular-location-and-translation-controls-p53-expression-in-b-cells
#4
Manuel D Díaz-Muñoz, Vladimir Yu Kiselev, Nicolas Le Novère, Tomaz Curk, Jernej Ule, Martin Turner
Post-transcriptional regulation of cellular mRNA is essential for protein synthesis. Here we describe the importance of mRNA translational repression and mRNA subcellular location for protein expression during B lymphocyte activation and the DNA damage response. Cytoplasmic RNA granules are formed upon cell activation with mitogens, including stress granules that contain the RNA binding protein Tia1. Tia1 binds to a subset of transcripts involved in cell stress, including p53 mRNA, and controls translational silencing and RNA granule localization...
September 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28887370/genome-reprogramming-in-saccharomyces-cerevisiae-upon-nonylphenol-exposure
#5
Ceyhun Bereketoglu, Kazim Yalcin Arga, Serpil Eraslan, Bulent Mertoglu
Bioaccumulative environmental estrogen, nonylphenol (NP; 4-nonylphenol), is widely used as a non-ionic surfactant and can affect human health. Since genomes of Saccharomyces cerevisiae and higher eukaryotes share many structural and functional similarities, we investigated subcellular effects of NP on S. cerevisiae BY4742 cells by analyzing genome-wide transcriptional profiles. We examined effects of low (1 mg/L NP) and high (5 mg/L NP) inhibitory concentration exposures for 120 or 180 min. After 120 and 180 min of 1 mg/L NP exposure, 187 (63 downregulated, 124 upregulated) and 103 genes (56 downregulated, 47 upregulated), respectively, were differentially expressed...
September 8, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28880957/mapping-the-stk4-hippo-signaling-network-in-prostate-cancer-cell
#6
Damien Ready, Kader Yagiz, Pooneh Amin, Yuksel Yildiz, Vincent Funari, Serdar Bozdag, Bekir Cinar
Dysregulation of MST1/STK4, a key kinase component of the Hippo-YAP pathway, is linked to the etiology of many cancers with poor prognosis. However, how STK4 restricts the emergence of aggressive cancer remains elusive. Here, we investigated the effects of STK4, primarily localized in the cytoplasm, lipid raft, and nucleus, on cell growth and gene expression in aggressive prostate cancer. We demonstrated that lipid raft and nuclear STK4 had superior suppressive effects on cell growth in vitro and in vivo compared with cytoplasmic STK4...
2017: PloS One
https://www.readbyqxmd.com/read/28877994/cadherin-complexes-recruit-mrnas-and-risc-to-regulate-epithelial-cell-signaling
#7
Antonis Kourtidis, Brian Necela, Wan-Hsin Lin, Ruifeng Lu, Ryan W Feathers, Yan W Asmann, E Aubrey Thompson, Panos Z Anastasiadis
Cumulative evidence demonstrates that most RNAs exhibit specific subcellular distribution. However, the mechanisms regulating this phenomenon and its functional consequences are still under investigation. Here, we reveal that cadherin complexes at the apical zonula adherens (ZA) of epithelial adherens junctions recruit the core components of the RNA-induced silencing complex (RISC) Ago2, GW182, and PABPC1, as well as a set of 522 messenger RNAs (mRNAs) and 28 mature microRNAs (miRNAs or miRs), via PLEKHA7. Top canonical pathways represented by these mRNAs include Wnt/β-catenin, TGF-β, and stem cell signaling...
September 6, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28874813/functionannotator-a-versatile-and-efficient-web-tool-for-non-model-organism-annotation
#8
Ting-Wen Chen, Ruei-Chi Gan, Yi-Kai Fang, Kun-Yi Chien, Wei-Chao Liao, Chia-Chun Chen, Timothy H Wu, Ian Yi-Feng Chang, Chi Yang, Po-Jung Huang, Yuan-Ming Yeh, Cheng-Hsun Chiu, Tzu-Wen Huang, Petrus Tang
Along with the constant improvement in high-throughput sequencing technology, an increasing number of transcriptome sequencing projects are carried out in organisms without decoded genome information and even on environmental biological samples. To study the biological functions of novel transcripts, the very first task is to identify their potential functions. We present a web-based annotation tool, FunctionAnnotator, which offers comprehensive annotations, including GO term assignment, enzyme annotation, domain/motif identification and predictions for subcellular localization...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28874536/microrna-277-targets-insulin-like-peptides-7-and-8-to-control-lipid-metabolism-and-reproduction-in-aedes-aegypti-mosquitoes
#9
Lin Ling, Vladimir A Kokoza, Changyu Zhang, Emre Aksoy, Alexander S Raikhel
Hematophagous female mosquitoes transmit numerous devastating human diseases, including malaria, dengue fever, Zika virus, and others. Because of their obligatory requirement of a vertebrate blood meal for reproduction, these mosquitoes need a lot of energy; therefore, understanding the molecular mechanisms linking metabolism and reproduction is of particular importance. Lipids are the major energy store providing the fuel required for host seeking and reproduction. They are essential components of the fat body, a metabolic tissue that is the insect analog of vertebrate liver and adipose tissue...
September 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28874523/escherichia-coli-responds-to-environmental-changes-using-enolasic-degradosomes-and-stabilized-dicf-srna-to-alter-cellular-morphology
#10
Oleg N Murashko, Sue Lin-Chao
Escherichia coli RNase E is an essential enzyme that forms multicomponent ribonucleolytic complexes known as "RNA degradosomes." These complexes consist of four major components: RNase E, PNPase, RhlB RNA helicase, and enolase. However, the role of enolase in the RNase E/degradosome is not understood. Here, we report that presence of enolase in the RNase E/degradosome under anaerobic conditions regulates cell morphology, resulting in Ecoli MG1655 cell filamentation. Under anaerobic conditions, enolase bound to the RNase E/degradosome stabilizes the small RNA (sRNA) DicF, i...
September 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28864474/the-scaffolding-protein-iqgap1-interacts-with-nlrc3-and-inhibits-type-i-ifn-production
#11
Aaron M Tocker, Emily Durocher, Kimberly D Jacob, Kate E Trieschman, Suzanna M Talento, Alma A Rechnitzer, David M Roberts, Beckley K Davis
Sensing of cytosolic nucleotides is a critical initial step in the elaboration of type I IFN. One of several upstream receptors, cyclic GMP-AMP synthase, binds to cytosolic DNA and generates dicyclic nucleotides that act as secondary messengers. These secondary messengers bind directly to stimulator of IFN genes (STING). STING recruits TNFR-associated NF-κB kinase-binding kinase 1 which acts as a critical node that allows for efficient activation of IFN regulatory factors to drive the antiviral transcriptome...
September 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28863891/black-carp-sting-functions-importantly-in-innate-immune-defense-against-rna-virus
#12
Liang Lu, Xu Wang, Sizhong Wu, Xuejiao Song, Ziqi Zou, Xinchi Xie, Jun Xiao, Song Chen, Hao Feng
Stimulator of interferon genes (STING) is a central and multifaceted mediator in the innate immune response of higher vertebrates. To explore its role in teleost fish, the STING homolog of black carp (Mylopharyngodon piceus) (bcSTING) has been cloned and characterized in this paper. bcSTING transcription in Mylopharyngodon piceus fin (MPF) cells increased remarkably in response to GCRV and SVCV infection, or poly (I:C) stimulation. bcSTING migrated around 42 KDa in immunoblot assay and was identified as a cytosolic protein locating on ER majorly through immunofluorescence staining...
August 30, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28854977/up-regulation-of-lncrna-casc9-promotes-esophageal-squamous-cell-carcinoma-growth-by-negatively-regulating-pdcd4-expression-through-ezh2
#13
Yuanyuan Wu, Liwen Hu, Yan Liang, Juan Li, Kai Wang, Xuedan Chen, Hui Meng, Xingying Guan, Kang Yang, Yun Bai
BACKGROUND: Abnormal expression of numerous long non-coding RNAs (lncRNAs) has been reported in esophageal squamous cell carcinoma (ESCC) recently, but the great majority of their roles and mechanisms remain largely unclear. We aim to identify the critical ESCC-associated lncRNAs and elucidate the functions and mechanisms in detail. METHODS: Microarrays were used to analyze the differentially expressed lncRNAs in ESCC tissues. qRT-PCR was used to verify the result of microarrays...
August 30, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28846638/rep1-modulates-autophagy-and-macropinocytosis-to-enhance-cancer-cell-survival
#14
Jungwon Choi, Hyena Kim, Young Ki Bae, Heesun Cheong
Rab escort protein 1 (REP1), a component of the Rab geranyl-geranyltransferase 2 complex, plays a role in Rab protein recruitment in proper vesicles during vesicle trafficking. In addition to having well-known tissue degenerative phenotypes in the REP1 mutant, REP1 is tightly associated with cancer development and contributes to cell growth and survival. However, the functional mechanism of REP1 in cancer progression is largely uninvestigated. Here, we show that REP1 plays a crucial role in regulating mammalian target of rapamycin (mTOR) signaling and its downstream pathways, as well as autophagy and macropinocytosis, which are essential for cancer cell survival during metabolic stresses including starvation...
August 28, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28841711/evidence-for-a-cytoplasmic-pool-of-ribosome-free-mrnas-encoding-inner-membrane-proteins-in-escherichia-coli
#15
Daniel Benhalevy, Ido Biran, Elena S Bochkareva, Rotem Sorek, Eitan Bibi
Translation-independent mRNA localization represents an emerging concept in cell biology. In Escherichia coli, mRNAs encoding integral membrane proteins (MPRs) are targeted to the membrane where they are translated by membrane associated ribosomes and the produced proteins are inserted into the membrane co-translationally. In order to better understand aspects of the biogenesis and localization of MPRs, we investigated their subcellular distribution using cell fractionation, RNA-seq and qPCR. The results show that MPRs are overrepresented in the membrane fraction, as expected, and depletion of the signal recognition particle-receptor, FtsY reduced the amounts of all mRNAs on the membrane...
2017: PloS One
https://www.readbyqxmd.com/read/28837131/detection-of-nucleic-acid-protein-interactions-in-plant-leaves-using-fluorescence-lifetime-imaging-microscopy
#16
Laurent Camborde, Alain Jauneau, Christian Brière, Laurent Deslandes, Bernard Dumas, Elodie Gaulin
DNA-binding proteins (DNA-BPs) and RNA-binding proteins (RNA-BPs) have critical roles in living cells in all kingdoms of life. Various experimental approaches exist for the study of nucleic acid-protein interactions in vitro and in vivo, but the detection of such interactions at the subcellular level remains challenging. Here we describe how to detect nucleic acid-protein interactions in plant leaves by using a fluorescence resonance energy transfer (FRET) approach coupled to fluorescence lifetime imaging microscopy (FLIM)...
September 2017: Nature Protocols
https://www.readbyqxmd.com/read/28834149/maternal-inheritance-of-nanog-ortholog-in-blunt-snout-bream
#17
Miao Yu, Ting Xue, Tiansheng Chen, Jian Fang, Qihua Pan, Yu Deng, Lingyu Li, Kai Chen, Yizhou Wang
The homeodomain transcription factor Nanog plays an essential role in maintaining pluripotency and self-renewal of embryonic stem cells in mammals. However, the evolutionary conservation of its ortholog in teleosts remains elusive. Here we isolated and characterized a Nanog homolog named as Ma-Nanog in blunt-snout bream (Megalobrama amblycephala). The full-length genomic sequence is 3,326 bp in length and consists of four exons encoding a homeodomain protein of 386 amino acid residues. Comparison of protein sequences revealed that Ma-Nanog is highly homologous to those in other teleosts, particularly in the homeodomain region...
August 23, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28833065/mesenteric-lymph-node-stromal-cell-derived-extracellular-vesicles-contribute-to-peripheral-de-novo-induction-of-foxp3-regulatory-t-cells
#18
Maria Pasztoi, Joern Pezoldt, Michael Beckstette, Christoph Lipps, Dagmar Wirth, Manfred Rohde, Krisztina Paloczi, Edit Iren Buzas, Jochen Huehn
Intestinal regulatory T cells (Tregs) are fundamental in peripheral tolerance towards commensals and food-borne antigens. Accordingly, gut-draining mesenteric lymph nodes (mLNs) represent a site of efficient peripheral de novo Treg induction when compared to skin-draining peripheral LNs (pLNs), and we had recently shown that LN stromal cells substantially contribute to this process. Here, we aimed to unravel the underlying molecular mechanisms and generated immortalized fibroblastic reticular cell lines (iFRCs) from mLNs and pLNs, allowing unlimited investigation of this rare stromal cell subset...
August 18, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/28829780/proteomic-analysis-of-potentilla-fruticosa-l-leaves-by-itraq-reveals-responses-to-heat-stress
#19
Yingtian Guo, Zhi Wang, Xuelian Guan, Zenghui Hu, Ze Zhang, Jian Zheng, Yizeng Lu
High temperature is an important environmental factor that affects plant growth and crop yield. Potentilla fruticosa L. has a developed root system and characteristics of resistance to several stresses (e.g., high temperature, cold, drought) that are shared by native shrubs in the north and west of China. To investigate thermotolerance mechanisms in P. fruticosa, 3-year-old plants were subjected to a high temperature of 42°C for 1, 2, and 3 days respectively before analysis. Then, we studied changes in cell ultrastructure using electron microscopy and investigated physiological changes in the leaves of P...
2017: PloS One
https://www.readbyqxmd.com/read/28820065/bcg-increased-membrane-expression-of-trim59-through-the-tlr2-tlr4-irf5-pathway-in-raw264-7-macrophages
#20
Jin Zheng, Tian Yuan, Yan Dongmei, Li Dong, Zhu Xun
OBJECTIVE: In our previous study, we showed that Bacillus Calmette-Guerin (BCG)-activated macrophages have the ability to directly kill tumor cells. One of the main properties of these macrophages is the high expression of tripartite motif family protein 59 (TRIM59). This study was conducted to investigate the mechanism of BCG-induced TRIM59 expression on macrophages and to identify the subcellular localization of TRIM59. METHODS: TRIM59 expression and TNF-α secretion were compared in RAW264...
August 18, 2017: Protein and Peptide Letters
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