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Posttranscriptional modification

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https://www.readbyqxmd.com/read/27903241/abundant-rna-editing-sites-of-chloroplast-protein-coding-genes-in-ginkgo-biloba-and-an-evolutionary-pattern-analysis
#1
Peng He, Sheng Huang, Guanghui Xiao, Yuzhou Zhang, Jianing Yu
BACKGROUND: RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27878160/chemo-enzymatic-modification-of-eukaryotic-mrna
#2
Fabian Muttach, Nils Muthmann, Andrea Rentmeister
Messenger RNA may not be very abundant in the cell but its central role in gene expression is indisputable. In addition to being the template for translation it can be subject for a variety of regulatory mechanisms affecting gene expression, ranging from simple structural changes to modifications and active transport. To elucidate and potentially control the underlying changes in vitro and in cells, site-specific modification and labeling strategies are required. In this perspective, we introduce chemo-enzymatic concepts for posttranscriptional modification focusing on eukaryotic mRNAs...
November 23, 2016: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/27834201/identification-of-ybey-protein-interactions-involved-in-16s-rrna-maturation-and-stress-regulation-in-escherichia-coli
#3
Maarten Vercruysse, Caroline Köhrer, Yang Shen, Sandra Proulx, Anubrata Ghosal, Bryan W Davies, Uttam L RajBhandary, Graham C Walker
: YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3' end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology...
November 8, 2016: MBio
https://www.readbyqxmd.com/read/27826833/dna-and-rna-pyrimidine-nucleobase-alkylation-at-the-carbon-5-position
#4
Yuri Motorin, Salifu Seidu-Larry, Mark Helm
The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modification in both DNA and RNA. The simplest modification of uridine at this position is methylation leading to thymine. Thymine is an integral part of the standard nucleobase repertoire of DNA that is synthesized at the nucleotide level. However, it also occurs in RNA, where it is synthesized posttranscriptionally at the polynucleotide level. The cytidine analogue 5-methylcytidine also occurs in both DNA and RNA, but is introduced at the polynucleotide level in both cases...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27811057/elp3-links-trna-modification-to-ires-dependent-translation-of-lef1-to-sustain-metastasis-in-breast-cancer
#5
Sylvain Delaunay, Francesca Rapino, Lars Tharun, Zhaoli Zhou, Lukas Heukamp, Martin Termathe, Kateryna Shostak, Iva Klevernic, Alexandra Florin, Hadrien Desmecht, Christophe J Desmet, Laurent Nguyen, Sebastian A Leidel, Anne E Willis, Reinhard Büttner, Alain Chariot, Pierre Close
Quantitative and qualitative changes in mRNA translation occur in tumor cells and support cancer progression and metastasis. Posttranscriptional modifications of transfer RNAs (tRNAs) at the wobble uridine 34 (U34) base are highly conserved and contribute to translation fidelity. Here, we show that ELP3 and CTU1/2, partner enzymes in U34 mcm(5)s(2)-tRNA modification, are up-regulated in human breast cancers and sustain metastasis. Elp3 genetic ablation strongly impaired invasion and metastasis formation in the PyMT model of invasive breast cancer...
October 17, 2016: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27800139/the-effect-of-microrna-375-overexpression-an-inhibitor-of-helicobacter-pylori-induced-carcinogenesis-on-lncrna-sox2ot
#6
Mohammad Shafiee, Seyed Ahmad Aleyasin, Seyed Javad Mowla, Mohammad Vasei, Seyed Amir Yazdanparast
BACKGROUND: Helicobacter pylori is a major human pathogenic bacterium in gastric mucosa. Although the association between gastric cancer and H. pylori has been well-established, the molecular mechanisms underlying H. pylori-induced carcinogenesis are still under investigation. MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression at the posttranscriptional level. Recently, studies have revealed that miRNAs are involved in immune response and host cell response to bacteria...
September 2016: Jundishapur Journal of Microbiology
https://www.readbyqxmd.com/read/27777593/genetic-and-epigenetic-studies-of-atopic-dermatitis
#7
REVIEW
Lianghua Bin, Donald Y M Leung
BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory disease caused by the complex interaction of genetic, immune and environmental factors. There have many recent discoveries involving the genetic and epigenetic studies of AD. METHODS: A retrospective PubMed search was carried out from June 2009 to June 2016 using the terms "atopic dermatitis", "association", "eczema", "gene", "polymorphism", "mutation", "variant", "genome wide association study", "microarray" "gene profiling", "RNA sequencing", "epigenetics" and "microRNA"...
2016: Allergy, Asthma, and Clinical Immunology
https://www.readbyqxmd.com/read/27770365/stem-loop-qrt-pcr-for-the-detection-of-plant-micrornas
#8
Erika Varkonyi-Gasic
Plant microRNAs (miRNAs) play important roles in the posttranscriptional regulation of protein-coding genes, and they are essential for a normal development and survival. Mature miRNAs are cleaved from larger precursor RNAs and are typically 21-22 nt long.The small size, the lack of a common feature like a poly(A) tail, 3' end-modifications, and presence of a precursor-all these factors affect the detection and hinder the quantification of miRNAs. The stem-loop qRT-PCR method described here is designed to detect and quantify mature miRNAs in a fast, specific, accurate, and reliable manner...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27734409/regulation-of-il-6-in-immunity-and-diseases
#9
Toshio Tanaka, Masashi Narazaki, Kazuya Masuda, Tadamitsu Kishimoto
Interleukin-6 (IL-6) is a prototypical cytokine with functional pleiotropy and plays an important role in host defense. When infections or tissue injuries occur, IL-6 is promptly produced by monocytes and macrophages and contributes to removal of infectious agents and restoration of damaged tissues through activation of immune, hematological, and acute-phase responses. Once stress is removed from the host, IL-6 synthesis ends, but uncontrolled excessive or persistent IL-6 production plays a pathological role in the development of various inflammatory diseases and cancers, indicating that IL-6 is a double-edged sword for the host...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27727240/social-stress-in-adolescents-induces-depression-and-brain-region-specific-modulation-of-the-transcription-factor-max
#10
L S Resende, C E Amaral, R B S Soares, A S Alves, L Alves-Dos-Santos, L R G Britto, S Chiavegatto
MAX is a conserved constitutive small phosphoprotein from a network of transcription factors that are extensively studied in tumorigenesis and whose functions affect cell proliferation, differentiation and death. Inspired by its higher expression during development and in regions involved in emotional behaviors, we hypothesized its involvement in cerebral changes caused by early-life stress. We studied the effects of repeated social stress during adolescence on behaviors and on MAX and its putative partner MYC...
October 11, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27717445/mirna-alterations-are-important-mechanism-in-maize-adaptations-to-low-phosphate-environments
#11
Zhaoxia Li, Xinrui Zhang, Xiuxia Liu, Yajie Zhao, Baomei Wang, Juren Zhang
Maize is a globally important crop, and a low phosphate (LP) supply frequently limits maize yields in many areas. microRNAs (miRNAs) play important roles in plant development and environmental adaptation. In this study, spatio-temporal miRNA transcript profiling and some of the target genes in the roots and leaves of the maize inbred line Q319 were analyzed in response to LP. Complex small RNA populations were detected after LP culture, and they displayed different patterns in the roots and leaves. Differentially expressed miRNAs can be grouped into 'early' miRNAs, which respond rapidly and are often non-specific to phosphate deficiency, and 'late' miRNAs, which alter the morphology, physiology or metabolism of plants upon prolonged phosphate deficiency...
November 2016: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/27668649/expression-and-activity-of-snail-transcription-factor-during-epithelial-to-mesenchymal-transition-emt-in-cancer-progression
#12
Izabela Papiewska-Pająk, Maria A Kowalska, Joanna Boncela
Inhibition of E-cadherin gene expression by transcription factor SNAIL is known to be a crucial element of Epithelial to Mesenchymal Transition; EMT. Epigenetic regulation of E-cadherin expression is regulated by SNAIL binding to E-box sequences in the CDH1 gene promoter and recruiting enzymes belonging to repressor complexes that are directly engaged in histone modifications and DNA methylation leading to the modification of chromatin structure. SNAIL involvement in cell acquisition of invasive phenotype is based on direct suppression of tight-junction and gap junction proteins...
2016: Postȩpy Higieny i Medycyny Doświadczalnej
https://www.readbyqxmd.com/read/27652271/involvement-of-histone-lysine-methylation-in-p21-gene-expression-in-rat-kidney-in-vivo-and-rat-mesangial-cells-in-vitro-under-diabetic-conditions
#13
Xiangjun Li, Chaoyuan Li, Xiaoxia Li, Peihe Cui, Qifeng Li, Qiaoyan Guo, Hongbo Han, Shujun Liu, Guangdong Sun
Diabetic nephropathy (DN), a common complication associated with type 1 and type 2 diabetes mellitus (DM), characterized by glomerular mesangial expansion, inflammation, accumulation of extracellular matrix (ECM) protein, and hypertrophy, is the major cause of end-stage renal disease (ESRD). Increasing evidence suggested that p21-dependent glomerular and mesangial cell (MC) hypertrophy play key roles in the pathogenesis of DN. Recently, posttranscriptional modifications (PTMs) have uncovered novel molecular mechanisms involved in DN...
2016: Journal of Diabetes Research
https://www.readbyqxmd.com/read/27622773/evolutionary-gain-of-alanine-mischarging-to-noncognate-trnas-with-a-g4-u69-base-pair
#14
Litao Sun, Ana Cristina Gomes, Weiwei He, Huihao Zhou, Xiaoyun Wang, David W Pan, Paul Schimmel, Tao Pan, Xiang-Lei Yang
Fidelity of translation, which is predominately dictated by the accuracy of aminoacyl-tRNA synthetases in pairing amino acids with correct tRNAs, is of central importance in biology. Yet, deliberate modifications of translational fidelity can be beneficial. Here we found human and not E. coli AlaRS has an intrinsic capacity for mispairing alanine onto nonalanyl-tRNAs including tRNA(Cys). Consistently, a cysteine-to-alanine substitution was found in a reporter protein expressed in human cells. All human AlaRS-mischarged tRNAs have a G4:U69 base pair in the acceptor stem...
October 5, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27573897/microrna-methylation-in-colorectal-cancer
#15
Sippy Kaur, Johanna E Lotsari-Salomaa, Riitta Seppänen-Kaijansinkko, Päivi Peltomäki
Epigenetic alterations such as DNA methylation, histone modifications and non-coding RNA (including microRNA) associated gene silencing have been identified as a major characteristic in human cancers. These alterations may occur more frequently than genetic mutations and play a key role in silencing tumor suppressor genes or activating oncogenes, thereby affecting multiple cellular processes. In recent years, studies have shown that microRNAs, that act as posttranscriptional regulators of gene expression are frequently deregulated in colorectal cancer (CRC), via aberrant DNA methylation...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27557899/microrna-epigenetic-signatures-in-human-disease
#16
REVIEW
Klara Piletič, Tanja Kunej
MicroRNAs (miRNAs) are short non-coding RNAs that act as important regulators of gene expression as part of the epigenetic machinery. In addition to posttranscriptional gene silencing by miRNAs, the epigenetic mechanisms also include DNA methylation, histone modifications and their crosstalk. Epigenetic modifications were reported to play an important role in many disease onsets and progressions and can be used to explain several features of complex diseases, such as late onset and fluctuation of symptoms. However, miRNAs not only function as a part of epigenetic machinery, but are also epigenetically modified by DNA methylation and histone modification like any other protein-coding gene...
October 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27540864/diastereoselectivity-of-5-methyluridine-osmylation-is-inverted-inside-an-rna-chain
#17
Lyudmil Tserovski, Mark Helm
In this study, we investigated the reaction of the osmium tetroxide-bipyridine complex with pyrimidines in RNA. This reagent, which reacts with the diastereotopic 5-6 double bond, thus leading to the formation of two diastereomers, was used in the past to label thymidine and 5-methylcytosine in DNA. In light of the growing interest in post-transcriptional RNA modifications, we addressed the question of whether this reagent could be used for labeling of the naturally occurring RNA modifications 5-methylcytosine and 5-methyluridine...
September 21, 2016: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/27509989/roles-of-microrna21-and-microrna29a-in-regulating-cell-adhesion-related-genes-in-bone-metastasis-secondary-to-prostate-cancer
#18
Maisarah Mohamad, Norhazlina Abdul Wahab, Rosna Yunus, Nor Azian Abdul Murad, Zulkifli Md Zainuddin, Murali Sundaram, Norfilza Mohd Mokhtar
BACKGROUND: There is an increasing concern in the role of microRNA (miRNA) in the pathogenesis of bone metastasis (BM) secondary to prostate cancer (CaP). In this exploratory study, we hypothesized that the expression of vinculin (VCL) and chemokine X3C ligand 1 (CX3CL1) might be downregulated in clinical samples, most likely due to the posttranscriptional modification by microRNAs. Targeted genes would be upregulated upon transfection of the bone metastatic prostate cancer cell line, PC3, with specific microRNA inhibitors...
2016: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/27450422/repression-of-mybl2-by-both-microrna858a-and-hy5-leads-to-the-activation-of-anthocyanin-biosynthetic-pathway-in-arabidopsis
#19
Yulong Wang, Yiqing Wang, Zhaoqing Song, Huiyong Zhang
Extensive studies in various plants show that the anthocyanin biosynthetic process is affected by environmental factors and regulated by many transcription factors through sophisticated regulatory networks. However, it remains largely unclear about the roles of microRNA in this process. Here, we demonstrate that miR858a is a positive regulator of anthocyanin biosynthesis in Arabidopsis seedlings. Overexpression of miR858a enhances the accumulation of anthocyanins, whereas the reduced miR858a activity results in low levels of anthocyanins in STTM858 transgenic plants...
October 10, 2016: Molecular Plant
https://www.readbyqxmd.com/read/27441695/who-watches-the-watchmen-roles-of-rna-modifications-in-the-rna-interference-pathway
#20
REVIEW
Samantha B Shelton, Calder Reinsborough, Blerta Xhemalce
RNA levels are widely thought to be predictive of RNA function. However, the existence of more than a hundred chemically distinct modifications of RNA alone is a major indication that these moieties may impart distinct functions to subgroups of RNA molecules that share a primary sequence but display distinct RNA "epigenetic" marks. RNAs can be modified on many sites, including 5' and 3' ends, the sugar phosphate backbone, or internal bases, which collectively provide many opportunities for posttranscriptional regulation through a variety of mechanisms...
July 2016: PLoS Genetics
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