journal
MENU ▼
Read by QxMD icon Read
search

RNA

journal
https://www.readbyqxmd.com/read/28630141/temperature-responsive-mirnas-in-drosophila-orchestrate-adaptation-to-different-ambient-temperatures
#1
Isabel Fast, Charlotte Hewel, Laura Wester, Julia Schumacher, Daniel Gebert, Hans Zischler, Christian Berger, David Rosenkranz
The majority of Drosophila genes are expressed in a temperature-dependent manner, but the way in which small RNAs may contribute to this effect is completely unknown as we currently lack an idea of how small RNA transcriptomes change as a function of temperature. Applying high throughput sequencing techniques complemented by quantitative real-time PCR experiments, we demonstrate that altered ambient temperature induces drastic, but reversible changes in sequence composition and total abundance of both, miRNA- and piRNA populations...
June 19, 2017: RNA
https://www.readbyqxmd.com/read/28630140/three-dimensional-structure-of-the-3-x-tail-of-hepatitis-c-virus-rna-in-monomeric-and-dimeric-states
#2
Angel Cantero-Camacho, Lixin Fan, Yun-Xing Wang, José Gallego
The 3'X domain is a 98-nucleotide region located at the 3' end of hepatitis C virus genomic RNA that plays essential functions in the viral life cycle. It contains an absolutely conserved, 16-base palindromic sequence that promotes viral RNA dimerization, overlapped with a 7-nucleotide tract implicated in a distal contact with a nearby functional sequence. Using small angle X-ray scattering measurements combined with model building guided by NMR spectroscopy, we have studied the stoichiometry, structure and flexibility of domain 3'X and two smaller subdomain sequences as a function of ionic strength, and obtained a three-dimensional view of the full-length domain in its monomeric and dimeric states...
June 19, 2017: RNA
https://www.readbyqxmd.com/read/28625967/rnase-ii-regulates-rnase-ph-and-is-essential-for-cell-survival-during-starvation-and-stationary-phase
#3
Shaheen Sulthana, Ernesto Quesada, Murray P Deutscher
RNase II is the most active exoribonuclease in Escherichia coli cell extracts. Yet, its removal appears to have no deleterious effect on growing cells. Here, we show that RNase II is required for cell survival during prolonged stationary phase and upon starvation. The absence of RNase II leads to greatly increased rRNA degradation and to the accumulation of rRNA fragments, both of which lead to a decline in cell survival. The deleterious effects of RNase II removal can be completely reversed by the simultaneous absence of a second exoribonuclease, RNase PH, an enzyme known to be required to initiate ribosome degradation in starving cells...
June 16, 2017: RNA
https://www.readbyqxmd.com/read/28611253/n6-methyladenosine-is-required-for-the-hypoxic-stabilization-of-specific-mrnas
#4
Nate J Fry, Brittany A Law, Olga R Ilkayeva, Christopher L Holley, Kyle D Mansfield
Post-transcriptional regulation of mRNA during oxygen deprivation, or hypoxia, can affect the survivability of cells. Hypoxia has been shown to increase stability of a subset of ischemia-related mRNAs, including VEGF. RNA binding proteins and miRNAs have been identified as important for post-transcriptional regulation of individual mRNAs, but corresponding mechanisms that regulate global stability are not well understood. Recently, mRNA modification by N6-methyladenosine (m6A) has been shown to be involved in post-transcriptional regulation processes including mRNA stability and promotion of translation, but the role of m6A in the hypoxia response is unknown...
June 13, 2017: RNA
https://www.readbyqxmd.com/read/28606943/role-of-terminator-hairpin-in-biogenesis-of-functional-hfq-binding-srnas
#5
Teppei Morita, Ryo Nishino, Hiroji Aiba
Many Rho-independent transcription terminators of the genes encoding bacterial Hfq-binding sRNAs possess a set of 7 or more T residues at the 3' end (Otaka et al. 2011; Ishikawa et al. 2012). Here, we have studied the role of terminator hairpin in biogenesis of sRNAs focusing on SgrS and RyhB in Esherichia coli. We constructed variant sRNA genes in which the GC-rich inverted repeat sequences are extended to stabilize the terminator hairpins. We demonstrate that the extension of the hairpin stem leads to generation of heterogeneous transcripts in which the polyU tail is shortened...
June 12, 2017: RNA
https://www.readbyqxmd.com/read/28600356/structural-basis-for-ligand-binding-to-the-guanidine-ii-riboswitch
#6
Caroline W Reiss, Scott A Strobel
The guanidine-II riboswitch, also known as mini-ykkC, is a conserved mRNA element with more than 800 examples in bacteria. It consists of two stemloops capped by identical, conserved tetraloops that are separated by a linker region of variable length and sequence. Like the guanidine-I riboswitch, it controls the expression of guanidine carboxylases and SugE-like genes. The guanidine-II riboswitch specifically binds free guanidinium cation and functions as a translationally-controlled on-switch. Here we report the structure of a P2 stemloop from the Pseudomonas aeruginosa guanidine-II riboswitch aptamer bound to guanidine at 1...
June 9, 2017: RNA
https://www.readbyqxmd.com/read/28592461/rbm24-promotes-u1-snrnp-recognition-of-the-mutated-5-splice-site-in-the-ikbkap-gene-of-familial-dysautonomia
#7
Kenji Ohe, Mayumi Yoshida, Akiko Nakano-Kobayashi, Motoyasu Hosokawa, Yukiya Sako, Maki Sakuma, Yukiko Okuno, Tomomi Usui, Kensuke Ninomiya, Takayuki Nojima, Naoyuki Kataoka, Masatoshi Hagiwara
The 5' splice site mutation (IVS20+6T>C) of the inhibitor of kappa light polypeptide gene enhancer in B cells, kinase complex-associated protein (IKBKAP) gene in familial dysautonomia (FD) is at the sixth intronic nucleotide of the 5' splice site. It is known to weaken U1 snRNP recognition and result in aberrantly spliced mRNA product in neuronal tissue, but normally spliced mRNA in other tissues. Aberrantly spliced IKBKAP mRNA abrogates IKK complex-associated protein (IKAP)/elongator protein 1 (ELP1) expression and results in a defect of neuronal cell development in FD...
June 7, 2017: RNA
https://www.readbyqxmd.com/read/28588079/focal-accumulation-of-preribosomes-outside-the-nucleolus-during-metaphase-anaphase-in-budding-yeast
#8
Giulia Moriggi, Sonia G Gaspar, Blanca Nieto, Xosé R Bustelo, Mercedes Dosil
Saccharomyces cerevisiae contains one nucleolus that remains intact in the mother-cell side of the nucleus throughout most of mitosis. Based on this, it is assumed that the bulk of ribosome production during cell division occurs in the mother cell. Here, we show that the ribosome synthesis machinery localizes not only in the nucleolus but also at a center that is present in the bud side of the nucleus after the initiation of mitosis. This center can be visualized by live microscopy as a punctate body located in close proximity to the nuclear envelope and opposite to the nucleolus...
June 6, 2017: RNA
https://www.readbyqxmd.com/read/28576826/archaeal-fibrillarin-nop5-heterodimer-2-o-methylates-rna-independently-of-the-c-d-guide-rnp-particle
#9
Miglė Tomkuvienė, Janina Ličytė, Ingrida Olendraitė, Zita Liutkevičiūtė, Béatrice Clouet-d'Orval, Saulius Klimašauskas
Archaeal fibrillarin (aFib) is a well-characterized S-Adenosyl methionine (SAM)-dependent RNA 2'-O-methyltransferase that is known to act in a large C/D ribonucleoprotein (RNP) complex together with Nop5 and L7Ae proteins and a box C/D guide RNA. In the reaction, the guide RNA is critical to direct the methylation reaction to a specific site in tRNA or rRNA by sequence complementarity. Here we show that Pyrococcus abyssi aFib-Nop5 heterodimer can alone perform a SAM-dependent 2'-O-methylation of 16S and 23S ribosomal RNAs in vitro independently of L7Ae and C/D guide RNAs...
June 2, 2017: RNA
https://www.readbyqxmd.com/read/28576825/identification-of-an-optimized-2-o-methylated-tri-nucleotide-rna-motif-inhibiting-toll-like-receptor-7-and-8
#10
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 as compared to 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...
June 2, 2017: RNA
https://www.readbyqxmd.com/read/28559491/antagonistic-actions-of-two-human-pan3-isoforms-on-global-mrna-turnover
#11
Chyi-Ying A Chen, Yueqiang Zhang, Yu Xiang, Leng Han, Ann-Bin Shyu
Deadenylation is a fundamental process that regulates eukaryotic gene expression. Mammalian deadenylation exhibits biphasic kinetics, with the Pan2-Pan3 and Ccr4-Caf1 deadenylase complexes mediating the first and second phase, respectively; however, the significance of the biphasic nature of deadenylation in mRNA turnover remains unclear. In this study, we discovered that two distinct isoforms of human Pan3 display opposing properties necessary for coordinating the two phases of deadenylation. The shorter isoform (Pan3S) interacts more strongly with PABP than the longer isoform (Pan3L) does...
May 30, 2017: RNA
https://www.readbyqxmd.com/read/28559490/adar-rna-editing-below-the-backbone
#12
Liam P Keegan, Anzer Khan, Dragana Vukic, Mary A O'Connell
ADAR RNA editing enzymes (Adenosine Deaminases acting on RNA), that convert adenosine bases to inosines were first identified biochemically thirty years ago. Since then studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster, which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins...
May 30, 2017: RNA
https://www.readbyqxmd.com/read/28546148/translation-initiation-factor-eif4g1-preferentially-binds-yeast-transcript-leaders-containing-conserved-oligo-uridine-motifs
#13
Boris Zinshteyn, Maria F Rojas Duran, Wendy V Gilbert
Translational control of gene expression plays essential roles in cellular stress responses and organismal development by enabling rapid, selective, and localized control of protein production. Translational regulation depends on context-dependent differences in the protein output of mRNAs, but the key mRNA features that distinguish efficiently translated mRNAs are largely unknown. Here we comprehensively determined the RNA-binding preferences of the initiation factor eIF4G to assess whether this core translation initiation factor has intrinsic sequence preferences that may contribute to preferential translation of specific mRNAs...
May 25, 2017: RNA
https://www.readbyqxmd.com/read/28539487/characterization-of-the-mammalian-rna-exonuclease-5-nef-sp-as-a-testis-specific-nuclear-3-%C3%A2-5-exoribonuclease
#14
Sara Silva, David Homolka, Ramesh S Pillai
Ribonucleases catalyse maturation of functional RNAs or mediate degradation of cellular transcripts, activities that are critical for gene expression control. Here we identify a previously uncharacterized mammalian nuclease family member NEF-sp [RNA exonuclease 5 (REXO5) or LOC81691] as a testis-specific factor. Recombinant human NEF-sp demonstrates a divalent metal ion-dependent 3'→5' exoribonuclease activity. This activity is specific to single-stranded RNA substrates and is independent of their length...
May 24, 2017: RNA
https://www.readbyqxmd.com/read/28522581/conformational-dynamics-of-the-frameshift-stimulatory-structure-in-hiv-1
#15
Dustin B Ritchie, Tonia R Cappellano, Collin Tittle, Negar Rezajooei, Logan Rouleau, William Ka Sikkema, Michael T Woodside
Programmed ribosomal frameshifting (PRF) in HIV-1 is thought to be stimulated by a hairpin in the mRNA, although a pseudoknot-like triplex has also been proposed. Because the conformational dynamics of the stimulatory structure under tension applied by the ribosomal helicase during translation may play an important role in PRF, we used optical tweezers to apply tension to the HIV stimulatory structure and monitor its unfolding and refolding dynamics. The folding and unfolding kinetics and energy landscape of the hairpin were measured by ramping the force on the hairpin up and down, providing a detailed biophysical characterisation...
May 18, 2017: RNA
https://www.readbyqxmd.com/read/28500251/expression-of-distinct-maternal-and-somatic-5-8s-18s-and-28s-rrna-types-during-zebrafish-development
#16
Mauro D Locati, Johanna F B Pagano, Geneviève Girard, Wim A Ensink, Marina van Olst, Selina van Leeuwen, Ulrike Nehrdich, Herman P Spaink, Han Rauwerda, Martijs J Jonker, Rob J Dekker, Timo M Breit
There is mounting evidence that the ribosome is not a static translation machinery, but a cell-specific, adaptive system. Ribosomal variations have mostly been studied at the protein level, even though the essential transcriptional functions are primarily performed by rRNAs. At the RNA level, oocyte-specific 5S rRNAs are long known for Xenopus. Recently, we described for zebrafish a similar system in which the sole maternal-type 5S rRNA present in eggs, is replaced completely during embryonic development by a somatic-type...
May 12, 2017: RNA
https://www.readbyqxmd.com/read/28495677/high-throughput-and-site-specific-identification-of-2-o-methylation-sites-using-ribose-oxidation-sequencing-riboxi-seq
#17
Yinzhou Zhu, Stephan P Pirnie, Gordon G Carmichael
Ribose methylation (2'-O methylation, 2'-OMe) occurs at high frequencies in rRNAs and other small RNAs, and is carried out using a shared mechanism across eukaryotes and archaea. As RNA modifications are important for ribosome maturation, and alterations in these modifications are associated with cellular defects and diseases, it is important to characterize the landscape of 2'-O methylation. Here we report the development of a highly sensitive and accurate method for ribose methylation detection using next generation sequencing...
May 11, 2017: RNA
https://www.readbyqxmd.com/read/28490506/polyadenylation-is-the-key-aspect-of-gld-2-function-in-c-elegans
#18
Marco Nousch, Ryuji Minasaki, Christian R Eckmann
In biology, the role of many enzymes extends beyond their dedicated catalytic activity by fulfilling important cellular roles in a catalysis-independent fashion. In this aspect, little is known about 3'-end RNA-modifying enzymes that belong to the class of nucleotidyl transferases. Among these are non-canonical poly(A) polymerases, a group of evolutionary conserved enzymes that are critical for gene expression regulation, by adding adenosines to the 3'end of mRNA targets. In this study, we investigate whether the functions of the cytoplasmic poly(A) polymerase (cytoPAP) GLD-2 in C...
May 10, 2017: RNA
https://www.readbyqxmd.com/read/28487382/nf45-and-nf90-nf110-coordinately-regulate-esc-pluripotency-and-differentiation
#19
Julia Ye, Hu Jin, Aleksandr Pankov, Jun Song, Robert Blelloch
While years of investigation have elucidated many aspects of embryonic stem cell (ESC) regulation, the contributions of post-transcriptional and translational mechanisms to the pluripotency network remain largely unexplored. In particular, little is known in ESCs about the function of RNA binding proteins (RBPs), the protein agents of post-transcriptional regulation. We performed an unbiased RNAi screen of RBPs in an ESC differentiation assay and identified two related genes, NF45 (Ilf2) and NF90/NF110 (Ilf3), whose knockdown promoted differentiation to an epiblast-like state...
May 9, 2017: RNA
https://www.readbyqxmd.com/read/28487381/improved-microrna-suppression-by-wpre-linked-tough-decoy-microrna-sponges
#20
Anne Kruse Hollensen, Rune Thomsen, Rasmus O Bak, Charlotte Christie Petersen, Eva Reumert Ermegaard, Lars Aagaard, Christian Kroun Damgaard, Jacob Giehm Mikkelsen
Our genes are posttranscriptionally regulated by microRNAs (miRNAs) inducing translational suppression and degradation of targeted mRNAs. Strategies to inhibit miRNAs in a spatiotemporal manner in a desired cell type or tissue, or at a desired developmental stage, can be crucial for understanding miRNA function and for pushing forward miRNA suppression as a feasible rationale for genetic treatment of disease. For such purposes, RNA polymerase II (RNApolII)-transcribed Tough Decoy (TuD) miRNA inhibitors are particularly attractive...
May 9, 2017: RNA
journal
journal
32304
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"