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RNA biogenesis

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https://www.readbyqxmd.com/read/29330460/enhanced-skeletal-muscle-ribosome-biogenesis-yet-attenuated-mtorc1-and-ribosome-biogenesis-related-signalling-following-short-term-concurrent-versus-single-mode-resistance-training
#1
Jackson J Fyfe, David J Bishop, Jonathan D Bartlett, Erik D Hanson, Mitchell J Anderson, Andrew P Garnham, Nigel K Stepto
Combining endurance training with resistance training (RT) may attenuate skeletal muscle hypertrophic adaptation versus RT alone; however, the underlying mechanisms are unclear. We investigated changes in markers of ribosome biogenesis, a process linked with skeletal muscle hypertrophy, following concurrent training versus RT alone. Twenty-three males underwent eight weeks of RT, either performed alone (RT group, n = 8), or combined with either high-intensity interval training (HIT+RT group, n = 8), or moderate-intensity continuous training (MICT+RT group, n = 7)...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330104/circular-rna-an-emerging-non-coding-rna-as-a-regulator-and-biomarker-in-cancer
#2
Bing Chen, Shenglin Huang
Circular RNA (circRNA) is a type of covalently closed non-coding RNA that may regulate gene expression in eukaryotes. The recent application of high-throughput RNA sequencing and bioinformatics approaches has revealed a large number of circRNAs in human cells. Emerging evidence indicates that many circRNAs have cell-type specific expression and are linked to physiological development and various diseases. Specially, circRNAs can either serve as oncogenic stimuli or tumor suppressors in cancer. circRNAs have also been shown to be enriched and stable in extracellular fluid, indicating the potential of circRNAs as cancer biomarkers...
January 9, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29327403/biogenesis-and-regulatory-hierarchy-of-phased-small-interfering-rnas-in-plants
#3
REVIEW
Pingchuan Deng, Sajid Muhammad, Min Cao, Liang Wu
Several varieties of small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are generated in plants to regulate development, genome stability, and response to adverse environments. Phased siRNA (phasiRNA) is a type of secondary siRNA that is processed from a miRNA-mediated cleavage of RNA transcripts, increasing silencing efficiency or simultaneously suppressing multiple target genes. Trans-acting siRNAs (ta-siRNAs) are a particular class of phasiRNA produced from non-coding transcripts that silence targets in trans...
January 11, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29322448/characterization-of-circular-rnas-circrna-associated-with-the-translation-machinery
#4
Deniz Bartsch, Anne Zirkel, Leo Kurian
A substantial proportion of the currently annotated genes in eukaryotes are proposed to function as RNA molecules (>200 bp) with no significant protein coding potential, currently classified as long noncoding RNAs (lncRNA). A distinct subgroup of lncRNAs is circular RNAs (circRNAs), which can be easily identified by unique junction reads, resulting from their biogenesis. CircRNAs are largely cytosolic and thought to either code for micro-peptides or facilitate gene regulation by sequestering microRNAs (miRNAs) or RNA-binding proteins (RBPs) from their targets...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29322444/constructing-gfp-based-reporter-to-study-back-splicing-and-translation-of-circular-rna
#5
Yun Yang, Zefeng Wang
Human transcriptome contains a large number of circular RNAs (circRNAs) that are mainly produced by back splicing of pre-mRNA. Here we describe a minigene reporter system containing a single exon encoding split GFP in reverse order, which can be efficiently back spliced to produce a circRNA encoding intact GFP gene. This simple reporter system can be adopted to study how different cis-elements and trans-factors affect circRNA production, and also can serve as a reliable system to measure the activity of IRES-mediated translation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29322436/detection-and-reconstruction-of-circular-rnas-from-transcriptomic-data
#6
Yi Zheng, Fangqing Zhao
Recent studies have shown that circular RNAs (circRNAs) are a novel class of abundant, stable, and ubiquitous noncoding RNA molecules in eukaryotic organisms. Comprehensive detection and reconstruction of circRNAs from high-throughput transcriptome data is an initial step to study their biogenesis and function. Several tools have been developed to deal with this issue, but they require many steps and are difficult to use. To solve this problem, we provide a protocol for researchers to detect and reconstruct circRNA by employing CIRI2, CIRI-AS, and CIRI-full...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321322/dengue-virus-selectively-annexes-endoplasmic-reticulum-associated-translation-machinery-as-a-strategy-for-co-opting-host-cell-protein-synthesis
#7
David W Reid, Rafael K Campos, Jessica R Child, Tianli Zheng, Kitti Wing Ki Chan, Shelton S Bradrick, Subhash G Vasudevan, Mariano A Garcia-Blanco, Christopher V Nicchitta
A primary question in Dengue virus (DENV) biology is the molecular strategy for recruitment of host cell protein synthesis machinery. Here we combined cell fractionation, ribosome profiling, and RNA-seq to investigate the subcellular organization of viral genome translation and replication as well as host cell translation and its response to DENV infection. We report that throughout the viral life cycle, DENV (+) and (-) strand RNAs were highly partitioned to the endoplasmic reticulum (ER), identifying the ER as the primary site of DENV translation...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29317670/tdrd5-binds-pirna-precursors-and-selectively-enhances-pachytene-pirna-processing-in-mice
#8
Deqiang Ding, Jiali Liu, Uros Midic, Yingjie Wu, Kunzhe Dong, Ashley Melnick, Keith E Latham, Chen Chen
Pachytene piRNAs are the most abundant piRNAs in mammalian adult testes. They are generated from long precursor transcripts by the primary piRNA biogenesis pathway but the factors involved in pachytene piRNA precursors processing are poorly understood. Here we show that the Tudor domain-containing 5 (TDRD5) protein is essential for pachytene piRNA biogenesis in mice. Conditional inactivation of TDRD5 in mouse postnatal germ cells reveals that TDRD5 selectively regulates the production of pachytene piRNAs from abundant piRNA-producing precursors, with little effect on low-abundant piRNAs...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29317647/investigation-of-piwi-interacting-rna-pathway-genes-role-in-idiopathic-non-obstructive-azoospermia
#9
Zeeba Kamaliyan, Sara Pouriamanesh, Mohsen Soosanabadi, Milad Gholami, Reza Mirfakhraie
Genes involved in piwi-interacting RNAs (piRNAs) pathway have an essential role in spermatogenesis. HIWI and TDRD proteins are critical for piRNA biogenesis and function. Therefore, Mutations and polymorphisms in HIWI and TDRD genes may play role in male infertility. The aim of the present study was to investigate the role of HIWI2 rs508485 (T>C) and HIWI3 rs11703684 (C>T) polymorphisms and mutational analysis of TDRD5 gene in idiopathic non-obstructive azoospermia in a case-control study including 226 non-obstructive azoospermia patients and 200 fertile males...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29316035/transcription-factor-eb-tfeb-influences-invasion-and-migration-in-oral-squamous-cell-carcinomas
#10
Hiroshi Sakamoto, Kentaro Yamashita, Kuniaki Okamoto, Tomoko Kadowaki, Eiko Sakai, Masahiro Umeda, Takayuki Tsukuba
OBJECTIVE: Transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis and plays an important role in various cancers. However, the function of TFEB in oral squamous cell carcinomas has not been examined. The aim of this study was to elucidate the role of TFEB in oral squamous cell carcinomas. MATERIALS AND METHODS: Expression levels of TFEB were examined in six different human oral squamous carcinoma cells: HSC2, HSC3, HSC4, SAS, OSC20, and SCC25...
January 9, 2018: Oral Diseases
https://www.readbyqxmd.com/read/29301509/assessment-of-pirna-biogenesis-and-function-in-testicular-germ-cell-tumors-and-their-precursor-germ-cell-neoplasia-in-situ
#11
Ildar V Gainetdinov, Yulia V Skvortsova, Sofia A Kondratieva, Alexey Klimov, Alexey A Tryakin, Tatyana L Azhikina
BACKGROUND: Aberrant overexpression of PIWI/piRNA pathway proteins is shown for many types of tumors. Interestingly, these proteins are downregulated in testicular germ cell tumors (TGCTs) compared to normal testis tissues. Here, we used germline and TGCT markers to assess the piRNA biogenesis and function in TGCTs and their precursor germ cell neoplasia in situ (GCNIS). METHODS: We used small RNA deep sequencing, qRT-PCR, and mining public RNAseq/small RNA-seq datasets to examine PIWI/piRNA gene expression and piRNA biogenesis at four stages of TGCT development: (i) germ cells in healthy testis tissues, (ii) germ cells in testis tissues adjacent to TGCTs, (iii) GCNIS cells and (iv) TGCT cells...
January 4, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29301498/pcaf-mediated-acetylation-of-lin28b-increases-let-7-biogenesis-in-lung-adenocarcinoma-h1299-cells
#12
Ting-Ting Qu, Fei Chen, Jing Wang, Yan-Jun Zhang, Mo-Bin Cheng, Wen-Zheng Sun, Yu-Fei Shen, Ye Zhang
BACKGROUND: Lin28B and its paralog Lin28A are small RNA binding proteins that have similar inhibitory effects, although they target separate steps in the maturation of let-7 miRNAs in mammalian cells. Because Lin28B participates in the promotion and development of tumors mostly by blocking the let-7 tumor suppressor family members, we sought to explore the associated mechanisms to gain insights into how Lin28B might be decreased in human cancer cells to increase let-7 levels and reverse malignancy...
January 4, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29286868/elongator-promotes-germination-and-early-post-germination-growth
#13
Magdalena Wołoszyńska, Olimpia Gagliardi, Filip Vandenbussche, Mieke Van Lijsebettens
The Elongator complex interacts with RNA polymerase II and via histone acetylation and DNA demethylation facilitates epigenetically the transcription of genes involved in diverse processes in plants, including growth, development, and immune response. Recently, we have shown that the Elongator complex promotes hypocotyl elongation and photomorphogenesis in Arabidopsis thaliana by regulating the photomorphogenesis and growth-related gene network that converges on genes implicated in cell wall biogenesis and hormone signaling...
December 29, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/29281264/piwi-interacting-rna-in-drosophila-biogenesis-transposon-regulation-and-beyond
#14
Haruna Yamashiro, Mikiko C Siomi
PIWI-interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity. To achieve this, upon being processed from piRNA precursors, most of which are transcripts of intergenic piRNA clusters, piRNAs bind PIWI proteins, germline-specific Argonaute proteins, to form effector complexes. The mechanism of this piRNA-mediated transposon silencing pathway is fundamentally similar to that of siRNA/miRNA-dependent gene silencing in that a small RNA guides its partner Argonaute protein to target gene transcripts for repression via RNA-RNA base pairing...
December 27, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/29277012/photoelectrochemical-biosensor-for-hen1-rna-methyltransferase-detection-using-peroxidase-mimics-ptcu-nfs-and-poly-u-polymerase-mediated-rna-extension
#15
Haiyan Wang, Libang Zhu, Junling Duan, Minghui Wang, Huanshun Yin, Po Wang, Shiyun Ai
2'-O-methyl group on the 3' terminal nucleotide in plant microRNAs, as one kind of RNA methylations, is caused by HEN1 RNA methyltransferase (HENMT1), which is thought to be crucial for ribosome biogenesis and function. Herein, a simple and label-free PEC biosensing method was proposed for assay of HENMT1 activity and inhibitor screening based on peroxidase mimic PtCu nanoframes (PtCu NFs) catalytic signal amplification. In this work, MoS2@Graphene quantum dots/Phosphorus-doped rodlike carbon nitride (MoS2@GQDs/P-RCN) heterojunction was used as photoactive materials...
December 21, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29276984/genetic-polymorphisms-offer-insight-into-the-causal-role-of-microrna-in-coronary-artery-disease
#16
REVIEW
Andrea Borghini, Maria Grazia Andreassi
There is growing interest in the potential of circulating microRNAs (miRNAs), a class of small and noncoding RNA molecules, as diagnostic and/or prognostic biomarkers in coronary artery disease (CAD). Despite this promising role, there are still widespread inconsistencies among studies, and important obstacles must be overcome before miRNAs can enter clinical practice. The study of single nucleotide polymorphisms (SNPs) in the miRNA regulatory network could help shed light on the causality of associations as well as validate the value of cardiovascular miRNAs...
December 15, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/29274231/structural-insights-into-the-assembly-and-polya-signal-recognition-mechanism-of-the-human-cpsf-complex
#17
Marcello Clerici, Marco Faini, Ruedi Aebersold, Martin Jinek
3' polyadenylation is a key step in eukaryotic mRNA biogenesis. In mammalian cells, this process is dependent on the recognition of the hexanucleotide AAUAAA motif in the pre-mRNA polyadenylation signal by the Cleavage and Polyadenylation Specificity Factor (CPSF) complex. A core CPSF complex comprising CPSF160, WDR33, CPSF30 and Fip1 is sufficient for AAUAAA motif recognition, yet the molecular interactions underpinning its assembly and mechanism of PAS recognition are not understood. Based on cross-linking-coupled mass spectrometry, crystal structure of the CPSF160-WDR33 subcomplex and biochemical assays, we define the molecular architecture of the core human CPSF complex, identifying specific domains involved in inter-subunit interactions...
December 23, 2017: ELife
https://www.readbyqxmd.com/read/29250093/xap5-circadian-timekeeper-positively-regulates-resistance-to-powdery-mildew8-1-mediated-immunity-in-arabidopsis
#18
Yong-Ju Xu, Yang Lei, Ran Li, Ling-Li Zhang, Zhi-Xue Zhao, Jing-Hao Zhao, Jing Fan, Yan Li, Hui Yang, Jing Shang, Shunyuan Xiao, Wen-Ming Wang
Ectopic expression of the Arabidopsis RESISTANCE TO POWDERY MILDEW8.1 (RPW8.1) boosts pattern-triggered immunity leading to enhanced resistance to different pathogens in Arabidopsis and rice. However, the underlying regulatory mechanism remains largely elusive. Here, we report that XAP5 CIRCADIAN TIMEKEEPER (XCT, At2g21150) positively regulates RPW8.1-mediated cell death and disease resistance. Forward genetic screen identified the b3-17 mutant that exhibited less cell death and susceptibility to powdery mildew and bacterial pathogens...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29248374/multi-omics-reveal-specific-targets-of-the-rna-binding-protein-puf3p-and-its-orchestration-of-mitochondrial-biogenesis
#19
Christopher P Lapointe, Jonathan A Stefely, Adam Jochem, Paul D Hutchins, Gary M Wilson, Nicholas W Kwiecien, Joshua J Coon, Marvin Wickens, David J Pagliarini
Coenzyme Q (CoQ) is a redox-active lipid required for mitochondrial oxidative phosphorylation (OxPhos). How CoQ biosynthesis is coordinated with the biogenesis of OxPhos protein complexes is unclear. Here, we show that the Saccharomyces cerevisiae RNA-binding protein (RBP) Puf3p regulates CoQ biosynthesis. To establish the mechanism for this regulation, we employed a multi-omic strategy to identify mRNAs that not only bind Puf3p but also are regulated by Puf3p in vivo. The CoQ biosynthesis enzyme Coq5p is a critical Puf3p target: Puf3p regulates the abundance of Coq5p and prevents its detrimental hyperaccumulation, thereby enabling efficient CoQ production...
December 12, 2017: Cell Systems
https://www.readbyqxmd.com/read/29247647/moesin-and-myosin-iia-modulate-phagolysosomal-biogenesis-in-macrophages
#20
Carolina P Gomez, Albert Descoteaux
Biogenesis of phagolysosomes is central to the elimination of pathogens by macrophages. We previously showed that Src homology region 2 domain-containing phosphatase 1 (SHP-1) participates in the regulation of phagosome maturation. Through proteomics, we identified moesin and the non-muscle myosin-IIA as proteins interacting with SHP-1 during phagocytosis. Silencing of either moesin or myosin IIA with small interfering RNA inhibited phagosomal acidification and recruitment of LAMP-1. Moreover, the intraphagosomal oxidative burst was impaired in the absence of either SHP-1 or myosin IIA but not moesin...
December 13, 2017: Biochemical and Biophysical Research Communications
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