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Rna editing

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https://www.readbyqxmd.com/read/28211909/a-crispr-cpf1-system-for-efficient-genome-editing-and-transcriptional-repression-in-plants
#1
Xu Tang, Levi G Lowder, Tao Zhang, Aimee A Malzahn, Xuelian Zheng, Daniel F Voytas, Zhaohui Zhong, Yiyi Chen, Qiurong Ren, Qian Li, Elida R Kirkland, Yong Zhang, Yiping Qi
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cpf1 has emerged as an effective genome editing tool in animals. Here we compare the activity of Cpf1 from Acidaminococcus sp. BV3L6 (As) and Lachnospiraceae bacterium ND2006 (Lb) in plants, using a dual RNA polymerase II promoter expression system. LbCpf1 generated biallelic mutations at nearly 100% efficiency at four independent sites in rice T0 transgenic plants. Moreover, we repurposed AsCpf1 and LbCpf1 for efficient transcriptional repression in Arabidopsis, and demonstrated a more than tenfold reduction in miR159b transcription...
February 17, 2017: Nature Plants
https://www.readbyqxmd.com/read/28209587/genome-surgery-using-cas9-ribonucleoproteins-for-the-treatment-of-age-related-macular-degeneration
#2
Kyoungmi Kim, Sung Wook Park, Jin Hyoung Kim, Seung Hwan Lee, Daesik Kim, Taeyoung Koo, Kwang-Eun Kim, Jeong Hun Kim, Jin-Soo Kim
RNA-guided genome surgery using CRISPR-Cas9 nucleases has shown promise for the treatment of diverse genetic diseases. Yet, the potential of such nucleases for therapeutic applications in nongenetic diseases is largely unexplored. Here, we focus on age-related macular degeneration (AMD), a leading cause of blindness in adults, which is associated with retinal overexpression of, rather than mutations in, the VEGFA gene. Subretinal injection of preassembled, Vegfa gene-specific Cas9 ribonucleoproteins (RNPs) into the adult mouse eye gave rise to mutagenesis at the target site in the retinal pigment epithelium...
February 16, 2017: Genome Research
https://www.readbyqxmd.com/read/28208729/altered-intracellular-milieu-of-adar2-deficient-motor-neurons-in-amyotrophic-lateral-sclerosis
#3
REVIEW
Takenari Yamashita, Megumi Akamatsu, Shin Kwak
Transactive response DNA-binding protein (TDP-43) pathology, and failure of A-to-I conversion (RNA editing) at the glutamine/arginine (Q/R) site of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor subunit GluA2, are etiology-linked molecular abnormalities that concomitantly occur in the motor neurons of most patients with amyotrophic lateral sclerosis (ALS). Adenosine deaminase acting on RNA 2 (ADAR2) specifically catalyzes GluA2 Q/R site-RNA editing. Furthermore, conditional ADAR2 knockout mice (AR2) exhibit a progressive ALS phenotype with TDP-43 pathology in the motor neurons, which is the most reliable pathological marker of ALS...
February 8, 2017: Genes
https://www.readbyqxmd.com/read/28208661/differential-binding-of-three-major-human-adar-isoforms-to-coding-and-long-non-coding-transcripts
#4
Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
RNA editing by deamination of adenosine to inosine is an evolutionarily conserved process involved in many cellular pathways, from alternative splicing to miRNA targeting. In humans, it is carried out by no less than three major adenosine deaminases acting on RNA (ADARs): ADAR1-p150, ADAR1-p110, and ADAR2. However, the first two derive from alternative splicing, so that it is currently impossible to delete ADAR1-p110 without also knocking out ADAR1-p150 expression. Furthermore, the expression levels of ADARs varies wildly among cell types, and no study has systematically explored the effect of each of these isoforms on the cell transcriptome...
February 11, 2017: Genes
https://www.readbyqxmd.com/read/28205546/crispr-cpf1-mediated-dna-free-plant-genome-editing
#5
Hyeran Kim, Sang-Tae Kim, Jahee Ryu, Beum-Chang Kang, Jin-Soo Kim, Sang-Gyu Kim
Cpf1, a type V CRISPR effector, recognizes a thymidine-rich protospacer-adjacent motif and induces cohesive double-stranded breaks at the target site guided by a single CRISPR RNA (crRNA). Here we show that Cpf1 can be used as a tool for DNA-free editing of plant genomes. We describe the delivery of recombinant Cpf1 proteins with in vitro transcribed or chemically synthesized target-specific crRNAs into protoplasts isolated from soybean and wild tobacco. Designed crRNAs are unique and do not have similar sequences (≤3 mismatches) in the entire soybean reference genome...
February 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28204845/mirnas-target-databases-developmental-methods-and-target-identification-techniques-with-functional-annotations
#6
REVIEW
Nagendra Kumar Singh
PURPOSE: microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by binding perfect or near perfect or imperfect complementary base pairs by RNA-induced silencing complex (RISC) formation during biogenesis process. One miRNA interacts with one or more mRNA genes and vice versa, hence takes part in causing various diseases...
February 15, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28202609/increased-nuclear-adar2-enhances-rna-editing
#7
(no author information available yet)
No abstract text is available yet for this article.
February 15, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28201607/crystal-structures-of-the-arabidopsis-thaliana-organellar-rna-editing-factors-morf1-and-morf9
#8
Sascha Haag, Magdalena Schindler, Leona Berndt, Axel Brennicke, Mizuki Takenaka, Gert Weber
No abstract text is available yet for this article.
February 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28199207/assessing-the-potential-function-of-adar1-in-virus-associated-sepsis
#9
Yugang Zhuang, Hu Peng, Yuanzhuo Chen, Shuqin Zhou, Yanqing Chen
Sepsis syndrome is a common and frequently fatal clinical condition. It is defined by the presence of both infection and an uncontrolled systemic inflammatory response. It represents a major, although largely unappreciated, healthcare problem worldwide. It is especially problematic in infants and toddlers who show markedly increased susceptibility to severe infections caused by various pathogens, including viruses. Viruses are important causative agents of sepsis. Host adenosine deaminase acting on RNA 1 (ADAR1) catalyzes adenosine to inosine (A-to-I) editing of RNA transcripts, thus changing viral RNAs and exerting antiviral and proviral effects...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28198371/method-for-dual-viral-vector-mediated-crispr-cas9-gene-disruption-in-primary-human-endothelial-cells
#10
Haixia Gong, Menglin Liu, Jeff Klomp, Bradley J Merrill, Jalees Rehman, Asrar B Malik
Human endothelial cells (ECs) are widely used to study mechanisms of angiogenesis, inflammation, and endothelial permeability. Targeted gene disruption induced by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-Associated Protein 9 (Cas9) nuclease gene editing is potentially an important tool for definitively establishing the functional roles of individual genes in ECs. We showed that co-delivery of adenovirus encoding EGFP-tagged Cas9 and lentivirus encoding a single guide RNA (sgRNA) in primary human lung microvascular ECs (HLMVECs) disrupted the expression of the Tie2 gene and protein...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28197904/roles-of-sumoylation-in-mrna-processing-and-metabolism
#11
Patricia Richard, Vasupradha Vethantham, James L Manley
SUMO has gained prominence as a regulator in a number of cellular processes. The roles of sumoylation in RNA metabolism, however, while considerable, remain less well understood. In this chapter we have assembled data from proteomic analyses, localization studies and key functional studies to extend SUMO's role to the area of mRNA processing and metabolism. Proteomic analyses have identified multiple putative sumoylation targets in complexes functioning in almost all aspects of mRNA metabolism, including capping, splicing and polyadenylation of mRNA precursors...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28196963/genetic-predisposition-to-acquire-a-polybasic-cleavage-site-for-highly-pathogenic-avian-influenza-virus-hemagglutinin
#12
Naganori Nao, Junya Yamagishi, Hiroko Miyamoto, Manabu Igarashi, Rashid Manzoor, Aiko Ohnuma, Yoshimi Tsuda, Wakako Furuyama, Asako Shigeno, Masahiro Kajihara, Noriko Kishida, Reiko Yoshida, Ayato Takada
Highly pathogenic avian influenza viruses with H5 and H7 hemagglutinin (HA) subtypes evolve from low-pathogenic precursors through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been observed to occur naturally only in these HA subtypes, little is known about the genetic basis for the acquisition of the polybasic HA cleavage site. Here we show that consecutive adenine residues and a stem-loop structure, which are frequently found in the viral RNA region encoding amino acids around the cleavage site of low-pathogenic H5 and H7 viruses isolated from waterfowl reservoirs, are important for nucleotide insertions into this RNA region...
February 14, 2017: MBio
https://www.readbyqxmd.com/read/28196870/biallelic-insertion-of-a-transcriptional-terminator-via-crispr-cas9-efficiently-silences-expression-of-protein-coding-and-non-coding-rna-genes
#13
Yangyang Liu, Xiao Han, Junting Yuan, Tuoyu Geng, Shihao Chen, Xuming Hu, Isabelle H Cui, Hengmi Cui
The type II bacterial CRISPR/Cas9 system is a simple, convenient and powerful tool for gene editing that allows for gene targeting. Here, we describe a CRISPR/Cas9-based approach for silencing both protein-coding and non-protein-coding genes by biallelic integration of a PolyA signal. Because of the integration of a BGH PolyA signal into the target genes, gene expression was drastically terminated. Two anti-antibiotic genes were used as markers in the selection of clonal cell lines with biallelic integration of a PolyA signal...
February 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28195574/muscle-specific-crispr-cas9-dystrophin-gene-editing-ameliorates-pathophysiology-in-a-mouse-model-for-duchenne-muscular-dystrophy
#14
Niclas E Bengtsson, John K Hall, Guy L Odom, Michael P Phelps, Colin R Andrus, R David Hawkins, Stephen D Hauschka, Joel R Chamberlain, Jeffrey S Chamberlain
Gene replacement therapies utilizing adeno-associated viral (AAV) vectors hold great promise for treating Duchenne muscular dystrophy (DMD). A related approach uses AAV vectors to edit specific regions of the DMD gene using CRISPR/Cas9. Here we develop multiple approaches for editing the mutation in dystrophic mdx(4cv) mice using single and dual AAV vector delivery of a muscle-specific Cas9 cassette together with single-guide RNA cassettes and, in one approach, a dystrophin homology region to fully correct the mutation...
February 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28195308/ca-2-permeable-ampa-receptors-associated-with-epileptogenesis-of-hypothalamic-hamartoma
#15
Hiroki Kitaura, Masaki Sonoda, Sayaka Teramoto, Hiroshi Shirozu, Hiroshi Shimizu, Tadashi Kimura, Hiroshi Masuda, Yosuke Ito, Hitoshi Takahashi, Shin Kwak, Shigeki Kameyama, Akiyoshi Kakita
Hypothalamic hamartoma (HH), composed of neurons and glia without apparent cytologic abnormalities, is a rare developmental malformation in humans. Patients with HH often have characteristic medically refractory gelastic seizures, and intrinsic epileptogenesis within the lesions has been speculated. Herein we provide evidence to suggest that in HH neurons, Ca(2+) permeability through α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors is aberrantly elevated. In needle biopsy specimens of HH tissue, field potential recordings demonstrated spontaneous epileptiform activities similar to those observed in other etiologically distinct epileptogenic tissues...
February 13, 2017: Epilepsia
https://www.readbyqxmd.com/read/28195163/targeted-gene-knock-in-by-crispr-cas-ribonucleoproteins-in-porcine-zygotes
#16
Ki-Eun Park, Anne Powell, Shelley E S Sandmaier, Chan-Mi Kim, Alan Mileham, David M Donovan, Bhanu P Telugu
The domestic pig is an important "dual purpose" animal model for agricultural and biomedical applications. There is an emerging consensus in the biomedical community for the use of large animal models such as pigs to either serve as an alternative, or complement investigations from the mouse. However, the use of pig has not proven popular due to technical difficulties and time required in generating models with desired genetic modifications. In this regard, the ability to directly modify the genome in the zygote and generate edited animals is highly desirable...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28193726/genetic-basis-of-melanin-pigmentation-in-butterfly-wings
#17
Linlin Zhang, Arnaud Martin, Michael W Perry, Karin R L van der Burg, Yuji Matsuoka, Antónia Monteiro, Robert D Reed
Despite the variety, prominence, and adaptive significance of butterfly wing patterns surprisingly little known about the genetic basis of wing color diversity. Even though there is intense interest in wing pattern evolution and development, the technical challenge of genetically manipulating butterflies has slowed efforts to functionally characterize color pattern development genes. To identify candidate wing pigmentation genes we used RNA-seq to characterize transcription across multiple stages of butterfly wing development, and between different color pattern elements, in the painted lady butterfly Vanessa cardui This allowed us to pinpoint genes specifically associated with red and black pigment patterns...
February 13, 2017: Genetics
https://www.readbyqxmd.com/read/28188894/emerging-rna-editing-biomarkers-will-foster-drug-development
#18
REVIEW
Siem van der Laan, Nicolas Salvetat, Dinah Weissmann, Franck Molina
Unanticipated adverse drug reactions (ADRs) on the central nervous system are a major cause of clinical attrition and market withdrawal. Current practices for their prospective assessment still lean on extensive analysis of rodent behaviour despite their highly controversial predictive value. Human-derived in vitro models that objectively quantify mechanism-related biomarkers can greatly contribute to better ADR prediction at early developmental stages. Adenosine-to-inosine RNA editing constitutes a physiological cellular process that translates environmental cues by regulating protein function at the synaptic level in health and disease...
February 7, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28188287/a-to-i-rna-editing-up-regulates-human-dihydrofolate-reductase-in-breast-cancer
#19
Masataka Nakano, Tatsuki Fukami, Saki Gotoh, Miki Nakajima
Dihydrofolate reductase (DHFR) plays a key role in folate metabolism and is a target molecule of methotrexate. An increase in the cellular expression level of DHFR is one of the mechanisms of tumor resistance to methotrexate. The present study investigated the possibility that adenosine-to-inosine RNA editing, which causes nucleotide conversion by adenosine deaminase acting on RNA (ADAR) enzymes, might modulate DHFR expression. In human breast adenocarcinoma-derived MCF-7 cells, 26 RNA editing sites were identified in the 3'-UTR of DHFR...
February 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28186130/identification-of-symmetrical-rna-editing-events-in-the-mitochondria-of-salvia-miltiorrhiza-by-strand-specific-rna-sequencing
#20
Bin Wu, Haimei Chen, Junjie Shao, Hui Zhang, Kai Wu, Chang Liu
Salvia miltiorrhiza is one of the most widely-used medicinal plants. Here, we systematically analyzed the RNA editing events in its mitochondria. We developed a pipeline using REDItools to predict RNA editing events from stand-specific RNA-Seq data. The predictions were validated using reverse transcription, RT-PCR amplification and Sanger sequencing experiments. Putative sequences motifs were characterized. Comparative analyses were carried out between S. miltiorrhiza, Arabidopsis thaliana and Oryza sativa...
February 10, 2017: Scientific Reports
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