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RNA Biology

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https://www.readbyqxmd.com/read/28440695/size-variable-zone-in-v3-region-of-16s-rrna
#1
Francisco Vargas-Albores, Luis Enrique Ortiz-Suárez, Enrique Villalpando-Canchola, Marcel Martínez-Porchas
The size distribution of complete 16S-rRNA sequences from the SILVA-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated. Overall, 513,309 sequences recorded in SILVA were used to estimate the size of hypervariable regions of the gene. Redundant sequences were treated as a single sequence to achieve a better representation of the molecular diversity. Nucleotides found in each position in 95% of the sequences were considered the consensus sequences for different size-groups (consensus95)...
April 25, 2017: RNA Biology
https://www.readbyqxmd.com/read/28440690/the-chemistries-and-consequences-of-dna-and-rna-methylation-and-demethylation
#2
Franziska R Traube, Thomas Carell
No abstract text is available yet for this article.
April 25, 2017: RNA Biology
https://www.readbyqxmd.com/read/28430077/host-pathogen-interactions-modulated-by-small-rnas
#3
Waqar Islam, Zujian Wu, Saif Ul Islam
Biological processes such as defense mechanisms and microbial offence strategies are regulated through RNA induced interference in eukaryotes. Genetic mutations are modulated through biogenesis of small RNAs which directly impacts upon host development. Plant defense mechanisms are regulated and supported by a diversified group of small RNAs which are involved in streamlining several RNA interference pathways leading towards the initiation of pathogen gene silencing mechanisms. In the similar context, pathogens also utilize the support of small RNAs to launch their offensive attacks...
April 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28430005/issues-in-current-microrna-target-identification-methods
#4
Hervé Seitz
microRNAs are currently believed to control a large diversity of physiological processes, through the collective repression of thousands of target genes. Both experimental and computational analyses indeed suggest that each microRNA regulates tens or hundreds of genes. But some observations suggest that the phenotypic consequences of many published miRNA/mRNA interactions are dubious. For example, the reported amplitude of miRNA-guided repression is very small, while biological processes tend to be robust to small changes in gene expression...
April 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28421898/targeting-the-nuclear-rna-exosome-poly-a-binding-proteins-enter-the-stage
#5
Nicola Meola, Torben Heick Jensen
Centrally positioned in nuclear RNA metabolism, the exosome deals with virtually all transcript types. This 3'-5' exo- and endo-nucleolytic degradation machine is guided to its RNA targets by adaptor proteins that enable substrate recognition. Recently, the discovery of the 'Poly(A) tail exosome targeting (PAXT)' connection as an exosome adaptor to human nuclear polyadenylated transcripts has relighted the interest of poly(A) binding proteins (PABPs) in both RNA productive and destructive processes.
April 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28421868/rknnmda-ranking-based-knn-for-mirna-disease-association-prediction
#6
Xing Chen, Qiao-Feng Wu, Gui-Ying Yan
Cumulative verified experimental studies have demonstrated that microRNAs (miRNAs) could be closely related with the development and progression of human complex diseases. Based on the assumption that functional similar miRNAs may have a strong correlation with phenotypically similar diseases and vice versa, researchers developed various effective computational models which combine heterogeneous biological datasets including disease similarity network, miRNA similarity network, and known disease-miRNA association network to identify potential relationships between miRNAs and diseases in biomedical research...
April 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28418268/the-folding-competence-of-hiv-1-tat-mediated-by-interaction-with-tar-rna
#7
Jung Min Kim, Hee Sun Choi, Baik Lin Seong
The trans-activator Tat protein of HIV-1 belongs to the large family of intrinsically disordered proteins (IDPs), and is known to recruit various host proteins for the transactivation of viral RNA synthesis. Tat protein interacts with the transactivator response RNA (TAR RNA), exhibiting RNA chaperone activities for structural rearrangement of interacting RNAs. Here, considering that Tat-TAR RNA interaction is mutually cooperative, we examined the potential role of TAR RNA as Chaperna - RNA that provides chaperone function to proteins - for the folding of HIV-1 Tat...
April 18, 2017: RNA Biology
https://www.readbyqxmd.com/read/28402218/rna-and-disease-and-development
#8
Michael F Jantsch, Andrea Barta
No abstract text is available yet for this article.
April 12, 2017: RNA Biology
https://www.readbyqxmd.com/read/28402213/engineering-and-expressing-circular-rnas-via-trna-splicing
#9
John J Noto, Casey A Schmidt, A Gregory Matera
Circular (circ)RNAs have recently become a subject of great biological interest. It is now clear that they represent a diverse and abundant class of RNAs with regulated expression and evolutionarily conserved functions. There are several mechanisms by which RNA circularization can occur in vivo. Here, we focus on the biogenesis of tRNA intronic circular RNAs (tricRNAs) in archaea and animals, and we detail their use as research tools for orthogonal, directed circRNA expression in vivo.
April 12, 2017: RNA Biology
https://www.readbyqxmd.com/read/28387604/des-ncrna-a-knowledgebase-for-exploring-information-about-human-micro-and-long-noncoding-rnas-based-on-literature-mining
#10
Adil Salhi, Magbubah Essack, Tanvir Alam, Vladan P Bajic, Lina Ma, Aleksandar Radovanovic, Benoit Marchand, Sebastian Schmeier, Zhang Zhang, Vladimir B Bajic
Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA ( www...
April 7, 2017: RNA Biology
https://www.readbyqxmd.com/read/28387584/deregulation-of-the-non-coding-genome-in-leukemia
#11
Susanna Teppo, Merja Heinäniemi, Olli Lohi
Methodological advances that allow deeper characterization of non-coding elements in the genome have started to reveal the full spectrum of deregulation in cancer. We generated an inducible cell model to track transcriptional changes after induction of a well-known leukemia-inducing fusion gene, ETV6-RUNX1. Our data revealed widespread transcriptional alterations outside coding elements in the genome. This adds to the growing list of various alterations in the non-coding genome in cancer and pinpoints their role in diseased cellular state...
April 7, 2017: RNA Biology
https://www.readbyqxmd.com/read/28362162/hypoxia-and-hypoglycemia-synergistically-regulate-mrna-stability
#12
Kristen R Carraway, Ellen M Johnson, Travis C Kauffmann, Nate J Fry, Kyle D Mansfield
Ischemic events, common in many diseases, result from decreased blood flow and impaired delivery of oxygen and glucose to tissues of the body. While much is known about the cellular transcriptional response to ischemia, much less is known about the posttranscriptional response to oxygen and glucose deprivation. The goal of this project was to investigate one such posttranscriptional response, the regulation of mRNA stability. To that end, we have identified a number of novel ischemia-related mRNAs that are synergistically stabilized by oxygen and glucose deprivation including VEGF, MYC, MDM2, and CYR61...
March 31, 2017: RNA Biology
https://www.readbyqxmd.com/read/28353398/a-fly-view-on-the-roles-and-mechanisms-of-the-m-6-a-mrna-modification-and-its-players
#13
Tina Lence, Matthias Soller, Jean-Yves Roignant
RNA modifications are an emerging layer of posttranscriptional gene regulation in eukaryotes. N(6)-methyladenosine (m(6)A) is amongst the most abundant modifications in messenger RNAs (mRNAs) that was shown to influence many physiological processes from yeast to mammals. Like DNA methylation, m(6)A in mRNA is dynamically regulated. A conserved methyltransferase complex catalyzes the deposition of the methyl group on adenosine, which can be removed by specific classes of demethylases. Furthermore, YTH-domain containing proteins can recognize this modification to mediate m(6)A-dependent activities...
March 29, 2017: RNA Biology
https://www.readbyqxmd.com/read/28346055/a-to-i-editing-in-disease-is-not-fake-news
#14
Prajakta Bajad, Michael F Jantsch, Liam Keegan, Mary O'Connell
Adenosine deaminases acting on RNA (ADARs) are zinc-containing enzymes that deaminate adenosine bases to inosines within dsRNA regions in transcripts. In short, structured dsRNA hairpins individual adenosine bases may be targeted specifically and edited with up to one hundred percent efficiency, leading to the production of alternative protein variants. However, the majority of editing events occur within longer stretches of dsRNA formed by pairing of repetitive sequences. Here, many different adenosine bases are potential targets but editing efficiency is usually much lower...
March 27, 2017: RNA Biology
https://www.readbyqxmd.com/read/28340329/a-close-up-view-of-codon-selection-in-eukaryotic-initiation
#15
Christoffer Lind, Mauricio Esguerra, Johan Åqvist
When given an option to choose among a set of alternatives and only one selection is right, one might stop and reflect over which one is best. However, the ribosome has no time to stop and make such reflections, proteins need to be produced and very fast. Eukaryotic translation initiation is an example of such a conundrum. Here, scanning for the correct codon match must be fast, efficient and accurate. We highlight our recent computational findings, which show how the initiation machinery manages to recognize one specific codon among many possible challengers, by fine-tuning the energetic landscape of base-pairing with the aid of the initiation factors eIF1 and eIF1A...
March 24, 2017: RNA Biology
https://www.readbyqxmd.com/read/28332918/artificial-and-natural-rna-interactions-between-bacteria-and-c-elegans
#16
Fabian Braukmann, David Jordan, Eric Miska
Nineteen years after Lisa Timmons and Andy Fire first described RNA transfer from bacteria to C. elegans in an experimental setting (48) the biologic role of this trans-kingdom RNA-based communication remains unknown. Here we summarize our current understanding on the mechanism and potential role of such social RNA.
March 23, 2017: RNA Biology
https://www.readbyqxmd.com/read/28318367/combinatorial-control-of-messenger-rnas-by-pumilio-nanos-and-brain-tumor-proteins
#17
René M Arvola, Chase A Weidmann, Traci M Tanaka Hall, Aaron C Goldstrohm
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of three Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurological processes. Here we synthesize thirty years of research with new insights into their molecular functions and mechanisms of action...
March 20, 2017: RNA Biology
https://www.readbyqxmd.com/read/28296624/dusp11-an-rna-phosphatase-that-regulates-host-and-viral-non-coding-rnas-in-mammalian-cells
#18
James M Burke, Christopher S Sullivan
Dual-specificity phosphatase 11 (DUSP11) is a conserved protein tyrosine phosphatase (PTP) in metazoans. The cellular substrates and physiological activities of DUSP11 remain largely unknown. In nematodes, DUSP11 is required for normal development and RNA interference against endogenous RNAs (endo-RNAi) via molecular mechanisms that are not well understood. However, mammals lack analogous endo-RNAi pathways and consequently, a role for DUSP11 in mammalian RNA silencing was unanticipated. Recent work from our lab demonstrated that DUSP11 activity alters the silencing potential of noncanonical viral miRNAs in mammalian cells...
March 15, 2017: RNA Biology
https://www.readbyqxmd.com/read/28296620/rna-as-a-means-of-inter-species-communication-and-manipulation-progresses-and-shortfalls
#19
Sassan Asgari
No abstract text is available yet for this article.
March 15, 2017: RNA Biology
https://www.readbyqxmd.com/read/28296577/genome-wide-identification-and-characterization-of-small-rnas-in-rhodobacter-capsulatus-and-identification-of-small-rnas-affected-by-loss-of-the-response-regulator-ctra
#20
Marc P Grüll, Lourdes Peña-Castillo, Martin E Mulligan, Andrew S Lang
Small non-coding RNAs (sRNAs) are involved in the control of numerous cellular processes through various regulatory mechanisms, and in the past decade many studies have identified sRNAs in a multitude of bacterial species using RNA sequencing (RNA-seq). Here, we present the first genome-wide analysis of sRNA sequencing data in Rhodobacter capsulatus, a purple nonsulfur photosynthetic alphaproteobacterium. Using a recently developed bioinformatics approach, sRNA-Detect, we detected 422 putative sRNAs from R...
March 15, 2017: RNA Biology
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