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RNA tag

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
Jiajia Wang, Hu Li, Renhuai Dai
Here, we describe the first complete mitochondrial genome (mitogenome) sequence of the leafhopper Taharana fasciana (Coelidiinae). The mitogenome sequence contains 15,161 bp with an A + T content of 77.9%. It includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding (A + T-rich) region; in addition, a repeat region is also present (GenBank accession no. KY886913). These genes/regions are in the same order as in the inferred insect ancestral mitogenome. All protein-coding genes have ATN as the start codon, and TAA or single T as the stop codons, except the gene ND3, which ends with TAG...
September 14, 2017: Genetica
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
Shengxi Chen, Rumit Maini, Xiaoguang Bai, Ryan C Nangreave, Larisa M Dedkova, Sidney M Hecht
Phosphorylated proteins play important roles in the regulation of many different cell networks. However, unlike the preparation of proteins containing unmodified proteinogenic amino acids, which can be altered readily by site-directed mutagenesis and expressed in vitro and in vivo, the preparation of proteins phosphorylated at predetermined sites cannot be done easily and in acceptable yields. To enable the synthesis of phosphorylated proteins for in vitro studies, we have explored the use of phosphorylated amino acids in which the phosphate moiety bears a chemical protecting group, thus eliminating the negative charges which have been shown to have a negative effect on protein translation...
September 12, 2017: Journal of the American Chemical Society
Patrizia D'Aquila, Paolina Crocco, Francesco De Rango, Cesare Indiveri, Dina Bellizzi, Giuseppina Rose, Giuseppe Passarino
Given the role of amino acid regulation for physiological and pathological cell proliferation, we investigated whether the variability of solute carrier family 1, member 5 (SLC1A5, namely ASCT2), encoding for ASCT2 protein, a major glutamine transporter, is related to longevity. A total of 607 differently aged unrelated individuals, 351 very old subjects (≥85 years, range 85-106 years, mean age 93.82 ± 4.44 years) and 256 younger controls (<85 years, range 64-84 years, mean age 73.60 ± 5.70 years) were analyzed...
September 8, 2017: Rejuvenation Research
Catherine Eichwald, Jonghwa Kim, Max L Nibert
Mammalian orthoreovirus protein μ2 is a component of the viral core particle. Its activities include RNA binding and hydrolysis of the γ-phosphate from NTPs and RNA 5´-termini, suggesting roles as a cofactor for the viral RNA-dependent RNA polymerase, λ3, first enzyme in 5´-capping of viral plus-strand RNAs, and/or prohibitory of RNA-5´-triphosphate-activated antiviral signaling. Within infected cells, μ2 also contributes to viral factories, cytoplasmic structures in which genome replication and particle assembly occur...
2017: PloS One
Xiangkun Huan, Yu He, Chi Huang, Younan Wang, Yi Zhu, Zekuan Xu, Li Yang, Huaxiang Cao
BACKGROUND: An escalating number of studies have provided identified evidence that sphingosine kinase 1 (SPHK1) plays an essential role in carcinogenesis. This present study was devised to seek the possible correlation of two tag single-nucleotide polymorphisms (SNPs) in SPHK1 (rs3744037 T>C, rs346801 C>T) with the susceptibility to gastric cancer (GC). METHODS: This present case-control study was comprised of 710 patients with GC and 710 gender- and age-matched cancer-free individuals...
September 1, 2017: Clinical Laboratory
Luke D Bussiere, Promisree Choudhury, Bryan Bellaire, Cathy L Miller
Within infected host cells, mammalian orthoreovirus (MRV) forms viral factories (VFs) which are sites of viral transcription, translation, assembly, and replication. MRV non-structural protein, μNS, comprises the structural matrix of VFs and is involved in recruiting other viral proteins to VF structures. Previous attempts have been made to visualize VF dynamics in live cells but due to current limitations in recovery of replicating reoviruses carrying large fluorescent protein tags, researchers have been unable to directly assess VF dynamics from virus-produced μNS...
September 6, 2017: Journal of Virology
Huanqiang Zhao, Fupin Hu, Han Yang, Baixing Ding, Xiaogang Xu, Chunyan He, Zelin Cui, Wen Shu, Qingzhong Liu
AIM: To explore the complete gene networks regulated by small RNA SprC and its targets in Staphylococcus aureus. MATERIALS & METHODS: The isobaric tags for relative and absolute quantitation and bioinformatic methods were utilized to identify and analyze the target proteins affected by SprC in S. aureus N315. RESULTS: Proteomic analysis showed that the expression of 44 proteins was modulated by SprC. Further, bioinformatic analysis displayed that these affected proteins mainly associated with metabolic and cellular process, biological regulation and catalytic activity...
September 6, 2017: Future Microbiology
J S Shincy, Mani Pankal, Jinu Jereena, Giri Yogesh Vengatagiri, Kshirsagar Rahul Vittalrao, Pethanen Sivakumar, Vincent Gopinath, Durairaj Sekar
MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules involved in the RNA silencing and post-transcriptional regulation of gene expression. miRNAs are well conserved in both plants and animals, and are thought to be a vital and evolutionarily ancient component of gene regulation and also act as oncogenes or tumor suppressors. It is known that Express Sequence Tags (EST) are a short sub-sequence of cDNA sequence, which contain information of condition or tissue specific transcripts (coding and non-coding) of an organism...
August 30, 2017: MicroRNA
Marco Brambilla, Francesca Martani, Paola Branduardi
The Saccharomyces cerevisiae poly(A)-binding protein Pab1 is a modular protein composed of four RNA recognition motifs (RRM), a proline-rich domain (P) and a C-terminus. Thanks to this modularity, Pab1 is involved in different interactions that regulate many aspects of mRNA metabolism, including the assembly of stress granules. In this work, we analyzed the contribution of each domain for the recruitment of the protein within stress granules by comparing the intracellular distribution of synthetic Pab1-GFP variants, lacking one or more domains, with the localization of the endogenous mCherry-tagged Pab1...
September 1, 2017: FEMS Yeast Research
Qi-Lin Zhang, Han-Yue Qiu, Ming-Zhong Liang, Bang Luo, Xiu-Qiang Wang, Jun-Yuan Chen
Amphioxus, a cephalochordate, is a key model animal for studying the evolution of vertebrate immunity. Recently, studies have revealed that microRNA (miRNA) expression profiles change significantly in the amphioxus gill after immune stimulation, but it remains largely unknown how gene expression responds to immune stress. Elucidating gene expression changes in the amphioxus gill will provide a deeper understanding of the evolution of gill immunity in vertebrates. Here, we used high-throughput RNA sequencing technology (RNA-seq) to conduct tag-based digital gene expression profiling (DGE) analyses of the gills of control Branchiostoma belcheri and of those exposed to the viral mimic, poly(I:C) (pIC)...
September 1, 2017: Fish & Shellfish Immunology
Birhanu M Kinfu, Maike Köster, Mareike Janus, Volkan Besirlioglu, Michael Roggenbuck, Richard Meurer, Ljubica Vojcic, Martin Borchert, Ulrich Schwaneberg, Jennifer Chow, Wolfgang R Streit
The exciting promises of functional metagenomics for the efficient discovery of novel biomolecules from nature are often hindered by factors associated with expression hosts. Aiming to shift functional metagenomics to a host independent innovative system, we here report on the cloning, heterologous expression and reconstitution of an RNA polymerase (RNAP) from the thermophilic Geobacillus sp. GHH01 and in vitro transcription thereafter. The five genes coding for RNAP subunits, a house keeping sigma factor and two transcription elongation factors were cloned and over expressed as His6 -tagged and/ or tag-free proteins...
August 26, 2017: Biotechnology and Bioengineering
Killian Quinn, Cinzia Traboni, Sujan Dily Penchala, Georgios Bouliotis, Nicki Doyle, Vincenzo Libri, Saye Khoo, Deborah Ashby, Jonathan Weber, Alfredo Nicosia, Riccardo Cortese, Antonello Pessi, Alan Winston
Long-acting injectable antiretroviral (LA-ARV) drugs with low toxicity profiles and propensity for drug-drug interactions are a goal for future ARV regimens. C34-PEG4-Chol is a novel cholesterol tagged LA HIV-fusion-inhibitor (FI). We assessed pre-clinical toxicology and first-in-human administration of C34-PEG4-Chol. Pre-clinical toxicology was conducted in 2 species. HIV-positive men were randomised to a single subcutaneous dose of C34-PEG4-Chol at incrementing doses or placebo. Detailed clinical (including injection site reaction (ISR) grading), plasma pharmacokinetic (time-to-minimum-effective-concentration (MEC, 25 ng/mL) and pharmacodynamic (plasma HIV RNA) parameters were assessed...
August 25, 2017: Scientific Reports
Satyanarayana Tatineni, Christian ELowsky, Robert Graybosch
Previously, we reported that coat protein (CP) of Wheat streak mosaic virus (WSMV; genus Tritimovirus, family Potyviridae) tolerates deletion of amino acids 36 to 84 for efficient systemic infection of wheat. In this study, we demonstrated that WSMV mutants with deletion of CP amino acids 58 to 84, but not 36 to 57, induced severe chlorotic streaks and spots, followed by acute chlorosis in wheat, maize, barley, and rye compared to mild to moderate chlorotic streaks and mosaic symptoms by wild-type virus. Deletion of CP amino acids 58 to 84 from WSMV genome accelerated cell-to-cell movement with increased accumulation of genomic RNAs and CP compared to wild-type virus...
August 25, 2017: Molecular Plant-microbe Interactions: MPMI
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
Ping Li, Maria Stumpf, Rolf Müller, Ludwig Eichinger, Gernot Glöckner, Angelika A Noegel
SUN1, a component of the LINC (Linker of Nucleoskeleton and Cytoskeleton) complex, functions in mammalian mRNA export through the NXF1-dependent pathway. It associates with mRNP complexes by direct interaction with NXF1. It also binds to the NPC through association with the nuclear pore component Nup153, which is involved in mRNA export. The SUN1-NXF1 association is at least partly regulated by a protein kinase C (PKC) which phosphorylates serine 113 (S113) in the N-terminal domain leading to reduced interaction...
August 22, 2017: Scientific Reports
Luis P Iñiguez, Mario Ramírez, William B Barbazuk, Georgina Hernández
BACKGROUND: The vast diversification of proteins in eukaryotic cells has been related with multiple transcript isoforms from a single gene that result in alternative splicing (AS) of primary transcripts. Analysis of RNA sequencing data from expressed sequence tags and next generation RNA sequencing has been crucial for AS identification and genome-wide AS studies. For the identification of AS events from the related legume species Phaseolus vulgaris and Glycine max, 157 and 88 publicly available RNA-seq libraries, respectively, were analyzed...
August 22, 2017: BMC Genomics
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
Christian Riml, Thomas Amort, Dietmar Rieder, Catherina Gasser, Alexandra Lusser, Ronald Micura
To understand the functional roles of RNA in the cell, it is essential to elucidate the dynamics of their production, processing and decay. A recent method for assessing mRNA dynamics is metabolic labeling with 4-thiouridine (4sU), followed by thio-selective attachment of affinity tags. Detection of labeled transcripts by affinity purification and hybridization to microarrays or by deep sequencing then reveals RNA expression levels. Here, we present a novel sequencing method (TUC-seq) that eliminates affinity purification and allows for direct assessment of 4sU-labeled RNA...
August 17, 2017: Angewandte Chemie
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