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Eva Schöller, Franziska Weichmann, Thomas Treiber, Sam Ringle, Nora Treiber, Andrew Flatley, Regina Feederle, Astrid Bruckmann, Gunter Meister
N6-methyladenine (m6A) is found on many eukaryotic RNAs including mRNAs. M6A modification has been implicated in mRNA stability and turn over, localization or translation efficiency. A heterodimeric enzyme complex composed of METTL3 and METTL14 generates m6A on mRNAs. METTL3/14 is found in the nucleus where it is localized to nuclear speckles and the splicing regulator WTAP is required for this distinct nuclear localization pattern. Although recent crystal structures revealed how the catalytic MT-A70 domains of METTL3 and METTL14 interact with each other, a more global architecture including WTAP and RNA interactions has not been reported so far...
January 18, 2018: RNA
Pamela Nicholson, Asimina Gkratsou, Christoph Josi, Martino Colombo, Oliver Mühlemann
The term "nonsense-mediated mRNA decay" (NMD) originally described the degradation of mRNAs with premature translation-termination codons (PTCs), but its meaning has recently been extended to be a translation-dependent post-transcriptional regulator of gene expression affecting 3-10 % of all mRNAs. The degradation of NMD target mRNAs involves both exonucleolytic and endonucleolytic pathways in mammalian cells. While the latter is mediated by the endonuclease SMG6, the former pathway has been reported to require a complex of SMG5-SMG7 or SMG5-PNRC2 binding to UPF1...
January 18, 2018: RNA
Natalie M McAdams, Rachel M Simpson, Runpu Chen, Yijun Sun, Laurie Read
The trypanosome RNA Editing Substrate Binding Complex (RESC) acts as the platform for mitochondrial uridine insertion/deletion RNA editing and facilitates the protein-protein and protein-RNA interactions required for the editing process. RESC is broadly comprised of two subcomplexes: GRBC (Guide RNA Binding Complex) and REMC (RNA Editing Mediator Complex). Here, we characterize the function and position in RESC organization of a previously unstudied RESC protein, MRB7260. We show that MRB7260 forms numerous RESC-related complexes, including a novel, small complex with the guide RNA binding protein, GAP1, which is a canonical GRBC component, and REMC components MRB8170 and TbRGG2...
January 12, 2018: RNA
Lela Lackey, Aaztli Coria, Chanin Woods, Evonne McArthur, Alain Laederach
The precise impact of inherited and somatic mutations on messenger RNA (mRNA) structure remains poorly understood. Recent technological advances that leverage next generation sequencing to obtain experimental structure data, such as SHAPE-MaP (Selective 2' Hydroxyl Acylation by Primer Extension and Mutational Profiling), can reveal structural effects of mutations especially when this data is rigorously incorporated in RNA structural modeling. Here we analyze the ability of SHAPE-MaP to detect the relatively subtle structural changes caused by single nucleotide mutations...
January 9, 2018: RNA
Olga Coll, Tanit Guitart, Ana Villalba, Catherine Papin, Martine Simonelig, Fatima Gebauer
Cytoplasmic polyadenylation is a widespread mechanism to regulate mRNA translation. In vertebrates, this process requires two sequence elements in target 3' UTRs, the U-rich cytoplasmic polyadenylation element and the AAUAAA hexanucleotide. In Drosophila melanogaster, cytoplasmic polyadenylation of Toll mRNA occurs independently of these canonical elements and requires a machinery that remains to be characterized. Here we identify Dicer-2 as a component of this machinery. Dicer-2, a factor previously involved in RNA interference (RNAi), interacts with the cytoplasmic poly(A) polymerase Wispy...
January 9, 2018: RNA
Qian Zhang, Zhefan Stephen Chen, Ying An, Haizhen Liu, Yonghui Hou, Wen Li, Kwok-Fai Lau, Alex Koon, Jacky Ngo, Edwin Chan
Polyglutamine (polyQ) diseases are a set of progressive neurodegenerative disorders ascribed by the expression of both expanded CAG RNA and misfolded polyQ protein. We previously reported that the direct interaction between expanded CAG RNA and nucleolar protein nucleolin (NCL) leads to impediment of pre-ribosomal RNA (pre-rRNA) transcription, and eventually triggers nucleolar stress-induced apoptosis in polyQ diseases. Here, we report a 21-amino acid peptide, named beta-structured inhibitor for neurodegenerative disease (BIND), effectively suppresses expanded CAG RNA toxicity...
January 2, 2018: RNA
Masaki Miyazawa, Alexander R Bogdan, Kazunori Hashimoto, Yoshiaki Tsuji
Intracellular iron is tightly regulated by coordinated expression of iron transport and storage genes, such as transferrin receptor-1 (TfR1) and ferritin. They are primarily regulated by iron through iron-induced dissociation of iron-regulatory proteins (IRPs) from iron-responsive elements (IREs) in the 3'-UTR (untranslated region) of TfR1 or 5'-UTR of ferritin mRNA, resulting in destabilization of TfR1 mRNA and release of ferritin translation block. Thus high iron decreases iron transport via TfR1 mRNA degradation and increases iron storage via ferritin translational upregulation...
January 2, 2018: RNA
Shoji Ohuchi, Beatrix Suess
Inhibitory aptamers against a protein are promising as antagonistic reagents and repressive genetic components. Typically, improvement of such aptamers is achieved by acquiring higher binding affinity. Here, we report an alternative mechanism for the improvement of aptamer activity. Recently, we reported a transcriptional activator based on an inhibitory RNA aptamer against lambda cI repressor. We improved the aptamer through in vitro selection (SELEX) from a randomly mutagenized aptamer pool, followed by in vivo screening and truncation...
December 28, 2017: RNA
Jennifer Perez-Boza, Michelle Lion, Ingrid Struman
Exosomes are small extracellular vesicles of around 100nm of diameter produced by most cell types. These vesicles carry nucleic acids, proteins, lipids and other biomolecules and function as carriers of biological information in processes of extracellular communication. The content of exosomes is regulated by the external and internal microenvironment of the parent cell, but the intrinsic mechanisms of loading of molecules into exosomes is still not completely elucidated. In this study, by the use of next generation sequencing we have characterized in depth the RNA composition of healthy endothelial cells and exosomes and provided an accurate profile of the different coding and non-coding RNA species found per compartment...
December 27, 2017: RNA
Katrin Kemmerer, Sandra Fischer, Julia E Weigand
HnRNP D, better known as AUF1, is an extensively studied protein that controls a variety of cellular pathways. Consequently, its expression has to be tightly regulated to prevent the onset of pathologies. In contrast, the cellular functions and regulation of its ubiquitously expressed paralog hnRNP DL are barely explored. Here, we present an intricate crosstalk between these two proteins. Both hnRNP D and DL are able to control their own expression by alternative splicing of cassette exons in their 3' UTRs...
December 20, 2017: RNA
Charlotte Nejad, Katherine A Pillman, Katherine J Siddle, Genevieve Pepin, Minna-Liisa Änkö, Claire E McCoy, Traude Beilharz, Lluís Quintana-Murci, Gregory J Goodall, Cameron P Bracken, Michael P Gantier
Endogenous microRNAs (miRNAs) often exist as multiple isoforms (known as "isomiRs") with predominant variation around their 3'-end. Increasing evidence suggests that different isomiRs of the same family can have diverse functional roles, as recently demonstrated with the example of miR-222-3p 3'-end variants. While isomiR levels from a same miRNA family can vary between tissues and cell types, change of templated isomiR stoichiometry to stimulation has not been reported to date. Relying on small RNA-sequencing analyses, we demonstrate here that miR-222-3p 3'-end variants >23 nt are specifically decreased upon interferon (IFN) β stimulation of human fibroblasts, while shorter isoforms are spared...
December 20, 2017: RNA
Matthew J Payea, Michael F Sloma, Yoshiko Kon, David L Young, Michael P Guy, Xiaoju Zhang, Thareendra De Zoysa, Stanley Fields, David H Mathews, Eric M Phizicky
Microorganisms have universally adapted their RNAs and proteins to survive at a broad range of temperatures and growth conditions. However, for RNAs, there is little quantitative understanding of the effects of mutations on function at high temperatures. To understand how variant tRNA function is affected by temperature change, we used the nonsense suppressor SUP4oc, of the yeast Saccharomyces cerevisiae to perform a high-throughput quantitative screen of tRNA function at two different growth temperatures. This screen yielded comparative values for 9,243 single and double variants...
December 19, 2017: RNA
Annamaria Sgromo, Tobias Raisch, Charlotte Backhaus, Csilla Keskeny, Vikram Alva, Oliver Weichenrieder, Elisa Izaurralde
Drosophila melanogaster Bag-of-marbles (Bam) promotes germline stem cell (GSC) differentiation by repressing the expression of mRNAs encoding stem cell maintenance factors. Bam interacts with Benign gonial cell neoplasm (Bgcn) and the CCR4 deadenylase, a catalytic subunit of the CCR4-NOT complex. Bam has been proposed to bind CCR4 and displace it from the CCR4-NOT complex. Here, we investigated the interaction of Bam with the CCR4-NOT complex by using purified recombinant proteins. Unexpectedly, we found that Bam does not interact with CCR4 directly but instead binds to the CAF40 subunit of the complex in a manner mediated by a conserved N-terminal CAF40-binding motif (CBM)...
December 18, 2017: RNA
Antto J Norppa, Tuuli M Kauppala, Harri A Heikkinen, Bhupendra Verma, Hideo Iwai, Mikko J Frilander
Mutations in the components of the minor spliceosome underlie several human diseases. A subset of patients with isolated growth hormone deficiency (IGHD) harbor mutations in the RNPC3 gene, which encodes the minor spliceosome-specific U11/U12-65K protein. Although a previous study showed that IGHD patient cells have defects in U12-type intron recognition, the biochemical effects of these mutations on the 65K protein have not been characterized. Here, we show that a proline-to-threonine missense mutation (P474T) and a nonsense mutation (R502X) in the C-terminal RNA recognition motif (C-RRM) of the 65K protein impair the binding of 65K to U12 and U6atac snRNAs...
December 18, 2017: RNA
Anupma Choudhary, Darya Vanichkina, Christine Ender, Joanna Crawford, Gregory Baillie, Andrew Calcino, Kelin Ru, Ryan Taft
MicroRNAs (miRNAs) are highly conserved ~22nt small noncoding RNAs that bind partially complementary sequences in target transcripts. MicroRNAs regulate both translation and transcript stability, and play important roles in development, cellular homeostasis and disease. There are limited approaches available to agnostically identify microRNA targets transcriptome-wide, and methods employing miRNA mimics, which in principle identify direct miRNA:transcript pairs, have low sensitivity and specificity. Here we describe a novel method to identify microRNA targets using miR-29b mimics containing 3-cyanovinylcarbazole (CNVK), a photolabile nucleoside analogue...
December 15, 2017: RNA
Rodrigo Maldonado, Michael Filarsky, Ingrid Grummt, Gernot Längst
Triplexes are non-canonical DNA structures, which are functionally associated with regulation of gene expression through ncRNA targeting to chromatin. Based on the rules of Hoogsteen base pairing, poly-purine sequences of a duplex can potentially form triplex structures with single-stranded oligonucleotides. Prediction of triplex-forming sequences by bioinformatics analyses have revealed enrichment of potential triplex targeting sites (TTS) at regulatory elements, mainly in promoters and enhancers, suggesting a potential function of RNA-DNA triplexes in transcriptional regulation...
December 8, 2017: RNA
Robert B Darnell, Shengdong Ke, James E Darnell
By using a cell fraction technique that separates chromatin associated nascent RNA, newly completed nucleoplasmic mRNA and cytoplasmic mRNA, we have shown that residues in exons are methylated (m6A) in nascent pre-mRNA and remain methylated in the same exonic residues in nucleoplasmic and cytoplasmic mRNA. Thus, there is no evidence of a substantial degree of demethylation in mRNA exons that would correspond to so-called "epigenetic" demethylation. The turnover rate of mRNA molecules is faster depending on m6A content in HeLa cell mRNA suggesting specification of mRNA stability may be the major role of m6A exon modification...
December 8, 2017: RNA
Boxuan Zhao, Sigrid Nachtergaele, Ian A Roundtree, Chuan He
We thank Darnell et al. in their Divergent Views article for noting our contributions to recent progress in the field of RNA modifications. We agree with many of the viewpoints expressed: that a majority of messenger RNA N6-methyladenosine (m6A) methylation occurs co-transcriptionally, that one of the main functions of m6A methylation on mRNA is to mark sets of transcripts for expedited turnover, and that this methylation may not dramatically affect splicing in HeLa cells. However, although the impact of m6A methylation on splicing appears to be modest in many cell lines, we suggest to be cautious because m6A methylation is enriched in long exons and overrepresented in transcripts with alternative splicing variants...
December 8, 2017: RNA
Patrick D Cherry, Laura K White, Kerri York, Jay R Hesselberth
RNA repair enzymes catalyze rejoining of an RNA molecule after cleavage of phosphodiester linkages. RNA repair in budding yeast is catalyzed by two separate enzymes that process tRNA exons during their splicing and HAC1 mRNA exons during activation of the unfolded protein response. The RNA ligase Trl1 joins 2',3'-cyclic phosphate and 5'-hydroxyl RNA fragments, creating a new phosphodiester linkage with a 2'-phosphate at the junction. The 2'-phosphate is subsequently removed by the 2'-phosphotransferase Tpt1, which catalyzes phosphate transfer to NAD+, producing nicotinamide and a unique ADP ribose metabolite...
December 6, 2017: RNA
Shih-Ting Kang, Yi-Shan Hsieh, Chi-Ting Feng, Yu-Ting Chen, Pok Eric Yang, Wei-Ming Chen
MicroRNA (miRNAs) are 18-25 nucleotides highly conserved, non-coding RNAs involved in gene regulations. Because of miRNAs' short length, the design of miRNA primers for PCR amplification remains a significant challenge. Adding to the challenge are miRNAs similar in sequences and miRNA family members which often only differ in sequences by one nucleotide. Here, we described a novel empirical-based method, miPrimer, which greatly reduces primer dimerization and increases primer specificity by factoring various intrinsic primer properties and employing four primer design strategies...
December 5, 2017: RNA
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