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RNA Biology

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https://www.readbyqxmd.com/read/28513325/developmental-transitions-in-arabidopsis-are-regulated-by-antisense-rnas-resulting-from-bidirectionally-transcribed-genes
#1
Katarzyna Krzyczmonik, Agata Wroblewska-Swiniarska, Szymon Swiezewski
Transcription terminators are DNA elements located at the 3' end of genes that ensure efficient cleavage of nascent RNA generating the 3' end of mRNA, as well as facilitating disengagement of elongating DNA-dependent RNA polymerase II. Surprisingly, terminators are also a potent source of antisense transcription. We have recently described an Arabidopsis antisense transcript originating from the 3' end of a master regulator of Arabidopsis thaliana seed dormancy DOG1. In this review, we discuss the broader implications of our discovery in light of recent developments in yeast and Arabidopsis...
May 17, 2017: RNA Biology
https://www.readbyqxmd.com/read/28498001/abce1-a-special-factor-that-orchestrates-translation-at-the-crossroad-between-recycling-and-initiation
#2
Eder Mancera-Martínez, Jailson Brito Querido, Leos Shivaya Valasek, Angelita Simonetti, Yaser Hashem
For many years initiation and termination of mRNA translation have been studied separately. However, a direct link between these two isolated stages has been suggested by the fact that some initiation factors also control termination and can even promote ribosome recycling; i.e. the last stage where post-terminating 80 S ribosomes are split to start a new round of initiation. Notably, it is now firmly established that, among other factors, ribosomal recycling critically requires the NTPase ABCE1. However, several earlier reports have proposed that ABCE1 also somehow participates in the initiation complex assembly...
May 12, 2017: RNA Biology
https://www.readbyqxmd.com/read/28497998/transcriptional-reprogramming-in-cellular-quiescence
#3
Benjamin Roche, Benoit Arcangioli, Robert A Martienssen
Most cells in nature are not actively dividing, yet are able to return to the cell cycle given the appropriate environmental signals. There is now ample evidence that quiescent G0 cells are not shut-down but still metabolically and transcriptionally active. Quiescent cells must maintain a basal transcriptional capacity to maintain transcripts and proteins necessary for survival. This implies a tight control over RNA polymerases: RNA pol II for mRNA transcription during G0, but especially RNA pol I and RNA pol III in order to maintain an appropriate level of structural RNAs, raising the possibility that specific transcriptional control mechanisms evolved in quiescent cells...
May 12, 2017: RNA Biology
https://www.readbyqxmd.com/read/28494198/microrna-338-modulates-cortical-neuronal-placement-and-polarity
#4
Aron Kos, Annetrude J de Mooij-Malsen, Hans van Bokhoven, Barry B Kaplan, Gerard J Martens, Sharon M Kolk, Armaz Aschrafi
The precise spatial and temporal regulation of gene expression orchestrates the many intricate processes during brain development. In the present study we examined the role of the brain-enriched microRNA-338 (miR-338) during mouse cortical development. Reduction of miR-338 levels in the developing mouse cortex, using a sequence-specific miR-sponge, resulted in a loss of neuronal polarity in the cortical plate and significantly reduced the number of neurons within this cortical layer. Conversely, miR-338 overexpression in developing mouse cortex increased the number of neurons, which exhibited a multipolar morphology...
May 11, 2017: RNA Biology
https://www.readbyqxmd.com/read/28488947/translation-control-learning-from-viruses-again
#5
Juana Díez, Jennifer Jungfleisch
Viruses are powerful tools to uncover cellular processes. Through viral studies we have recently identified a novel translational control mechanism that involves the DEAD-box helicase Dhh1/DDX6 and RNA folding within coding sequences (CDSs). All Dhh1-dependent mRNAs, viral and cellular ones, (i) contain long and highly structured CDSs, (ii) are directly bound by Dhh1 with a specific pattern, (iii) are activated at the translation initiation step and (iv) express proteins associated with the endoplasmic reticulum...
May 10, 2017: RNA Biology
https://www.readbyqxmd.com/read/28488916/observing-the-fate-of-trna-and-its-modifications-by-nucleic-acid-isotope-labeling-mass-spectrometry-nail-ms
#6
Matthias Heiss, Valentin F Reichle, Stefanie Kellner
RNA in yeast, especially rRNA and tRNA are heavily modified to fulfill their function in protein translation. Using biosynthetic stable isotope labeled internal standards we quantified 12 modified nucleosides in tRNA from S. cerevisiae over 24 hours. We observed different quantities of modified nucleosides in dependence of the growth phase. To elucidate the underlying mechanism of the observed tRNA epitranscriptome adaptation, it is necessary to distinguish the pre-existing tRNA pool and its modifications from newly-synthesized tRNAs...
May 10, 2017: RNA Biology
https://www.readbyqxmd.com/read/28486008/special-focus-on-the-cajal-body
#7
Karla M Neugebauer
No abstract text is available yet for this article.
May 9, 2017: RNA Biology
https://www.readbyqxmd.com/read/28453393/cleavage-and-polyadenylation-ending-the-message-expands-gene-regulation
#8
Jonathan Neve, Radhika Patel, Zhiqiao Wang, Alastair Louey, André Martin Furger
Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3'end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes...
April 28, 2017: RNA Biology
https://www.readbyqxmd.com/read/28448743/circular-rnas-with-hammerhead-ribozymes-encoded-in-eukaryotic-genomes-the-enemy-at-home
#9
Marcos de la Peña, Amelia Cervera
A new family of non-autonomous retrotransposons with self-cleaving hammerhead ribozymes, the so called retrozymes, has recently been found encoded in a number of plant genomes. These retroelements can be actively transcribed, and their RNAs accumulate in the cells as abundant non-coding circular RNAs (circRNAs) of small size (600-1000 nt). Related circRNAs with self-cleaving ribozymes had already been described in plants, and belong to a group of infectious RNA agents with an uncertain origin: the viroids and viroid-like satellites of plant RNA viruses...
April 27, 2017: RNA Biology
https://www.readbyqxmd.com/read/28440695/size-variable-zone-in-v3-region-of-16s-rrna
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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 biologic data sets 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
#16
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
#17
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
#18
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
#19
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
#20
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
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