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https://www.readbyqxmd.com/read/29127211/mechanistic-implications-of-enhanced-editing-by-a-hypertribe-rna-binding-protein
#1
Weijin Xu, Reazur Rahman, Michael Rosbash
We previously developed TRIBE, a method for the identification of cell-specific RNA binding protein targets. TRIBE expresses an RBP of interest fused to the catalytic domain (cd) of the RNA editing enzyme ADAR and performs Adenosine-to-Inosine editing on RNA targets of the RBP. However, target identification is limited by the low editing efficiency of the ADARcd. Here we describe HyperTRIBE, which carries a previously characterized hyperactive mutation (E488Q) of the ADARcd. HyperTRIBE identifies dramatically more editing sites, many of which are also edited by TRIBE but at a much lower editing frequency...
November 10, 2017: RNA
https://www.readbyqxmd.com/read/29127210/hiv-1-nc-induced-stress-granule-assembly-and-translation-arrest-are-inhibited-by-the-dsrna-binding-protein-staufen1
#2
Shringar Rao, Alessandro Cinti, Abdelkrim Temzi, Raquel Amorim, Ji Chang You, Andrew J Mouland
The nucleocapsid (NC) is an N-terminal protein derived from the HIV-1 Gag precursor polyprotein, pr55Gag. NC possesses key functions at several pivotal stages of viral replication. For example, an interaction between NC and the host, double-stranded RNA-binding protein Staufen1 was shown to regulate several steps in the viral replication cycle, such as Gag multimerisation and genomic RNA encapsidation. In this work, we observed that the overexpression of NC leads to the induction of stress granule (SG) assembly...
November 10, 2017: RNA
https://www.readbyqxmd.com/read/29122971/poly-a-site-choice-and-pol2-ctd-serine-5-status-govern-lncrna-control-of-phosphate-responsive-tgp1-gene-expression-in-fission-yeast
#3
Ana M Sanchez, Stewart Shuman, Beate Schwer
Expression of fission yeast glycerophosphate transporter Tgp1 is repressed in phosphate-rich medium and induced during phosphate starvation. Repression is enforced by transcription of the nc-tgp1 locus upstream of tgp1 to produce a long noncoding (lnc) RNA. Here we identify two essential elements of the nc-tgp1 promoter: a TATA box (-30)TATATATA(-23) and a HomolD box (-64)CAGTCACA(-57), mutations of which inactivate the nc-tgp1 promoter and de-repress the downstream tgp1 promoter under phosphate-replete conditions...
November 9, 2017: RNA
https://www.readbyqxmd.com/read/29122970/a-novel-form-of-rna-double-helix-based-on-g%C3%A2-u-and-c%C3%A2-a-wobble-base-pairing
#4
Ankur Garg, Udo Heinemann
Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA double helix in overall A conformation, which includes a unique, central stretch of six consecutive wobble base pairs (W helix) with two G·U and four rare C·A(+) wobble pairs. Four adenines within the W helix are N1-protonated and wobble-base-paired with the opposing cytosine through two regular hydrogen bonds...
November 9, 2017: RNA
https://www.readbyqxmd.com/read/29114019/native-elongating-transcript-sequencing-reveals-global-anti-correlation-between-sense-and-antisense-nascent-transcription-in-fission-yeast
#5
Maxime Wery, Camille Gautier, Marc Descrimes, Mayuko Yoda, Hervé Vennin-Rendos, Valérie Migeot, Daniel Gautheret, Damien Hermand, Antonin Morillon
Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site...
November 7, 2017: RNA
https://www.readbyqxmd.com/read/29114018/accurate-detection-of-chemical-modifications-in-rna-by-mutational-profiling-map-with-shapemapper-2
#6
Steven Busan, Kevin M Weeks
Mutational profiling (MaP) enables detection of sites of chemical modification in RNA as sequence changes during reverse transcription (RT), subsequently read out by massively parallel sequencing. We introduce ShapeMapper 2, which integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to now identify RNA adduct sites as accurately as achieved by careful manual analysis of electrophoresis data, the prior highest-accuracy standard...
November 7, 2017: RNA
https://www.readbyqxmd.com/read/29114017/a-microrna-feedback-loop-regulates-global-microrna-abundance-during-aging
#7
Sachi Inukai, Zachary Pincus, Alexandre de Lencastre, Frank J Slack
Expression levels of many microRNAs (miRNAs) change during aging, notably declining globally in a number of organisms and tissues across taxa. However, little is known about the mechanisms or the biological relevance for this change. We investigated the network of genes that controls miRNA transcription and processing during C. elegans aging. We found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs. In particular, miR-71, known to influence lifespan and itself upregulated during aging, represses alg-1/Argonaute expression post-transcriptionally during aging...
November 7, 2017: RNA
https://www.readbyqxmd.com/read/29109157/an-ultra-processive-accurate-reverse-transcriptase-encoded-by-a-metazoan-group-ii-intron
#8
Chen Zhao, Fei Liu, Anna Marie Pyle
Group II introns and non-LTR retrotransposons encode a phylogenetically-related family of highly processive reverse transcriptases (RTs) that are essential for mobility and persistence of these retroelements. Recent crystallographic studies on members of this RT family have revealed that they are structurally distinct from the retroviral RTs that are typically used in biotechnology. However, quantitative, structure-guided analysis of processivity, efficiency and accuracy of this alternate RT family has been lacking...
November 6, 2017: RNA
https://www.readbyqxmd.com/read/29101277/application-of-a-schizosaccharomyces-pombe-edc1-fused-dcp1-dcp2-decapping-enzyme-for-transcription-start-site-mapping
#9
David Russell Paquette, Jeffrey S Mugridge, David E Weinberg, John David Gross
Changes in the 5' leader of an mRNA can have profound effects on its translational efficiency with little effect on abundance. Sequencing-based methods to accurately map the 5' leader by identifying the first transcribed nucleotide rely on enzymatic removal of the 5' eukaryotic cap structure by tobacco acid pyrophosphatase (TAP). However, commercial TAP production has been problematic and has now been discontinued. RppH, a bacterial enzyme that can also cleave the 5' cap, and Cap-Clip, a plant-derived enzyme, have been marketed as TAP replacements...
November 3, 2017: RNA
https://www.readbyqxmd.com/read/29093021/the-rna-exosome-and-rna-exosome-linked-disease
#10
Derrick J Morton, Emily G Kuiper, Stephanie K Jones, Sara W Leung, Anita H Corbett, Milo B Fasken
The RNA exosome is an evolutionarily conserved, ribonuclease complex that is critical for both processing and degradation of a variety of RNAs. Cofactors that associate with the RNA exosome likely dictate substrate specificity for this complex. Recently, mutations in genes encoding both structural subunits of the RNA exosome and its cofactors have been linked to human disease. Mutations in the RNA exosome genes EXOSC3 and EXOSC8 cause pontocerebellar hypoplasia type 1b (PCH1b) and type 1c (PCH1c), respectively, which are similar autosomal recessive, neurodegenerative diseases...
November 1, 2017: RNA
https://www.readbyqxmd.com/read/29089381/drosophila-sister-of-sex-lethal-is-a-repressor-of-translation
#11
Rebecca Moschall, Daniela Strauss, Marina Garcia-Bayert, Fatima Gebauer, Jan Medenbach
The RNA-binding protein Sex Lethal (Sxl) is an important post-transcriptional regulator of gene expression in female Drosophila To prevent the assembly of the dosage compensation complex in female flies, Sxl acts as a repressor of msl-2 mRNA translation. It employs two distinct and mutually reinforcing blocks to translation that operate on the 5' and 3' untranslated regions (UTRs) of msl-2 mRNA, respectively. While 5' UTR-mediated translational control involves an upstream open reading frame, 3' UTR-mediated regulation strictly requires the co-repressor protein Upstream of N-ras (Unr) which is recruited to the msl-2 mRNA by Sxl...
October 31, 2017: RNA
https://www.readbyqxmd.com/read/29079635/cefra-seq-reveals-broad-asymmetric-mrna-and-non-coding-rna-distribution-profiles-in-drosophila-and-human-cells
#12
Louis Philip Benoit Bouvrette, Neal A L Cody, Julie Bergalet, Fabio Alexis Lefebvre, Cédric Diot, Xiaofeng Wang, Mathieu Blanchette, Eric Lécuyer
Cells are highly asymmetrical, a feature that relies on the sorting of molecular constituents, including proteins, lipids and nucleic acids, to distinct subcellular locales. The localization of RNA molecules is an important layer of gene regulation required to modulate localized cellular activities, although its global prevalence remains unclear. We combine biochemical cell fractionation with RNA sequencing (CeFra-seq) analysis to assess the prevalence and conservation of RNA asymmetric distribution on a transcriptome-wide scale in Drosophila and human cells...
October 27, 2017: RNA
https://www.readbyqxmd.com/read/29079634/small-rna-mediated-regulation-of-dna-dosage-in-the-ciliate-oxytricha
#13
Jaspreet S Khurana, Derek Clay, Sandrine Moreira, Xing Wang, Laura F Landweber
Dicer-dependent small non-coding RNAs play important roles in gene regulation in a wide variety of organisms. Endogenous small interfering RNAs (siRNAs) are part of an ancient pathway of transposon control in plants and animals. The ciliate, Oxytricha trifallax, has approximately 16,000 gene-sized chromosomes in its somatic nucleus. Long non-coding RNAs establish high ploidy levels at the onset of sexual development, but the factors that regulate chromosome copy numbers during cell division and growth have been a mystery...
October 27, 2017: RNA
https://www.readbyqxmd.com/read/29054886/the-ssu-processome-interactome-in-saccharomyces-cerevisiae-reveals-potential-new-protein-subcomplexes
#14
Nicholas G Vincent, J Michael Charette, Susan J Baserga
Ribosome assembly is an evolutionarily conserved and energy intensive process required for cellular growth, proliferation, and maintenance. In yeast, assembly of the small ribosomal subunit (SSU) requires approximately 75 assembly factors that act in coordination to form the SSU processome, a 6 MDa ribonucleoprotein complex. The SSU processome is required for processing, modifying, and folding the pre-ribosomal RNA (rRNA) to prepare it for incorporation into the mature SSU. Although the protein composition of the SSU processome has been known for some time, the interaction network of the proteins required for its assembly has remained poorly defined...
October 20, 2017: RNA
https://www.readbyqxmd.com/read/29051199/assessment-and-comparison-of-thermal-stability-of-phosphorothioate-dna-dna-rna-2-f-rna-and-lna-in-the-context-of-phi29-prna-3wj
#15
Xijun Piao, Hongzhi Wang, Daniel W Binzel, Peixuan Guo
The question of whether RNA is more stable or unstable comparing to DNA or other nucleic acids has long been an extensive scrutiny and public attention. In these days, thermodynamically-stable and degradation-resistant RNA motifs have been utilized in RNA nanotechnology to build desired architectures and integrate multiple functional groups. Here we report the effects of phosphorothioate deoxyribonucleotides (PS-DNA), deoxyribonucleotides (DNA), ribonucleotides (RNA), 2'-F nucleotides (2'-F) and locked nucleic acids (LNA) on the thermal and in vivo stability of RNA and the three-way junction (3WJ) of bacteriophage phi29 motor pRNA...
October 19, 2017: RNA
https://www.readbyqxmd.com/read/29042507/selection-of-functional-2a-sequences-within-foot-and-mouth-disease-virus-requirements-for-the-npgp-motif-with-a-distinct-codon-bias
#16
Jonas Kjær, Graham J Belsham
Foot-and-mouth disease virus (FMDV) has a positive-sense ssRNA genome including a single, large, open reading frame. Splitting of the encoded polyprotein at the 2A/2B junction is mediated by the 2A peptide (18 residues long) which induces a non-proteolytic, co-translational, "cleavage" at its own C-terminus. A conserved feature among variants of 2A is the C-terminal motif N16P17G18/P19 where P19 is the first residue of 2B. It has been shown previously that certain amino acid substitutions can be tolerated at residues E14, S15 and N16 within the 2A sequence of infectious FMDVs but no variants at residues P17, G18 or P19 have been identified...
October 17, 2017: RNA
https://www.readbyqxmd.com/read/29042506/non-watson-crick-rna-synthesis-suited-to-origin-functions
#17
Deepa Puthenvedu, Irene Majerfeld, Michael Yarus
A templated RNA synthesis is characterized in which G5'pp5'G accelerates synthesis of A5'pp5'A from pA and chemically activated ImpA precursors. Similar acceleration is not observable in the presence of UppU, CppC, AppG, AppA or pG alone. Thus, it seems likely that AppA is templated by GppG via a form or forms of G:A base-pairing. AppA also appears, more slowly, via a previously known untemplated 2nd order chemical route. Such AppA synthesis requires only ordinary near-neutral solutions containing monovalent and divalent salts, and rates are only slightly sensitive to variation in pH...
October 17, 2017: RNA
https://www.readbyqxmd.com/read/29042505/binding-synergy-as-an-essential-step-for-trna-editing-and-modification-enzyme-co-dependence-in-trypanosoma-brucei
#18
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/29030489/glyoxals-as-in-vivo-rna-structural-probes-of-guanine-base-pairing
#19
David Mitchell, Laura E Ritchey, Hongmarn Park, Paul Babitzke, Sarah M Assmann, Philip C Bevilacqua
Elucidation of the folded structures that RNA forms in vivo is vital to understanding its functions. Chemical reagents that modify the Watson-Crick (WC) face of unprotected nucleobases are particularly useful in structure elucidation. Dimethyl sulfate penetrates cell membranes and informs on RNA base pairing and secondary structure but only modifies the WC face of adenines and cytosines. We present glyoxal, methylglyoxal, and phenylglyoxal as potent in vivo reagents that target the WC face of guanines as well as cytosines and adenines...
October 13, 2017: RNA
https://www.readbyqxmd.com/read/28986506/sbp1-modulates-translation-of-pab1-mrna-in-a-poly-a-and-rgg-dependent-manner
#20
Alberto Brandariz Núñez, Fuxing Zeng, Quan Ngoc Lam, Hong Jin
RNA-binding protein Sbp1 facilitates the decapping pathway in mRNA metabolism and inhibits global mRNA translation by an unclear mechanism. Here we report molecular interactions responsible for Sbp1-mediated translation inhibition of mRNA encoding the polyadenosine-binding protein (Pab1), an essential translation factor that stimulates mRNA translation and inhibits mRNA decapping in eukaryotic cells. We demonstrate that the two distal RRMs of Sbp1 bind to the poly(A)-sequence in the 5' UTR of the Pab1 mRNA specifically and cooperatively while the central RGG domain of the protein interacts directly with Pab1...
October 6, 2017: RNA
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