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Daniel Sprague, Shafagh Waters, Jessime M Kirk, Jeremy Wang, Paul Samollow, Paul Waters, J Mauro Calabrese
The marsupial inactive X chromosome expresses a long noncoding RNA (lncRNA) called Rsx that has been proposed to be the functional analogue of eutherian Xist. Despite the possibility that Xist and Rsx encode related functions, the two lncRNAs harbor no linear sequence similarity. However, both lncRNAs harbor domains of tandemly repeated sequence. In Xist, these repeat domains are known to be critical for function. Using k-mer based comparison, we show that the repeat domains of Xist and Rsx unexpectedly partition into two major clusters that each harbor substantial levels of non-linear sequence similarity...
May 16, 2019: RNA
Paolo A Lorenzini, Resilind Se Chew, Cheryl Weiqi Tan, Jing Yen Yong, Fan Zhang, Jie Zheng, Xavier Roca
Altered splicing contributes to the pathogenesis of human blood disorders including MyeloDysplastic Syndromes (MDS) and leukemias. Here we characterized the transcriptomic regulation of PRPF40B, which is a splicing factor mutated in a small fraction of MDS patients. We generated a full PRPF40B knockout in K562 cell line by CRISPR/Cas9 technology, and rescued its levels by transient overexpression of wild-type, P383L or P540S MDS alleles. Using RNA sequencing we identified hundreds of differentially expressed genes and alternative splicing events in the knockout that are rescued by wild-type PRPF40B, with a majority also rescued by MDS alleles, pointing to mild effects of these mutations...
May 14, 2019: RNA
Mohamed Nasef, Mary C Muffly, Andrew B Beckman, Sebastian J Rowe, Forrest C Walker, Asma Hatoum-Aslan, Jack A Dunkle
CRISPR-Cas systems are a class of adaptive immune systems in prokaryotes that use small CRISPR RNAs (crRNAs) in conjunction with CRISPR-associated (Cas) nucleases to recognize and degrade foreign nucleic acids. Recent studies have revealed that Type III CRISPR-Cas systems synthesize second messenger molecules previously unknown to exist in prokaryotes, cyclic oligoadenylates (cOA). These molecules activate the Csm6 nuclease to promote RNA degradation and may also coordinate additional cellular responses to foreign nucleic acids...
May 10, 2019: RNA
Meng Jiang, Ling Liu, Chengye Hong, Debo Chen, Xihu Yao, Xiaoyuan Chen, Chen Lin, Rongqin Ke
Visualization of gene expression at single RNA molecule level represents a great challenge to both imaging technologies and molecular engineering. Here we show a single molecule chromogenic in situ hybridization (smCISH) assay that enables counting and localizing individual RNA molecules in fixed cells and tissue under bright field microscopy. Our method is based on in situ padlock probe assay directly using RNA as ligation template and rolling circle amplification combined with enzyme catalyzed chromogenic reaction for amplification product visualization...
May 7, 2019: RNA
Emily R Garnett, Jo E Lomax, Bassem Mohammed, David Gailani, John P Sheehan, Ronald T Raines
Biological roles for extracellular RNA (eRNA) have become apparent. For example, eRNA can induce contact activation in blood via activation of the plasma proteases factor XII (FXII) and factor XI (FXI). We sought to reveal the biological role of the secretory enzyme ribonuclease 1 (RNase 1) in an organismal context by generating and analyzing RNase 1 knockout ( Rnase1 -/- ) mice. We found that these mice are viable, healthy, and fertile, though larger than Rnase1 +/+ mice. Rnase1 -/- plasma contains more RNA than does the plasma of Rnase1 +/+ mice...
May 3, 2019: RNA
Xueyin Wang, Karen J Goodrich, Erin G Conlon, Jianchao Gao, Annette H Erbse, James L Manley, Thomas R Cech
Some neurological disorders, including Amyotrophic Lateral Sclerosis (ALS), Frontotemporal Dementia (FTD), Fragile X Syndrome, Huntington's Disease, Myotonic Dystrophy, and various ataxias, can be caused by expansions of short nucleic acid sequence repeats in specific genes. A possible disease mechanism involves the transcribed repeat RNA binding an RNA-binding protein (RBP), resulting in its sequestration and thus dysfunction. Polycomb Repressive Complex 2 (PRC2), the histone methyltransferase that deposits the H3K27me3 mark of epigenetically silenced chromatin, binds G-rich RNAs and has especially high affinity for G-quadruplex (G-Q) structures...
May 2, 2019: RNA
Perrine Lavalou, Helene Eckert, Louise Damy, Florian Constanty, Sara Majello, Angelo Bitetti, Antoine Graindorge, Alena Shkumatava
The number of annotated long noncoding RNAs (lncRNAs) continues to grow, however their functional characterization in model organisms has been hampered by the lack of reliable genetic inactivation strategies. While partial or full deletions of lncRNA loci disrupt lncRNA expression, they do not permit the formal association of a phenotype with the encoded transcript. Here, we examined several alternative strategies for generating lncRNA null alleles in zebrafish and found that they often resulted in unpredicted changes to lncRNA expression...
May 1, 2019: RNA
Alex G Johnson, Christopher P Lapointe, Jinfan Wang, Nicholas C Corsepius, Junhong Choi, Gabriele Fuchs, Joseph D Puglisi
Receptor for activated C kinase 1 (RACK1) is a eukaryote-specific ribosomal protein implicated in diverse biological functions. To engineer ribosomes for specific fluorescent labeling, we selected RACK1 as a target given its location on the small ribosomal subunit and other properties. However, prior results suggested that RACK1 has roles both on and off the ribosome, and such an exchange might be related to its various cellular functions and hinder our ability to use RACK1 as a stable fluorescent tag for the ribosome...
April 25, 2019: RNA
Annum Munir, Leonora Abdullahu, Ankan Banerjee, Masad J Damha, Stewart Shuman
The enzyme Tpt1 removes the 2'-PO4 at the splice junction generated by fungal tRNA ligase; it does so via a two-step reaction in which: (i) the internal RNA 2'-PO4 attacks NAD+ to form an RNA-2'-phospho-ADP-ribosyl intermediate; and (ii) transesterification of the ribose O2'' to the 2'-phosphodiester yields 2'-OH RNA and ADP-ribose-1'',2''-cyclic phosphate products. The role that Tpt1 enzymes play in taxa that have no fungal-type RNA ligase remains obscure. An attractive prospect is that Tpt1 enzymes might catalyze reactions other than internal RNA 2'-PO4 removal, via their unique NAD+ -dependent transferase mechanism...
April 24, 2019: RNA
Isabel Freund, Daniel K Buhl, Sebastien Boutin, Annika Kotter, Florian Pichot, Virginie Marchand, Tim Vierbuchen, Holger Heine, Yuri Motorin, Mark Helm, Alexander H Dalpke, Tatjana Eigenbrod
Bacterial RNA has emerged as important activator of innate immune responses by stimulating Toll-like receptors TLR7 and TLR8 in humans. Guanosine 2'-O-methylation at position 18 (Gm18) in bacterial tRNA was shown to antagonize tRNA induced TLR7/8 activation, suggesting a potential role of Gm18 as immune escape mechanism. This modification also occurs in eukaryotic tRNA, yet a physiological immune function remained to be tested. We therefore set out to investigate the immune modulatory role of Gm18 in both prokaryotic and eukaryotic microorganisms, Escherichia coli and Saccharomyces cerevisiae, and in human cells...
April 24, 2019: RNA
Victoria V Smirnova, Ekaterina D Shestakova, Dmitry V Bikmetov, Anastasiya A Chugunova, Ilya A Osterman, Marina V Serebryakova, Olga V Sergeeva, Timofei S Zatsepin, Ivan N Shatsky, Ilya M Terenin
Poly(rC)-binding protein 2 (PCBP2, hnRNP E2) is one of the most abundant RNA-binding proteins in mammalian cells. In humans, it exists in seven isoforms, which are assumed to play similar roles in cells. The protein is shown to bind 3' untranslated regions (3' UTRs) of many mRNAs and regulate their translation and/or stability, but nothing is known about functional consequences of PCBP2 binding to 5' UTRs. Here we show that the PCBP2 isoform f interacts with the 5' UTRs of mRNAs encoding eIF4G2 (a translation initiation factor with yet unknown mechanism of action, also known as DAP5) and Cyclin I, and inhibits their translation in vitro and in cultured cells, while the PCBP2 isoform e only affects Cyclin I translation...
April 22, 2019: RNA
Ruth Barral-Arca, Jacobo Pardo-Seco, Xabi Bello, Federico Martinon-Torres, Antonio Salas
There is a growing body of evidence suggesting that patterns of gene expression vary within and between human populations. However, the impact of this variation in human diseases has been poorly explored, in part owing to the lack of a standardized protocol to estimate biogeographical ancestry from gene expression studies. Here we examine several studies that provide new solid evidence indicating that the ancestral background of individuals impacts gene expression patterns. Next, we test a procedure to infer genetic ancestry from RNAseq data in 25 datasets where information on ethnicity was reported...
April 22, 2019: RNA
Mitzli X Velasco, Adam Kosti, Gabriela D A Guardia, Marcia C Santos, Allison Tegge, Mei Qiao, Bruna R S Correa, Greco Hernandez, Erzsebet Kokovay, Pedro A F Galante, Luiz O Penalva
RNA binding proteins (RBPs) and miRNAs are critical gene expression regulators that interact with one another in cooperative and antagonistic fashions. We identified Musashi1 (Msi1) and miR-137 as regulators of a molecular switch between self-renewal and differentiation. Msi1 and miR-137 have opposite expression patterns and functions, and Msi1 is repressed by miR-137. Msi1 is a stem-cell protein implicated in self-renewal while miR-137 functions as a pro-neuronal differentiation miRNA. In gliomas, miR-137 functions as a tumor suppressor while Msi1 is a pro-oncogenic factor...
April 19, 2019: RNA
Ya-Lan Tan, Chen-Jie Feng, Lei Jin, Ya-Zhou Shi, Wenbing Zhang, Zhi-Jie Tan
Knowledge-based statistical potentials have been shown to be efficient in protein structure evaluation/prediction, and the core difference between various statistical potentials is attributed to the choice of reference states. However, for RNA 3D structure evaluation, a comprehensive examination on reference states is still lacking. In this work, we built six statistical potentials based on six reference states widely used in protein structure evaluation, including averaging, quasi-chemical approximation, atom-shuffled, finite-ideal-gas, spherical-non-interacting and random-walk-chain reference states, and examined the six reference states against three RNA test sets including six subsets...
April 17, 2019: RNA
Ahmad Siam, Mai Baker, Leah Amit, Gal Regev, Alona Rabner, Rauf Ahmad Najar, Mercedes Bentata, Sara Dahan, Klil Cohen, Sarah Araten, Yuval Nevo, Gillian Kay, Yael Mandel-Gutfreund, Maayan Salton
Splicing of precursor mRNA (pre-mRNA) is an important regulatory step in gene expression. Recent evidence points to a regulatory role of chromatin-related proteins in alternative splicing regulation. Using an unbiased approach, we have identified the acetyltransferase p300 as a key chromatin-related regulator of alternative splicing. p300 promotes genome-wide exon inclusion in both a transcription-dependent and ‑independent manner. Using CD44 as a paradigm, we found that p300 regulates alternative splicing by modulating the binding of splicing factors to pre-mRNA...
April 15, 2019: RNA
Mateusz Wawro, Karolina Wawro, Jakub Kochan, Aleksandra Solecka, Weronika Sowinska, Agata Lichawska-Cieslar, Jolanta Jura, Aneta Kasza
ZC3H12B is the most enigmatic member of the ZC3H12 protein family. The founding member of this family, Regnase-1/MCPIP1/ZC3H12A, is a well-known modulator of inflammation and is involved in the degradation of inflammatory mRNAs. In this study, for the first time, we characterized the properties of the ZC3H12B protein. We show that the biological role of ZC3H12B depends on an intact NYN/PIN RNase domain. Using RNA immunoprecipitation,experiments utilizing actinomycin D and ELISA, we show that ZC3H12B binds endogenous proinflammatory interleukin-6 (IL-6) mRNA in vivo, regulates its turnover and results in reduced production of IL-6 protein upon proinflammattory stimulation with IL 1β...
April 15, 2019: RNA
Susan E Liao, Suresh K Kandasamy, Li Zhu, Ryuya Fukunaga
Drosophila Belle (human ortholog DDX3) is a conserved DEAD-box RNA helicase implicated in regulating gene expression. However, the molecular mechanisms by which Belle/DDX3 regulates gene expression are poorly understood. Here we performed systematic mutational analysis of Belle to determine the contributions of conserved motifs within Belle to its in vivo function. We found that Belle RNA-binding and RNA-unwinding activities and intrinsically disordered regions (IDRs) are required for Belle in vivo function...
April 12, 2019: RNA
Jeffrey Zuber, David H Mathews
Nearest neighbor parameters for estimating the folding stability of RNA are commonly used in secondary structure prediction, for generating folding ensembles of structures, and for analyzing RNA function. Previously, we demonstrated that we could quantify the uncertainties in each nearest neighbor parameter by perturbing the underlying optical melting data within experimental error and rederiving the parameters, which accounts for the substantial correlations that exist between the parameters. In this contribution, we describe a method to estimate uncertainty in the estimated folding stabilities of RNA structures, accounting for correlations in the nearest neighbor parameters...
April 5, 2019: RNA
Lee-Ya Chu, Sashank Agrawal, Yi-Ping Chen, Wei-Zen S Yang, Hanna S Yuan
Human RNA exoribonuclease 2 (Rexo2) is an evolutionarily conserved 3'-to-5' DEDDh-family exonuclease located primarily in mitochondria. Rexo2 degrades small RNA oligonucleotides of less than five nucleotides (nanoRNA) in a way similar to E. coli Oligoribonuclease (ORN), suggesting that it plays a role in RNA turnover in mitochondria. However, how Rexo2 preferentially binds and degrades nanoRNA remains elusive. Here, we show that Rexo2 binds small RNA and DNA oligonucleotides with the highest affinity, and it is most robust in degrading small nanoRNA into mononucleotides in the presence of magnesium ions...
March 29, 2019: RNA
Winston R Becker, Inga Jarmoskaite, Pavanapuresan P Vaidyanathan, William J Greenleaf, Daniel Herschlag
Post-translational gene regulation requires a complex network of RNA/protein interactions. Cooperativity, which tunes response sensitivities, originates from protein-protein interactions in many systems. For RNA binding proteins, cooperativity can also be mediated through RNA structure. RNA structural cooperativity (RSC) arises when binding of one protein induces a redistribution of RNA conformational states that enhance access (positive cooperativity) or block access (negative cooperativity) to additional binding sites...
March 26, 2019: RNA
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