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RNA Biology

Ishita Jain, Leonid Minakhin, Vladimir Mekler, Vasily Sitnik, Natalia Rubanova, Konstantin Severinov, Ekaterina Semenova
Target binding by CRISPR-Cas ribonucleoprotein effectors is initiated by the recognition of double-stranded PAM motifs by the Cas protein moiety followed by destabilization, localized melting, and interrogation of the target by the guide part of CRISPR RNA moiety. The latter process depends on seed sequences, parts of the target that must be strictly complementary to CRISPR RNA guide. Mismatches between the target and CRISPR RNA guide outside the seed have minor effects on target binding, thus contributing to off-target activity of CRISPR-Cas effectors...
July 19, 2018: RNA Biology
Simon Huck, Josephine Bock, Jörg Girardello, Marc Gauert, Ümit Pul
In this communication, we report the adaptation of the CRISPR-Cas9 technology in Ustilago trichophora prototrophic wild-type isolate obtained from its natural host Echinochloa crus-galli. The established CRISPR vector and method enable a rapid and marker-free introduction of Cas9-induced non-homologous end-joining (NHEJ) dependent mutation at the targeted gene. Moreover, the method allows a specific modification of the chromosomal DNA sequence by Cas9-induced homologous recombination using short DNA repair templates...
July 12, 2018: RNA Biology
Wolfgang R Hess, Shengwei Hou, Manuel Brenes-Álvarez, Viktoria Reimann, Omer S Alkhnbashi, Rolf Backofen, Alicia M Muro-Pastor
Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor >40 different putative CRISPR repeat-spacer cassettes, while the number of cas gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria...
July 11, 2018: RNA Biology
Kawanda Foster, Joshua Kalter, Walter Woodside, Rebecca M Terns, Michael P Terns
CRISPR-Cas systems provide prokaryotes with RNA-based adaptive immunity against viruses and plasmids. A unique feature of Type III CRISPR-Cas systems is that they selectively target transcriptionally-active invader DNA, and can cleave both the expressed RNA transcripts and source DNA. The Type III-A effector crRNP (CRISPR RNA-Cas protein complex), which contains Cas proteins Csm1-5, recognizes and degrades invader RNA and DNA in a crRNA-guided, manner. Interestingly, Type III-A systems also employ Csm6, an HEPN family ribonuclease that does not stably associate with the Type III-A effector crRNP, but nevertheless contributes to defense via mechanistic details that are still being determined...
July 11, 2018: RNA Biology
Huafeng Zhang, Dongzhe Li, Yi Zhang, Jianqiang Li, Shengli Ma, Jianwei Zhang, Yuanyuan Xiong, Wengang Wang, Ning Li, Lei Xia
Objective The present study was designed to investigate the molecular mechanism and biological roles of lncRNA brain-derived neurotrophic factor antisense (lncRNA BDNF-AS) in acute spinal cord injury (ASCI). Methods The rat model of ASCI and hypoxic cellular model were established to detect the expression of BDNF-AS, miR-130b-5p, PR (PRDI-BF1 and RIZ) domain protein 5 (PRDM5) and cleaved caspase 3 (c-caspase 3) using qRT-PCR and western blot. Basso, Beattie and Bresnahan (BBB) score was carried out to assess neurological function...
July 11, 2018: RNA Biology
Teyuan Chyou, Chris M Brown
Type II CRISPR-Cas9 systems require a small RNA called the trans-activating CRISPR RNA (tracrRNA) in order to function. The prediction of these non-coding RNAs in prokaryotic genomes is challenging because they have dissimilar structures, having short stems (3-6 bp) and non-canonical base-pairs e.g. G-A. Much of the tracrRNA is involved in base-pairing interactions with the CRISPR RNA, or itself, or in RNA-protein interactions with Cas9. Here we develop a new bioinformatic tool to predict tracrRNAs. On an experimentally verified test set the algorithm achieved a high sensitivity and specificity, and a low false discovery rate (FDR) on genome analysis...
July 11, 2018: RNA Biology
Joice de Faria Poloni, Diego Bonatto
Cancer metastasis is defined as the dissemination of malignant cells from the primary tumor site, leading to colonization of distant organs and the establishment of a secondary tumor. Metastasis is frequently associated with chemoresistance and is the major cause of cancer-related mortality. Metastatic cells need to acquire the ability to resist to stresses provided by different environments, such as reactive oxygen species, shear stress, hemodynamic forces, stromal composition, and immune responses, to colonize other tissues...
July 9, 2018: RNA Biology
Demián Cazalla
Viruses masterfully regulate host gene expression during infection. Many do so, in part, by expressing non-coding RNAs. Recent work has shown that HSUR 2, a viral non-coding RNA expressed by the oncogenic Herpesvirus saimiri, regulates mRNA expression through a novel mechanism. HSUR 2 base pairs with both target mRNAs and host miRNAs in infected cells. This results in HSUR 2-dependent recruitment of host miRNAs and associated Ago proteins to target mRNAs, and the subsequent destabilization of target mRNAs. Using this mechanism, this virus regulates key cellular pathways during viral infection...
July 9, 2018: RNA Biology
Zhen Liao, Jonas Kjellin, Marc P Hoeppner, Manfred Grabherr, Fredrik Söderbom
Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals...
July 3, 2018: RNA Biology
Wei Lun Ng, Taznim Begam Mohd Mohidin, Kirti Shukla
Circular RNAs (circRNAs) are a large class of endogenously expressed non-coding RNAs formed by covalently closed loops through back-splicing. High throughput sequencing technologies have identified thousands of circRNAs with high sequence conservation and cell type specific expression in eukaryotes. CircRNAs play multiple important roles in cellular physiology functioning as miRNA sponges, transcriptional regulators, RBP binding molecules, templates for protein translation, and immune regulators. In a clinical context, circRNAs expression is correlated with patient's clinicopathological features in cancers including breast, liver, gastric, colorectal, and lung cancer...
June 28, 2018: RNA Biology
Noé Dubois, Keith K Khoo, Shannon Ghossein, Tanja Seissler, Philippe Wolff, William J McKinstry, Johnson Mak, Jean-Christophe Paillart, Roland Marquet, Serena Bernacchi
The Pr55Gag precursor specifically selects the HIV-1 genomic RNA (gRNA) from a large excess of cellular and partially or fully spliced viral RNAs and drives the virus assembly at the plasma membrane. During these processes, the NC domain of Pr55Gag interacts with the gRNA, while its C-terminal p6 domain binds cellular and viral factors and orchestrates viral particle release. Gag∆p6 is a truncated form of Pr55Gag lacking the p6 domain usually used as a default surrogate for wild type Pr55Gag for in vitro analysis...
June 28, 2018: RNA Biology
Soh Ishiguro, Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei
Adenosine deaminases acting on RNA (ADARs) catalyze the deamination of adenosine (A) to inosine (I). A-to-I RNA editing targets double-stranded RNA (dsRNA), and increases the complexity of gene regulation by modulating base pairing-dependent processes such as splicing, translation, and microRNA (miRNA)-mediated gene silencing. This study investigates the genome-wide binding preferences of the nuclear constitutive isoforms ADAR1-p110 and ADAR2 on human miRNA species by RNA immunoprecipitation of ADAR-bound small RNAs (RIP-seq)...
June 27, 2018: RNA Biology
Aleksandra Swida-Barteczka, Anja Krieger-Liszkay, Wolfgang Bilger, Ulrike Voigt, Götz Hensel, Zofia Szweykowska-Kulinska, Karin Krupinska
In this article a novel mechanism of retrograde signaling by chloroplasts during stress is described. This mechanism involves the DNA/RNA binding protein WHIRLY1 as a regulator of microRNA levels. By virtue of its dual localization in chloroplasts and the nucleus of the same cell, WHIRLY1 was proposed as an excellent candidate coordinator of chloroplast function and nuclear gene expression. Comparison of wild-type and transgenic plants with an RNAi-mediated knockdown of WHIRLY1 showed, that the transgenic plants were unable to cope with continuous high light conditions...
June 27, 2018: RNA Biology
Finn Kirpekar, Lykke H Hansen, Julie Mundus, Stine Tryggedsson, Patrícia Teixeira Dos Santos, Eleni Ntokou, Birte Vester
All organisms contain RNA modifications in their ribosomal RNA (rRNA), but the importance, positions and exact function of these are still not fully elucidated. Various functions such as stabilising structures, controlling ribosome assembly and facilitating interactions have been suggested and in some cases substantiated. Bacterial rRNA contains much fewer modifications than eukaryotic rRNA. The rRNA modification patterns in bacteria differ from each other, but too few organisms have been mapped to draw general conclusions...
June 27, 2018: RNA Biology
Eric D Nguyen, Maggie M Balas, April M Griffin, Justin T Roberts, Aaron M Johnson
Long noncoding RNAs (lncRNAs) often carry out their functions through associations with adaptor proteins. We recently identified heterogeneous ribonucleoprotein (hnRNP) A2/B1 as an adaptor of the human HOTAIR lncRNA. hnRNP A2 and B1 are splice isoforms of the same gene. The spliced version of HOTAIR preferentially associates with the B1 isoform, which we hypothesize contributes to RNA-RNA matching between HOTAIR and transcripts of target genes in breast cancer. Here we used enhanced cross-linking immunoprecipitation (eCLIP) to map the direct interactions between A2/B1 and RNA in breast cancer cells...
June 23, 2018: RNA Biology
Farah Mustafa, Valérie Vivet-Boudou, Ayesha Jabeen, Lizna M Ali, Rawan M Kalloush, Roland Marquet, Tahir A Rizvi
Packaging the mouse mammary tumor virus (MMTV) genomic RNA (gRNA) requires the entire 5' untranslated region (UTR) in conjunction with the first 120 nucleotides of the gag gene. This region includes several palindromic (pal) sequence(s) and stable stem loops (SLs). Among these, stem loop 4 (SL4) adopts a bifurcated structure consisting of three stems, two apical loops, and an internal loop. Pal II, located in one of the apical loops, mediates gRNA dimerization, a process intricately linked to packaging. We thus hypothesized that the bifurcated SL4 structure could constitute the major gRNA packaging determinant...
June 21, 2018: RNA Biology
Kirtika H Asrani, Lei Cheng, Christopher J Cheng, Romesh R Subramanian
Arginase I (ARG1) deficiency is an autosomal recessive urea cycle disorder, caused by deficiency of the enzyme Arginase I, resulting in accumulation of arginine in blood. Current Standard of Care (SOC) for ARG1 deficiency in patients or those having detrimental mutations of ARG1 gene is diet control. Despite diet and drug therapy with nitrogen scavengers, ~25% of patients suffer from severe mental deficits and loss of ambulation. 75% of patients whose symptoms can be managed through diet therapy continue to suffer neuro-cognitive deficits...
June 20, 2018: RNA Biology
Yael Yair-Helman, Uri Gophna
CRISPR-Cas systems are a highly effective immune mechanism for prokaryotes, providing defense against invading foreign DNA. By definition, all CRISPR-Cas systems have short repeats interspersing their spacers. These repeats play a key role in preventing cleavage of self DNA and in the integration of new spacers. Here we focus on the phenomenon of repeat modularity, namely the unexpectedly high degree of repeat conservation across different systems within a genome or between different species. We hypothesize that modularity can be beneficial for CRISPR-Cas containing organisms, because it facilitates horizontal acquisition of "pre-immunized" CRISPR arrays and allows the utilization of spacers acquired by one system for use by other systems within the same cell...
June 20, 2018: RNA Biology
Shiraz A Shah, Omer S Alkhnbashi, Juliane Behler, Wenyuan Han, Qunxin She, Wolfgang R Hess, Roger A Garrett, Rolf Backofen
A study was undertaken to identify conserved proteins that are encoded adjacent to cas gene cassettes of Type III CRISPR-Cas (Clusters of Regularly IntersSpaced Palindromic Repeats - CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families...
June 18, 2018: RNA Biology
Oscar Vargas-Rodriguez, Markus Englert, Anna Merkuryev, Takahito Mukai, Dieter Söll
In many organisms, the UGA stop codon is recoded to insert selenocysteine (Sec) into proteins. Sec incorporation in bacteria is directed by an mRNA element, known as the Sec-insertion sequence (SECIS), located downstream of the Sec codon. Unlike other aminoacyl-tRNAs, Sec-tRNASec is delivered to the ribosome by a dedicated elongation factor, SelB. We recently identified a series of tRNASec -like tRNA genes distributed across Bacteria that also encode a canonical tRNASec . These tRNAs contain sequence elements generally recognized by cysteinyl-tRNA synthetase (CysRS)...
June 18, 2018: RNA Biology
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