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https://www.readbyqxmd.com/read/28736447/prokaryotic-argonaute-proteins-novel-genome-editing-tools
#1
REVIEW
Jorrit W Hegge, Daan C Swarts, John van der Oost
Argonaute proteins constitute a highly diverse family of nucleic acid-guided proteins. They were first discovered in eukaryotes as key proteins in RNA interference systems, but homologous prokaryotic Argonaute proteins (pAgos) have also been found in archaea and bacteria. In this Progress article, we focus on long pAgo variants, a class of pAgos that are involved in nucleic acid-guided host defence against invading nucleic acids, and discuss the potential of pAgos in genome editing.
July 24, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28733609/suppression-of-hbv-replication-by-the-expression-of-nickase-and-nuclease-dead-cas9
#2
Takeshi Kurihara, Takasuke Fukuhara, Chikako Ono, Satomi Yamamoto, Kentaro Uemura, Toru Okamoto, Masaya Sugiyama, Daisuke Motooka, Shota Nakamura, Masato Ikawa, Masashi Mizokami, Yoshihiko Maehara, Yoshiharu Matsuura
Complete removal of hepatitis B virus (HBV) DNA from nuclei is difficult by the current therapies. Recent reports have shown that a novel genome-editing tool using Cas9 with a single-guide RNA (sgRNA) system can cleave the HBV genome in vitro and in vivo. However, induction of a double-strand break (DSB) on the targeted genome by Cas9 risks undesirable off-target cleavage on the host genome. Nickase-Cas9 cleaves a single strand of DNA, and thereby two sgRNAs are required for inducing DSBs. To avoid Cas9-induced off-target mutagenesis, we examined the effects of the expressions of nickase-Cas9 and nuclease dead Cas9 (d-Cas9) with sgRNAs on HBV replication...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729683/a-positive-feedback-loop-mediated-by-sigma-x-enhances-expression-of-the-streptococcal-regulator-comr
#3
Rabia Khan, Roger Junges, Heidi A Åmdal, Tsute Chen, Donald A Morrison, Fernanda C Petersen
Natural transformation is used by bacteria to take up DNA from their surroundings and incorporate it into their genomes. Streptococci do so during a transient period of competence, triggered by pheromones that they produce, secrete and sense under conditions influenced by the environment. In Streptococcus mutans, Streptococcus suis, and species of the bovis, salivarius and pyogenic groups of streptococci, the pheromone XIP is sensed by the intra-cellular regulator ComR, that in turn activates the transcription of comS, encoding the XIP precursor, and of sigX, encoding the only known alternative sigma factor in streptococci...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729655/a-crispr-cas9-guidance-rna-screen-platform-for-hiv-provirus-disruption-and-hiv-aids-gene-therapy-in-astrocytes
#4
Zaohua Huang, Madahavan Nair
HIV/AIDS remains a major health threat despite significant advances in the prevention and treatment of HIV infection. The major reason is the inability of existing treatments to eradicate the multiple HIV reservoirs in the human body, including astrocytes in the human brain. CRISPR/Cas9 system is an emerging gene-editing technique with the potential to eliminate or disrupt HIV provirus in HIV reservoir cells, which may lead to a complete cure of HIV/AIDS. The key components of CRISPR/Cas9 are guide RNAs (gRNAs) which determine specific sequence targeting of DNAs...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28727142/genomic-and-transcriptomic-heterogeneity-of-colorectal-tumors-arising-in-lynch-syndrome
#5
Hans Binder, Lydia Hopp, Michal R Schweiger, Steve Hoffmann, Frank Jühling, Martin Kerick, Bernd Timmermann, Susann Siebert, Christina Grimm, Lilit Nersisyan, Arsen Arakelyan, Maria Herberg, Peter Buske, Henry Loeffler-Wirth, Maciej Rosolowski, Christoph Engel, Jens Przybilla, Martin Peifer, Nicolaus Friedrichs, Gabriela Moeslein, Margarete Odenthal, Michelle Hussong, Sophia Peters, Stefanie Holzapfel, Jacob Nattermann, Robert Hueneburg, Wolff Schmiegel, Brigitte Royer-Pokora, Stefan Aretz, Michael Kloth, Matthias Kloor, Reinhard Buettner, Jörg Galle, Markus Loeffler
Colorectal cancer (CRC) arising in Lynch Syndrome (LS) comprises tumors with constitutional mutations in DNA mismatch-repair genes. Whole-genome and transcriptome studies of LS-CRC are still missing to address questions about similarities and differences of mutation and gene expression characteristics between LS-CRC and sporadic CRC, about the molecular heterogeneity of LS-CRC and about specific mechanisms of LS-CRC genesis linked to dysfunctional mismatch-repair in LS colonic mucosa and the possible role of immune editing...
July 20, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28724960/sgrna-expression-of-cripsr-cas9-system-based-on-mirna-polycistrons-as-a-versatile-tool-to-manipulate-multiple-and-tissue-specific-genome-editing
#6
Chen Xie, Yan-Lian Chen, Dong-Fang Wang, Yi-Lin Wang, Tian-Peng Zhang, Hui Li, Fu Liang, Yong Zhao, Guang-Ya Zhang
CRISPR/Cas9-mediated genome editing is a next-generation strategy for genetic modifications. Typically, sgRNA is constitutively expressed relying on RNA polymerase III promoters. Polymerase II promoters initiate transcription in a flexible manner, but sgRNAs generated by RNA polymerase II promoter lost their nuclease activity. To express sgRNAs in a tissue-specific fashion and endow CRISPR with more versatile function, a novel system was established in a polycistron, where miRNAs (or shRNAs) and sgRNAs alternately emerged and co-expressed under the control of a single polymerase II promoter...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#7
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28720816/functional-divergence-and-origin-of-the-dag-like-gene-family-in-plants
#8
Meijie Luo, Manjun Cai, Jianhua Zhang, Yurong Li, Ruyang Zhang, Wei Song, Ke Zhang, Hailin Xiao, Bing Yue, Yonglian Zheng, Yanxin Zhao, Jiuran Zhao, Fazhan Qiu
The nuclear-encoded DAG-like (DAL) gene family plays critical roles in organelle C-to-U RNA editing in Arabidopsis thaliana. However, the origin, diversification and functional divergence of DAL genes remain unclear. Here, we analyzed the genomes of diverse plant species and found that: DAL genes are specific to spermatophytes, all DAL genes share a conserved gene structure and protein similarity with the inhibitor I9 domain of subtilisin genes found in ferns and mosses, suggesting that DAL genes likely arose from I9-containing proproteases via exon shuffling...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717061/apobec-mediated-genomic-alterations-link-immunity-and-viral-infection-during-human-papillomavirus-driven-cervical-carcinogenesis
#9
Lanting Chen, Xuemin Qiu, Na Zhang, Yan Wang, Mingyan Wang, Dajin Li, Ling Wang, Yan Du
Cervical cancer is one of the most frequently diagnosed cancers and is a major cause of death from gynecologic cancers worldwide; the cancer burden from cervical cancer is especially heavy in less developed countries. Most cases of cervical cancer are caused by persistent infection with carcinogenic human papillomavirus (HPV) genotypes 16 and 18. Non-resolving inflammation caused by HPV infection provides a microenvironment that facilitates cancer development. Molecular alterations during the process of HPV-induced carcinogenesis are characterized by DNA methylation within the HPV genome, promoter hypermethylation of tumor suppressor genes in the host genome, as well as genomic instability caused by viral DNA integrating into the host genome...
July 17, 2017: Bioscience Trends
https://www.readbyqxmd.com/read/28717048/rna-seq-of-rice-yellow-stem-borer-scirpophaga-incertulas-reveals-molecular-insights-during-four-larval-developmental-stages
#10
Renuka P, Maganti S Madhav, Padmakumari A P, Kalyani M Barbadikar, Sathendra K Mangrauthia, Vijaya Sudhakara Rao K, Soma S Marla, Ravindra Babu V
The yellow stem borer (YSB), Scirpophaga incertulas is a prominent pest in the rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on biology and mechanisms underlying growth and differentiation of YSB. To understand and identify the genes involved in YSB development and infestation, so as to design pest control strategies, we performed de novo transcriptome at 1(st), 3(rd), 5(th) and 7(th) larval developmental stages employing Illumina Hi-seq...
July 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28716651/significance-of-a-to-i-rna-editing-of-transcripts-modulating-pharmacokinetics-and-pharmacodynamics
#11
REVIEW
Masataka Nakano, Miki Nakajima
RNA editing is a post-transcriptional process that alters the nucleotide sequence of RNA transcripts to generate transcriptome diversity. Among the various types of RNA editing, adenosine-to-inosine (A-to-I) RNA editing is the most frequent type of RNA editing in mammals. Adenosine deaminases acting on RNA (ADAR) enzymes, ADAR1 and ADAR2, convert adenosines in double-stranded RNA structures into inosines by hydrolytic deamination. Inosine forms a base pair with cytidine as if it were guanosine; therefore, the conversion may affect the amino acid sequence, splicing, microRNA targeting, and miRNA maturation...
July 15, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28714361/rna-editing-is-induced-by-type-i-interferon-in-esophageal-squamous-cell-carcinoma
#12
Jinyao Zhang, Zhaoli Chen, Zefang Tang, Jianbing Huang, Xueda Hu, Jie He
In recent years, abnormal RNA editing has been shown to play an important role in the development of esophageal squamous cell carcinoma, as such abnormal editing is catalyzed by ADAR (adenosine deaminases acting on RNA). However, the regulatory mechanism of ADAR1 in esophageal squamous cell carcinomas remains largely unknown. In this study, we investigated ADAR1 expression and its association with RNA editing in esophageal squamous cell carcinomas. RNA sequencing applied to esophageal squamous cell carcinoma clinical samples showed that ADAR1 expression was correlated with the expression of STAT1, STAT2, and IRF9...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28712496/engineering-molecular-immunity-against-plant-viruses
#13
Syed Shan-E-Ali Zaidi, Manal Tashkandi, Magdy M Mahfouz
Genomic engineering has been used to precisely alter eukaryotic genomes at the single-base level for targeted gene editing, replacement, fusion, and mutagenesis, and plant viruses such as Tobacco rattle virus have been developed into efficient vectors for delivering genome-engineering reagents. In addition to altering the host genome, these methods can target pathogens to engineer molecular immunity. Indeed, recent studies have shown that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems that target the genomes of DNA viruses can interfere with viral activity and limit viral symptoms in planta, demonstrating the utility of this system for engineering molecular immunity in plants...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28712495/on-improving-crispr-for-editing-plant-genes-ribozyme-mediated-guide-rna-production-and-fluorescence-based-technology-for-isolating-transgene-free-mutants-generated-by-crispr
#14
Yubing He, Rongchen Wang, Xinhua Dai, Yunde Zhao
CRISPR/Cas9-mediated genome editing technology has been used to successfully edit numerous genes in various organisms including plants. There are still two major challenges in using CRISPR/Cas9 technology for gene editing in plants. First, there are very limited choices of promoters that are suitable for in vivo production of single-guide RNAs (sgRNAs), which is complementary to the target sequence and which guides Cas9 to generate double-strand breaks at the target site. It is especially difficult to produce sgRNA molecules with temporal and spatial precision...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28710381/evaluation-and-diagnostic-potential-of-circulating-extracellular-vesicle-associated-micrornas-in-adrenocortical-tumors
#15
Pál Perge, Henriett Butz, Raffaele Pezzani, Irina Bancos, Zoltán Nagy, Krisztina Pálóczi, Gábor Nyírő, Ábel Decmann, Erna Pap, Michaela Luconi, Massimo Mannelli, Edit I Buzás, Miklós Tóth, Marco Boscaro, Attila Patócs, Peter Igaz
There is no available blood marker for the preoperative diagnosis of adrenocortical malignancy. The objective of this study was to investigate the expression of extracellular vesicle-associated microRNAs and their diagnostic potential in plasma samples of patients suffering from adrenocortical tumors. Extracellular vesicles were isolated either by using Total Exosome Isolation Kit or by differential centrifugation/ultracentrifugation. Preoperative plasma extracellular vesicle samples of 6 adrenocortical adenomas (ACA) and 6 histologically verified adrenocortical cancer (ACC) were first screened by Taqman Human Microarray A-cards...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28710037/rna-editing-independently-occurs-at-three-mir-376a-1-sites-and-may-compromise-the-stability-of-the-microrna-hairpin
#16
Alicia Gallego, Diego A Hartasánchez, Marina Brasó-Vives, Eva Garcia-Ramallo, Maria Lopez-Valenzuela, Neus Baena, Miriam Guitart, Hugo Fernández-Bellon, Ivanela Kondova, Ronald Bontrop, Yukio Kawahara, Yolanda Espinosa-Parrilla
RNA editing is being recognized as an important post-transcriptional mechanism that may have crucial roles in introducing genetic variation and phenotypic diversity. Despite microRNA editing recurrence, defining its biological relevance is still under extended debate. To better understand microRNA editing function and regulation we performed an exhaustive characterization of the A-to-I site-specific patterns in mir-376a-1, a mammalian microRNA which RNA editing is involved in the regulation of development and in disease...
July 11, 2017: Gene
https://www.readbyqxmd.com/read/28709658/ngago-gdna-system-efficiently-suppresses-hepatitis-b-virus-replication-through-accelerating-decay-of-pregenomic-rna
#17
Zhuanchang Wu, Siyu Tan, Leiqi Xu, Lifen Gao, Haizhen Zhu, Chunhong Ma, Xiaohong Liang
Covalently closed circular DNA (cccDNA) in the hepatocytes nucleus is responsible for persistent infection of Hepatitis B virus (HBV). Current antiviral therapy drugs nucleos(t)ide analogs or interferon fail to eradicate HBV cccDNA. Genome editing technique provides an effective approach for HBV treatment through targeting viral cccDNA. Natronobacterium gregoryi Argonaute (NgAgo)-guide DNA (gDNA) system with powerful genome editing prompts us to explore its application in inhibiting HBV replication. Preliminary function verification indicated that NgAgo/EGFP-gDNA obviously inhibited EGFP expression...
July 12, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28706995/disabling-cas9-by-an-anti-crispr-dna-mimic
#18
Jiyung Shin, Fuguo Jiang, Jun-Jie Liu, Nicolas L Bray, Benjamin J Rauch, Seung Hyun Baik, Eva Nogales, Joseph Bondy-Denomy, Jacob E Corn, Jennifer A Doudna
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated gene editing in human cells. However, the mechanism of CRISPR-Cas9 inhibition is not known, and the potential applications for Cas9 inhibitor proteins in mammalian cells have not been fully established...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28705213/the-therapeutic-landscape-of-hiv-1-via-genome-editing
#19
REVIEW
Alexander Kwarteng, Samuel Terkper Ahuno, Godwin Kwakye-Nuako
Current treatment for HIV-1 largely relies on chemotherapy through the administration of antiretroviral drugs. While the search for anti-HIV-1 vaccine remain elusive, the use of highly active antiretroviral therapies (HAART) have been far-reaching and has changed HIV-1 into a manageable chronic infection. There is compelling evidence, including several side-effects of ARTs, suggesting that eradication of HIV-1 cannot depend solely on antiretrovirals. Gene therapy, an expanding treatment strategy, using RNA interference (RNAi) and programmable nucleases such as meganuclease, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR-Cas9) are transforming the therapeutic landscape of HIV-1...
July 14, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28699694/the-epigenomics-of-schizophrenia-in-the-mouse
#20
REVIEW
Behnam Javidfar, Royce Park, Bibi S Kassim, Lucy K Bicks, Schahram Akbarian
Large-scale consortia including the Psychiatric Genomics Consortium, the Common Minds Consortium, BrainSeq and PsychENCODE, and many other studies taken together provide increasingly detailed insights into the genetic and epigenetic risk architectures of schizophrenia (SCZ) and offer vast amounts of molecular information, but with largely unexplored therapeutic potential. Here we discuss how epigenomic studies in human brain could guide animal work to test the impact of disease-associated alterations in chromatin structure and function on cognition and behavior...
July 12, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
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