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Rna editing

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https://www.readbyqxmd.com/read/29223796/species-specific-rna-a-to-i-editing-of-mosquito-rdl-modulates-gaba-potency-and-influences-agonistic-potentiating-and-antagonistic-actions-of-ivermectin
#1
Jennina Taylor-Wells, Anish Senan, Isabel Bermudez, Andrew K Jones
The insect GABA receptor, RDL, is the target of several classes of pesticides. The peptide sequences of RDL are generally highly conserved between diverse insects. However, RNA A-to-I editing can effectively alter amino acid residues of RDL in a species specific manner, which can affect the potency of GABA and possibly insecticides. We report here that RNA A-to-I editing alters the gene products of Rdl in three mosquito disease vectors, recoding five amino acid residues in RDL of Aedes aegypti and six residues in RDLs of Anopheles gambiae and Culex pipiens, which is the highest extent of editing in RDL observed to date...
December 6, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29223164/the-mitochondrial-genome-of-the-moss-brachythecium-rivulare-hypnales-brachytheciaceae
#2
D V Goryunov, M D Logacheva, M S Ignatov, I A Milyutina, A V Fedorova, A V Troitsky
The mitochondrial genome of the pleurocarpous moss Brachythecium rivulare has been sequenced and annotated. The genome consists of 104,460 base pairs and has approximately the same gene set and organization as other bryophyte mitogenomes. Whole mitochondrial genome comparison between B. rivulare and Physcomitrella patens, Tetraphis pellucida, Anomodon rugelii, and Anomodon attenuatus was performed. The primary cause of bryophyte mitochondrial gene length variation was found to be numerous indels in the introns...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29222070/regulation-of-trna-biogenesis-in-plants-and-its-link-to-plant-growth-and-response-to-pathogens
#3
REVIEW
Adriana Santos Soprano, Juliana Helena Costa Smetana, Celso Eduardo Benedetti
tRNA biology has fascinated scientists over the years. Besides their fundamental role in protein translation, new evidence indicates that tRNA-derived molecules also regulate gene expression and protein synthesis in all domains of life. In this review, we will highlight some of the recent findings linking tRNA transcription and modification with plant cell growth and response to pathogens. In fact, mutations in proteins directly involved in tRNA synthesis and modification most often lead to pleiotropic effects on plant growth and immunity...
December 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29221488/divergent-susceptibilities-to-aav-sacas9-grna-vector-mediated-genome-editing-in-a-single-cell-derived-cell-population
#4
Salma G Morsy, Jason M Tonne, Yaxi Zhu, Brian Lu, Karol Budzik, James W Krempski, Sherine A Ali, Mohamed A El-Feky, Yasuhiro Ikeda
OBJECTIVE: Recombinant adeno-associated virus (AAV)-based vectors are characterized by their robust and safe transgene delivery. The CRISPR/Cas9 and guide RNA (gRNA) system present a promising genome-editing platform, and a recent development of a shorter Cas9 enzyme from Staphylococcus aureus (SaCas9) allows generation of high titer single AAV vectors which carry both saCas9- and gRNA-expression cassettes. Here, we used two AAV-SaCas9 vectors with distinct GFP-targeted gRNA sequences and determined the impact of AAV-SaCas9-gRNA vector treatment in a single cell clone carrying a GFP-expression cassette...
December 8, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29220521/trypanosomatid-mitochondrial-rna-editing-dramatically-complex-transcript-repertoires-revealed-with-a-dedicated-mapping-tool
#5
Evgeny S Gerasimov, Anna A Gasparyan, Iosif Kaurov, Boris Tichý, Maria D Logacheva, Alexander A Kolesnikov, Julius Lukeš, Vyacheslav Yurchenko, Sara L Zimmer, Pavel Flegontov
RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3' to 5' on a transcript, resulting in a population of partially edited as well as pre-edited and completely edited molecules for each mitochondrial cryptogene of these protozoans. Often, the number of uridines inserted and deleted exceed the number of nucleotides that are genome-encoded...
December 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29219081/whole-genome-analysis-of-crispr-cas9-sgrna-off-target-homologies-via-an-efficient-computational-algorithm
#6
Hong Zhou, Michael Zhou, Daisy Li, Joseph Manthey, Ekaterina Lioutikova, Hong Wang, Xiao Zeng
BACKGROUND: The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA, single guide RNA (sgRNA), to cleave double stranded DNA, allowing the introduction of wanted mutations. Unfortunately, it has been reported repeatedly that the sgRNA can also guide Cas9 to off-target sites where the DNA sequence is homologous to sgRNA. RESULTS: Using human genome and Streptococcus pyogenes Cas9 (SpCas9) as an example, this article mathematically analyzed the probabilities of off-target homologies of sgRNAs and discovered that for large genome size such as human genome, potential off-target homologies are inevitable for sgRNA selection...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29218706/genome-wide-rna-seq-identifies-fas-fasl-mediated-tumoricidal-activity-of-embryonic-stem-cells
#7
Yatong Li, Yongna Fan, Jing Xu, Peng Zhang, Taijiao Jiang, Menghua Dai, Limin Li
The discovery of tumor tropism of stem cells revealed the intimate relationship between stem cells and tumor cells, but the functional role of stem cells in tumorigenesis is poorly understood. To investigate embryonic stem cell (ESC) and tumor cell interactions, we co-cultured mouse ESCs with mouse melanoma B16-F10 cells or mouse pancreatic tumor Pan02 cells, and found that ESCs significantly inhibited tumor cell proliferation. Coculture of ESCs and tumor cells resulted in significant inhibition of tumorigenesis in vivo...
December 8, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29216369/the-pentatricopeptide-repeat-protein-mef31-is-required-for-editing-at-site-581-of-the-tatc-transcript-and-indirectly-influences-editing-at-site-586-of-the-same-transcript
#8
Anita Arenas-M, Enrique González-Durán, Isabel Gómez, Matthias Burger, Axel Brennicke, Mizuki Takenaka, Xavier Jordana
Pentatricopeptide repeat (PPR) proteins constitute the largest family of proteins in angiosperms and most members are predicted to play roles in the maturation of organellar RNAs. Here we describe the novel Mitochondrial Editing Factor 31 (MEF31), an E-PPR protein involved in editing at two near sites in the same transcript encoding subunit C of the twin-arginine translocation (tat) pathway. MEF31 is essential for editing at site tatC-581 and application of the recently proposed amino acid code for RNA recognition by PPR proteins supports the view that MEF31 directly targets this site by recognizing its cis sequence...
December 4, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29213323/defined-tetra-allelic-gene-disruption-of-the-4-coumarate-coenzyme-a-ligase-1-pv4cl1-gene-by-crispr-cas9-in-switchgrass-results-in-lignin-reduction-and-improved-sugar-release
#9
Jong-Jin Park, Chang Geun Yoo, Amy Flanagan, Yunqiao Pu, Smriti Debnath, Yaxin Ge, Arthur J Ragauskas, Zeng-Yu Wang
Background: The development of genome editing technologies offers new prospects in improving bioenergy crops like switchgrass (Panicum virgatum). Switchgrass is an outcrossing species with an allotetraploid genome (2n = 4x = 36), a complexity which forms an impediment to generating homozygous knock-out plants. Lignin, a major component of the plant cell wall and a contributor to cellulosic feedstock's recalcitrance to decomposition, stands as a barrier to efficient biofuel production by limiting enzyme access to cell wall polymers during the fermentation process...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29213239/dynamic-editome-of-zebrafish-under-aminoglycosides-treatment-and-its-potential-involvement-in-ototoxicity
#10
Sijia Yan, Yulan Lu, Lin He, Xinzhi Zhao, Lihua Wu, Huizhong Zhu, Menglin Jiang, Yu Su, Wei Cao, Weidong Tian, Qinghe Xing
RNA editing is an important co- and post-transcriptional event that generates RNA and protein diversity. Aminoglycosides are a group of bactericidal antibiotics and a mainstay of antimicrobial therapy for several life-threatening infections. However, aminoglycosides can induce ototoxicity, resulting in damage to the organs responsible for hearing and balance. At low concentrations, aminoglycosides can bind to many RNA sequences and critically influence RNA editing. We used a bioinformatics approach to investigate the effect of aminoglycosides on global mRNA editing events to gain insight into the interactions between mRNA editing and aminoglycoside ototoxicity...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29213066/crispr-cas9-mediated-mutation-of-mouse-il-1%C3%AE-nuclear-localisation-sequence-abolishes-expression
#11
Michael J D Daniels, Antony D Adamson, Neil Humphreys, David Brough
Inflammation is a host defense process against infection. Inflammatory mediators include cytokines of the interleukin-1 family, such as IL-1α and IL-1β. Unlike IL-1β, IL-1α carries an N-terminal nuclear localisation sequence (NLS) and is trafficked to the nucleus. The importance of IL-1α nuclear localisation is poorly understood. Here, we used CRISPR/Cas9 to make inactivating mutations to the NLS on the Il1a gene. A colony of NLS mutant mice was successfully generated with precise knock-in mutations to incapacitate NLS function...
December 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29212218/optimized-guide-rna-structure-for-genome-editing-via-cas9
#12
Jianyong Xu, Wei Lian, Yuning Jia, Lingyun Li, Zhong Huang
The genome editing tool Cas9-gRNA (guide RNA) has been successfully applied in different cell types and organisms with high efficiency. However, more efforts need to be made to enhance both efficiency and specificity. In the current study, we optimized the guide RNA structure of Streptococcus pyogenes CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system to improve its genome editing efficiency. Comparing with the original functional structure of guide RNA, which is composed of crRNA and tracrRNA, the widely used chimeric gRNA has shorter crRNA and tracrRNA sequence...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29209299/natural-antisense-transcripts-at-the-interface-between-host-genome-and-mobile-genetic-elements
#13
Hany S Zinad, Inas Natasya, Andreas Werner
Non-coding RNAs are involved in epigenetic processes, playing a role in the regulation of gene expression at the transcriptional and post-transcriptional levels. A particular group of ncRNA are natural antisense transcripts (NATs); these are transcribed in the opposite direction to protein coding transcripts and are widespread in eukaryotes. Their abundance, evidence of phylogenetic conservation and an increasing number of well-characterized examples of antisense-mediated gene regulation are indicative of essential biological roles of NATs...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29208987/genome-wide-dna-methylation-changes-associated-with-olfactory-learning-and-memory-in-apis-mellifera
#14
You Li, Li-Zhen Zhang, Yao Yi, Wan-Wan Hu, Ya-Hui Guo, Zhi-Jiang Zeng, Zachary-Y Huang, Zi-Long Wang
The honeybee is a model organism for studying learning and memory formation and its underlying molecular mechanisms. While DNA methylation is well studied in caste differentiation, its role in learning and memory is not clear in honeybees. Here, we analyzed genome-wide DNA methylation changes during olfactory learning and memory process in A. mellifera using whole genome bisulfite sequencing (WGBS) method. A total of 853 significantly differentially methylated regions (DMRs) and 963 differentially methylated genes (DMGs) were identified...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208606/emerging-role-of-crispr-cas9-technology-for-micrornas-editing-in-cancer-research
#15
REVIEW
Guillermo Aquino-Jarquin
MicroRNAs (miRNA) are small, noncoding RNA molecules with a master role in the regulation of important tasks in different critical processes of cancer pathogenesis. Because there are different miRNAs implicated in all the stages of cancer, for example, functioning as oncogenes, this makes these small molecules suitable targets for cancer diagnosis and therapy. RNA-mediated interference has been one major approach for sequence-specific regulation of gene expression in eukaryotic organisms. Recently, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system, first identified in bacteria and archaea as an adaptive immune response to invading genetic material, has been explored as a sequence-specific molecular tool for editing genomic sequences for basic research in life sciences and for therapeutic purposes...
December 5, 2017: Cancer Research
https://www.readbyqxmd.com/read/29207996/crispr-cas9-mediated-gene-deletions-in-lager-yeast-saccharomyces-pastorianus
#16
Arthur R Gorter de Vries, Philip A de Groot, Marcel van den Broek, Jean-Marc G Daran
BACKGROUND: The ease of use of CRISPR-Cas9 reprogramming, its high efficacy, and its multiplexing capabilities have brought this technology at the forefront of genome editing techniques. Saccharomyces pastorianus is an aneuploid interspecific hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus that has been domesticated for centuries and is used for the industrial fermentation of lager beer. For yet uncharacterised reasons, this hybrid yeast is far more resilient to genetic alteration than its ancestor S...
December 5, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29207527/efficient-generation-of-somatic-cell-nuclear-transfer-competent-porcine-cells-with-mutated-alleles-at-multiple-target-loci-by-using-crispr-cas9-combined-with-targeted-toxin-based-selection-system
#17
Masahiro Sato, Kazuchika Miyoshi, Shingo Nakamura, Masato Ohtsuka, Takayuki Sakurai, Satoshi Watanabe, Hiroaki Kawaguchi, Akihide Tanimoto
The recent advancement in genome editing such a CRISPR/Cas9 system has enabled isolation of cells with knocked multiple alleles through a one-step transfection. Somatic cell nuclear transfer (SCNT) has been frequently employed as one of the efficient tools for the production of genetically modified (GM) animals. To use GM cells as SCNT donor, efficient isolation of transfectants with mutations at multiple target loci is often required. The methods for the isolation of such GM cells largely rely on the use of drug selection-based approach using selectable genes; however, it is often difficult to isolate cells with mutations at multiple target loci...
December 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29205437/mrna-traffic-control-reviewed-n6-methyladenosine-m6-a-takes-the-driver-s-seat
#18
REVIEW
Abhirami Visvanathan, Kumaravel Somasundaram
Messenger RNA is a flexible tool box that plays a key role in the dynamic regulation of gene expression. RNA modifications variegate the message conveyed by the mRNA. Similar to DNA and histone modifications, mRNA modifications are reversible and play a key role in the regulation of molecular events. Our understanding about the landscape of RNA modifications is still rudimentary in contrast to DNA and histone modifications. The major obstacle has been the lack of sensitive detection methods since they are non-editing events...
December 4, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29203771/alu-dependent-rna-editing-of-gli1-promotes-malignant-regeneration-in-multiple-myeloma
#19
Elisa Lazzari, Phoebe K Mondala, Nathaniel Delos Santos, Amber C Miller, Gabriel Pineda, Qingfei Jiang, Heather Leu, Shawn A Ali, Anusha-Preethi Ganesan, Christina N Wu, Caitlin Costello, Mark Minden, Raffaella Chiaramonte, A Keith Stewart, Leslie A Crews, Catriona H M Jamieson
Despite novel therapies, relapse of multiple myeloma (MM) is virtually inevitable. Amplification of chromosome 1q, which harbors the inflammation-responsive RNA editase adenosine deaminase acting on RNA (ADAR)1 gene, occurs in 30-50% of MM patients and portends a poor prognosis. Since adenosine-to-inosine RNA editing has recently emerged as a driver of cancer progression, genomic amplification combined with inflammatory cytokine activation of ADAR1 could stimulate MM progression and therapeutic resistance. Here, we report that high ADAR1 RNA expression correlates with reduced patient survival rates in the MMRF CoMMpass data set...
December 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/29202216/type-ii-c-crispr-cas9-biology-mechanism-and-application
#20
Aamir Mir, Alireza Edraki, Jooyoung Lee, Erik J Sontheimer
Genome editing technologies have been revolutionized by the discovery of prokaryotic RNA-guided defense system called CRISPR-Cas. Cas9, a single effector protein found in type II CRISPR systems, has been at the heart of this genome editing revolution. Nearly half of the Cas9s discovered so far belong to the type II-C subtype, but have not been explored extensively. Type II-C CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins. Cas9s are central players in type II-C systems since they function in multiple steps of the CRISPR pathway, including adaptation and interference...
December 4, 2017: ACS Chemical Biology
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