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Posttranscriptional modification

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https://www.readbyqxmd.com/read/28917036/selenocysteine-trna-ser-sec-the-central-component-of-selenoprotein-biosynthesis-isolation-identification-modification-and-sequencing
#1
Bradley A Carlson, Byeong Jae Lee, Petra A Tsuji, Paul R Copeland, Ulrich Schweizer, Vadim N Gladyshev, Dolph L Hatfield
The selenocysteine (Sec) tRNA([Ser]Sec) population consists of two isoforms that differ from each other by a single 2'-O-methylribosyl moiety at position 34 (Um34). These two isoforms, which are encoded in a single gene, Trsp, and modified posttranscriptionally, are involved individually in the synthesis of two subclasses of selenoproteins, designated housekeeping and stress-related selenoproteins. Techniques used in obtaining these isoforms for their characterization include extraction of RNA from mammalian cells and tissues, purifying the tRNA([Ser]Sec) population by one or more procedures, and finally resolving the two isoforms from each other...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28914256/mettl3-mettl14-mediated-mrna-n-6-methyladenosine-modulates-murine-spermatogenesis
#2
Zhen Lin, Phillip J Hsu, Xudong Xing, Jianhuo Fang, Zhike Lu, Qin Zou, Ke-Jia Zhang, Xiao Zhang, Yuchuan Zhou, Teng Zhang, Youcheng Zhang, Wanlu Song, Guifang Jia, Xuerui Yang, Chuan He, Ming-Han Tong
Spermatogenesis is a differentiation process during which diploid spermatogonial stem cells (SSCs) produce haploid spermatozoa. This highly specialized process is precisely controlled at the transcriptional, posttranscriptional, and translational levels. Here we report that N(6)-methyladenosine (m(6)A), an epitranscriptomic mark regulating gene expression, plays essential roles during spermatogenesis. We present comprehensive m(6)A mRNA methylomes of mouse spermatogenic cells from five developmental stages: undifferentiated spermatogonia, type A1 spermatogonia, preleptotene spermatocytes, pachytene/diplotene spermatocytes, and round spermatids...
September 15, 2017: Cell Research
https://www.readbyqxmd.com/read/28889729/role-of-post-transcriptional-regulation-of-mrna-stability-on-the-expression-of-cytokine-coding-genes-in-renal-inflammation
#3
Eva Feigerlová, Shyue-Fang Battaglia-Hsu
Mechanisms that control mammalian gene expression, notably mRNA stability and translation, have major functions in the modulation of the cellular response to internal and external stimuli. Altered posttranscriptional regulation of gene expression has been associated with many diseases. Such types of deregulation have also recently been noted on the inflammatory cytokines pertinent to kidney inflammation. In this article, we summarize briefly the recent knowledge obtained from both human and experimental systems on the details of posttranscriptional regulation of gene expression related to the control of mRNA stability and discuss their relevance in regulating cytokine expression linked to the inflammatory processes in kidney...
September 8, 2017: Minerva Medica
https://www.readbyqxmd.com/read/28888611/comparison-of-mammary-lipid-metabolism-in-dairy-cows-and-goats-fed-diets-supplemented-with-starch-plant-oil-or-fish-oil
#4
L Bernard, P G Toral, Y Chilliard
A direct comparison of cow and goat performance and milk fatty acid (FA) responses to diets known to induce milk fat depression in the bovine has suggested interspecies differences in rumen and mammary lipid metabolism. Thus, this study was conducted to infer some potential mechanisms responsible for the differences in mammary lipogenesis due to diet and ruminant species. To meet this objective, 12 cows and 15 goats were fed a basal diet (control), a similar diet supplemented with 2.2% fish oil (FO), or a diet containing 5...
September 6, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28882223/micrornas-and-epigenetics
#5
Catia Moutinho, Manel Esteller
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression mainly at the posttranscriptional level. Similar to protein-coding genes, their expression is also controlled by genetic and epigenetic mechanisms. Disruption of these control processes leads to abnormal expression of miRNAs in cancer. In this chapter, we discuss the supportive links between miRNAs and epigenetics in the context of carcinogenesis. miRNAs can be epigenetically regulated by DNA methylation and/or specific histone modifications...
2017: Advances in Cancer Research
https://www.readbyqxmd.com/read/28856171/genetic-factors-in-tendon-injury-a-systematic-review-of-the-literature
#6
REVIEW
Natalie H Vaughn, Hayk Stepanyan, Robert A Gallo, Aman Dhawan
BACKGROUND: Tendon injury such as tendinopathy or rupture is common and has multiple etiologies, including both intrinsic and extrinsic factors. The genetic influence on susceptibility to tendon injury is not well understood. PURPOSE: To analyze the published literature regarding genetic factors associated with tendon injury. STUDY DESIGN: Systematic review; Level of evidence, 3. METHODS: A systematic review of published literature was performed in concordance with the Preferred Reporting Items of Systematic Reviews and Meta-analysis (PRISMA) guidelines to identify current evidence for genetic predisposition to tendon injury...
August 2017: Orthopaedic Journal of Sports Medicine
https://www.readbyqxmd.com/read/28835691/proteomic-analysis-of-phytase-transgenic-and-non-transgenic-maize-seeds
#7
Yanhua Tan, Zheng Tong, Qian Yang, Yong Sun, Xiang Jin, Cunzhi Peng, Anping Guo, Xuchu Wang
Proteomics has become a powerful technique for investigating unintended effects in genetically modified crops. In this study, we performed a comparative proteomics of the seeds of phytase-transgenic (PT) and non-transgenic (NT) maize using 2-DE and iTRAQ techniques. A total of 148 differentially expressed proteins (DEPs), including 106 down-regulated and 42 up-regulated proteins in PT, were identified. Of these proteins, 32 were identified through 2-DE and 116 were generated by iTRAQ. It is noteworthy that only three proteins could be detected via both iTRAQ and 2-DE, and most of the identified DEPs were not newly produced proteins but proteins with altered abundance...
August 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798901/translational-dysregulation-in-cancer-molecular-insights-and-potential-clinical-applications-in-biomarker-development
#8
REVIEW
Christos Vaklavas, Scott W Blume, William E Grizzle
Although transcript levels have been traditionally used as a surrogate measure of gene expression, it is increasingly recognized that the latter is extensively and dynamically modulated at the level of translation (messenger RNA to protein). Over the recent years, significant progress has been made in dissecting the complex posttranscriptional mechanisms that regulate gene expression. This advancement in knowledge came hand in hand with the progress made in the methodologies to study translation both at gene-specific as well as global genomic level...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28794999/modulation-of-the-p53-family-network-by-rna-binding-proteins
#9
Chris Lucchesi, Jin Zhang, Xinbin Chen
Since its discovery more than three decades ago, tumor suppressor p53 has been shown to play pivotal roles in both maintaining genomic integrity and tumor suppression. p53 functions as a transcription factor responding to a multitude of cellular stressors, regulating the transcription of many genes involved in cell-cycle arrest, senescence, autophagy, and apoptosis. Extensive work has revealed that p53 is one of the most commonly mutated tumor suppressor genes. The last three decades have demonstrated that p53 activity is controlled through transcriptional regulation and posttranslational modifications...
December 2016: Translational Cancer Research
https://www.readbyqxmd.com/read/28760958/two-interacting-ppr-proteins-are-major-arabidopsis-editing-factors-in-plastid-and-mitochondria
#10
Damien Guillaumot, Mauricio Lopez-Obando, Kevin Baudry, Alexandra Avon, Guillem Rigaill, Andéol Falcon de Longevialle, Benjamin Broche, Mizuki Takenaka, Richard Berthomé, Geert De Jaeger, Etienne Delannoy, Claire Lurin
RNA editing is converting hundreds of cytosines into uridines during organelle gene expression of land plants. The pentatricopeptide repeat (PPR) proteins are at the core of this posttranscriptional RNA modification. Even if a PPR protein defines the editing site, a DYW domain of the same or another PPR protein is believed to catalyze the deamination. To give insight into the organelle RNA editosome, we performed tandem affinity purification of the plastidial CHLOROPLAST BIOGENESIS 19 (CLB19) PPR editing factor...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28754764/plastome-sequences-of-an-ancient-fern-lineage-reveal-remarkable-changes-in-gene-content-and-architecture
#11
Paulo H Labiak, Kenneth G Karol
PREMISE OF THE STUDY: Comparative analyses of plastid genomes have suggested that gene order and content are relatively stable across the main groups of land plants, with significant changes rarely reported. We examine plastome organization and RNA editing in ferns and report changes that add valuable information on plastome evolution in land plants. METHODS: Using next-generation sequencing methods, we fully sequenced plastomes from three species of Schizaeaceae, and compared their plastomes with other groups of land plants to study changes in gene composition, plastome architecture, and putative RNA editing sites...
July 28, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28703578/detection-of-a-subset-of-posttranscriptional-transfer-rna-modifications-in-vivo-with-a-restriction-fragment-length-polymorphism-based-method
#12
Thomas F Wulff, Rafael J Argüello, Marc Molina Jordàn, Helena Roura Frigolé, Glenn Hauquier, Liudmila Filonava, Noelia Camacho, Evelina Gatti, Philippe Pierre, Lluís Ribas de Pouplana, Adrian G Torres
Transfer RNAs (tRNAs) are among the most heavily modified RNA species. Posttranscriptional tRNA modifications (ptRMs) play fundamental roles in modulating tRNA structure and function and are being increasingly linked to human physiology and disease. Detection of ptRMs is often challenging, expensive, and laborious. Restriction fragment length polymorphism (RFLP) analyses study the patterns of DNA cleavage after restriction enzyme treatment and have been used for the qualitative detection of modified bases on mRNAs...
August 8, 2017: Biochemistry
https://www.readbyqxmd.com/read/28695513/methodology-to-identify-poly-adp-ribose-polymerase-1-parp1-mrna-targets-by-par-clip
#13
Manana Mekishvili, Elena Matveeva, Yvonne Fondufe-Mittendorf
There is a long list of important RNA-binding proteins (RBP) involved in different steps of gene expression through posttranscriptional modifications: pre-mRNA splicing, mRNA stabilization, polyadenylation, mRNA export from nucleus to the cytoplasm, and translation. The critical role of RNA-protein interaction necessitates a continuous identification of proteins involved in this process. Here we describe the identification of Poly-ADP-Ribose Polymerase 1 (PARP1) as an RNA binding protein involved in RNA splicing...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623126/crystal-structure-of-trna-his-guanylyltransferase-from-saccharomyces-cerevisiae
#14
Kitaik Lee, Eun Hye Lee, Jonghyeon Son, Kwang Yeon Hwang
tRNA maturation involves several steps, including processing, splicing, CCA addition, and posttranscriptional modifications. tRNA(His) guanylyltransferase (Thg1) is the only enzyme known to catalyze templated nucleotide addition in the 3'-5' direction, unlike other DNA and RNA polymerases. For a better understanding of its unique catalytic mechanism at the molecular level, we determined the crystal structure of GTP-bound Thg1 from Saccharomyces cerevisiae at the maximum resolution of 3.0 Å. The structure revealed the enzyme to have a tetrameric conformation that is well conserved among different species, and the GTP molecule was clearly bound at the active site, coordinating with two magnesium ions...
August 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28601222/synthesis-function-and-heterogeneity-of-snorna-guided-posttranscriptional-nucleoside-modifications-in-eukaryotic-ribosomal-rnas
#15
Anthony K Henras, Célia Plisson-Chastang, Odile Humbert, Yves Romeo, Yves Henry
Ribosomal RNAs contain numerous 2'-O-methylated nucleosides and pseudouridines. Methylation of the 2' oxygen of ribose moieties and isomerization of uridines into pseudouridines are catalyzed by C/D and H/ACA small nucleolar ribonucleoprotein particles, respectively. We review the composition, structure, and mode of action of archaeal and eukaryotic C/D and H/ACA particles. Most rRNA modifications cluster in functionally crucial regions of the rRNAs, suggesting they play important roles in translation. Some of these modifications promote global translation efficiency or modulate translation fidelity...
2017: Enzymes
https://www.readbyqxmd.com/read/28601221/posttranscriptional-rna-pseudouridylation
#16
Meemanage D De Zoysa, Yi-Tao Yu
Pseudouridine (Ψ) is the most abundant posttranscriptional modification in noncoding RNAs. Pseudouridines are often clustered in important regions of rRNAs (ribosomal RNAs), snRNAs (small nuclear RNAs), and tRNAs (transfer RNAs), contributing to RNA function. Pseudouridylation is governed by two independent mechanisms. The first involves single protein enzymes called pseudouridine synthases (PUSs) that alone recognize the substrate and catalyze the isomerization of uridine to pseudouridine (RNA-independent pseudouridylation)...
2017: Enzymes
https://www.readbyqxmd.com/read/28601219/the-importance-of-being-modified-the-role-of-rna-modifications-in-translational-fidelity
#17
Paul F Agris, Amithi Narendran, Kathryn Sarachan, Ville Y P Väre, Emily Eruysal
The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon...
2017: Enzymes
https://www.readbyqxmd.com/read/28576825/identification-of-an-optimized-2-o-methylated-trinucleotide-rna-motif-inhibiting-toll-like-receptors-7-and-8
#18
Felix C F Schmitt, Isabel Freund, Markus A Weigand, Mark Helm, Alexander H Dalpke, Tatjana Eigenbrod
Bacterial RNA serves an important function as activator of the innate immune system. In humans bacterial RNA is sensed by the endosomal receptors TLR7 and TLR8. Differences in the posttranscriptional modification profile of prokaryotic when compared with eukaryotic RNA allow innate immune cells to discriminate between "host" and "foreign" RNA. Ribose 2'-O-methylation is of particular importance and has been reported to antagonize TLR7/8 activation. Yet, the exact sequence context in which 2'-O-methylation has to occur to mediate its inhibitory activity remains largely undefined...
September 2017: RNA
https://www.readbyqxmd.com/read/28567652/pull-down-assay-to-characterize-ca-2-calmodulin-binding-to-plant-receptor-kinases
#19
Christine Kaufmann, Margret Sauter
Plant receptor-like kinases (RLKs) are regulated by posttranscriptional modification and by interaction with regulatory proteins. A common modification of RLKs is (auto)phosphorylation, and a common regulatory protein is the calcium sensor calmodulin (CaM). We have developed protocols to detect the interaction of an RLK with CaM. The interaction with CaM was shown by bimolecular fluorescence complementation (BiFC) (see Chapter 14) and pull-down assay (this chapter). Both methods offer unique advantages. BiFC is useful in showing interaction of soluble as well as of membrane-bound proteins in planta...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28567651/bifc-assay-to-detect-calmodulin-binding-to-plant-receptor-kinases
#20
Cornelia Fischer, Margret Sauter, Petra Dietrich
Plant receptor-like kinases (RLKs) are regulated at various levels including posttranscriptional modification and interaction with regulatory proteins. Calmodulin (CaM) is a calcium-sensing protein that was shown to bind to some RLKs such as the PHYTOSULFOKINE RECEPTOR1 (PSKR1). The CaM-binding site is embedded in subdomain VIa of the kinase domain. It is possible that many more of RLKs interact with CaM than previously described. To unequivocally confirm CaM binding, several methods exist. Bimolecular fluorescence complementation (BiFC) and pull-down assays have been successfully used to study CaM binding to PSKR1 and are described in this chapter (BiFC) and in Chapter 15 (pull down)...
2017: Methods in Molecular Biology
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