keyword
MENU ▼
Read by QxMD icon Read
search

Posttranscriptional modification

keyword
https://www.readbyqxmd.com/read/29143920/distinguishing-the-disease-associated-snps-based-on-composition-frequency-analysis
#1
Wenling Li, Menglong Li, Xuemei Pu, Yanzhi Guo
Single-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and thus arouse posttranscriptional level abnormality. Therefore, SNP has a strong correlation with diseases. Although enormous SNPs have been experimentally identified, only a tiny proportion of them are truly disease-associated SNPs (dSNPs) that relate to microRNA modification and then are involved in disease causing process...
November 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29130189/identifying-the-m-6-a-methylome-by-affinity-purification-and-sequencing
#2
Phillip J Hsu, Chuan He
N (6)-methyladenosine (m(6)A) is the most abundant internal modification in eukaryotic mRNA, and is newly emerging as a key posttranscriptional mRNA regulator. Recent research has uncovered insight into the location and function of m(6)A sites on a large scale, in part due to the transcriptome-wide identification of m(6)A sites by high-throughput sequencing (m(6)A-seq). Here, we present a protocol for m(6)A-seq, which maps the m(6)A methylome by affinity purification and sequencing.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29111692/fingerprints-of-modified-rna-bases-from-deep-sequencing-profiles
#3
Anna M Kietrys, Willem A Velema, Eric T Kool
Posttranscriptional modifications of RNA bases are not only found in many noncoding RNAs but have also recently been identified in coding (messenger) RNAs as well. They require complex and laborious methods to locate, and many still lack methods for localized detection. Here we test the ability of next-generation sequencing (NGS) to detect and distinguish between ten modified bases in synthetic RNAs. We compare ultradeep sequencing patterns of modified bases, including miscoding, insertions and deletions (indels), and truncations, to unmodified bases in the same contexts...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29073095/broad-role-for-ybx1-in-defining-the-small-noncoding-rna-composition-of-exosomes
#4
Matthew J Shurtleff, Jun Yao, Yidan Qin, Ryan M Nottingham, Morayma M Temoche-Diaz, Randy Schekman, Alan M Lambowitz
RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with contaminants, lack of knowledge of the mechanisms of RNA sorting into EVs, and limitations of conventional RNA-sequencing methods. Here we present our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) to characterize the RNA extracted from HEK293T cell EVs isolated by flotation gradient ultracentrifugation and from exosomes containing the tetraspanin CD63 further purified from the gradient fractions by immunoisolation...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29042505/binding-synergy-as-an-essential-step-for-trna-editing-and-modification-enzyme-co-dependence-in-trypanosoma-brucei
#5
Katherine Mary McKenney, Mary Anne T Rubio, Juan D Alfonzo
Transfer RNAs acquire a variety of naturally occurring chemical modifications during their maturation; these fine-tune their structure and decoding properties in a manner critical for protein synthesis. We recently reported that in the eukaryotic parasite, Trypanosoma brucei, a methylation and deamination event are unexpectedly interconnected, whereby the tRNA adenosine deaminase (TbADAT2/3) and the 3-methylcytosine methyltransferase (TbTrm140) strictly rely on each other for activity, leading to formation of m(3)C and m(3)U at position 32 in several tRNAs...
October 17, 2017: RNA
https://www.readbyqxmd.com/read/29040360/elucidating-the-editome-bioinformatics-approaches-for-rna-editing-detection
#6
Maria Angela Diroma, Loredana Ciaccia, Graziano Pesole, Ernesto Picardi
RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved through the availability of high-throughput RNA sequencing (RNA-Seq) technologies. Accurate bioinformatics pipelines are essential for the analysis of next-generation sequencing (NGS) data to ensure the correct identification of edited sites...
October 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28984054/rna-uridylation-a-key-posttranscriptional-modification-shaping-the-coding-and-noncoding-transcriptome
#7
REVIEW
Caroline De Almeida, Hélène Scheer, Hélène Zuber, Dominique Gagliardi
RNA uridylation is a potent and widespread posttranscriptional regulator of gene expression. RNA uridylation has been detected in a range of eukaryotes including trypanosomes, animals, plants, and fungi, but with the noticeable exception of budding yeast. Virtually all classes of eukaryotic RNAs can be uridylated and uridylation can also tag viral RNAs. The untemplated addition of a few uridines at the 3' end of a transcript can have a decisive impact on RNA's fate. In rare instances, uridylation is an intrinsic step in the maturation of noncoding RNAs like for the U6 spliceosomal RNA or mitochondrial guide RNAs in trypanosomes...
October 5, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28968025/-the-role-of-interactions-of-transposons-with-epigenetic-factors-in-the-aging-process
#8
R N Mustafin, E K Khusnutdinova
The review considers modern theories of aging mechanisms and data on epigenetic regulation of ontogenesis. Transposons may be the material bases of the epigenetic control system, their movements affect the differentiation of cells and can cause genomic instability. Control systems aimed at protecting against foreign DNA (splicing machine, microRNA processing) became the basis of regulatory networks of genomes underlying cell differentiation. Transposon sequences are the basis for non-coding RNAs that suppress the expression of the transposons themselves and protein-coding genes at the posttranscriptional level, as well as by altering the activity of methyltransferases and modifying the histone modification...
2017: Advances in Gerontology, Uspekhi Gerontologii
https://www.readbyqxmd.com/read/28917036/selenocysteine-trna-ser-sec-the-central-component-of-selenoprotein-biosynthesis-isolation-identification-modification-and-sequencing
#9
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
#10
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...
October 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
#11
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
#12
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...
November 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28882223/micrornas-and-epigenetics
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
93507
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"