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https://www.readbyqxmd.com/read/29453099/impact-of-integrated-viral-dna-on-the-goal-to-clear-hepatitis-b-surface-antigen-with-different-therapeutic-strategies
#1
REVIEW
Magnus Lindh, Gustaf E Rydell, Simon B Larsson
A hallmark of hepatitis B virus (HBV) infection is the presence of hepatitis B surface antigen (HBsAg) in the serum of patients. Sustained loss of HBV DNA and HBsAg from the blood are main goals for treatment, and considered as functional cure. It is rarely achieved with long-term nucleoside analogue treatment though, both because cccDNA, the template for viral replication, is not completely cleared, and probably also because hepatocytes with HBV DNA integrated into their chromosomes persist and continue to produce large amounts of HBsAg...
February 13, 2018: Current Opinion in Virology
https://www.readbyqxmd.com/read/29451311/impaired-phloem-loading-in-zmsweet13a-b-c-sucrose-transporter-triple-knock-out-mutants-in-zea-mays
#2
Margaret Bezrutczyk, Thomas Hartwig, Marc Horshman, Si Nian Char, Jinliang Yang, Bing Yang, Wolf B Frommer, Davide Sosso
Crop yield depends on efficient allocation of sucrose from leaves to seeds. In Arabidopsis, phloem loading is mediated by a combination of SWEET sucrose effluxers and subsequent uptake by SUT1/SUC2 sucrose/H + symporters. ZmSUT1 is essential for carbon allocation in maize, but the relative contribution to apoplasmic phloem loading and retrieval of sucrose leaking from the translocation path is not known. Here we analysed the contribution of SWEETs to phloem loading in maize. We identified three leaf-expressed SWEET sucrose transporters as key components of apoplasmic phloem loading in Zea mays L...
February 16, 2018: New Phytologist
https://www.readbyqxmd.com/read/29450416/a-g-quadruplex-motif-at-the-3-end-of-sgrnas-improves-crispr-cas9-based-genome-editing-efficiency
#3
Smita Nahar, Paras Sehgal, Mohd Azhar, Manish Rai, Amrita Singh, Sridhar Sivasubbu, Debojyoti Chakraborty, Souvik Maiti
Originating as a component of prokaryotic adaptive immunity, the type II CRISPR/Cas9 system has been repurposed for targeted genome editing in various organisms. Although Cas9 can bind and cleave DNA efficiently under in vitro conditions, its activity inside a cell can vary dramatically between targets owing to the differences between genomic loci and the availability of enough Cas9/sgRNA (single guide RNA) complex molecules for cleavage. Most methods have so far relied on Cas9 protein engineering or base modifications in the sgRNA sequence to improve CRISPR/Cas9 activity...
February 16, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29449833/stem-loop-rna-hairpins-in-giant-viruses-invading-rrna-like-repeats-and-a-template-free-rna
#4
Hervé Seligmann, Didier Raoult
We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo , other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29449511/crispr-cas12a-target-binding-unleashes-indiscriminate-single-stranded-dnase-activity
#5
Janice S Chen, Enbo Ma, Lucas B Harrington, Maria Da Costa, Xinran Tian, Joel M Palefsky, Jennifer A Doudna
CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind and cut DNA as components of bacterial adaptive immune systems. Like CRISPR-Cas9, Cas12a has been harnessed for genome editing based on its ability to generate targeted, double-stranded DNA (dsDNA) breaks. Here we show that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA (ssDNA) cleavage activity by Cas12a that completely degrades ssDNA molecules. We find that target-activated, non-specific ssDNase cleavage is also a property of other type V CRISPR-Cas12 enzymes...
February 15, 2018: Science
https://www.readbyqxmd.com/read/29445326/structure-function-studies-of-the-%C3%AE-4-subunit-reveal-evolutionary-loss-of-a-glyr-subtype-involved-in-startle-and-escape-responses
#6
Sophie Leacock, Parnayan Syed, Victoria M James, Anna Bode, Koichi Kawakami, Angelo Keramidas, Maximiliano Suster, Joseph W Lynch, Robert J Harvey
Inhibitory glycine receptors (GlyRs) are pentameric ligand-gated anion channels with major roles in startle disease/hyperekplexia (GlyR α1), cortical neuronal migration/autism spectrum disorder (GlyR α2), and inflammatory pain sensitization/rhythmic breathing (GlyR α3). However, the role of the GlyR α4 subunit has remained enigmatic, because the corresponding human gene ( GLRA4 ) is thought to be a pseudogene due to an in-frame stop codon at position 390 within the fourth membrane-spanning domain (M4). Despite this, a recent genetic study has implicated GLRA4 in intellectual disability, behavioral problems and craniofacial anomalies...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29445025/strong-conservation-of-inbred-mouse-strain-microrna-loci-but-broad-variation-in-brain-micrornas-due-to-rna-editing-and-isomir-expression
#7
Kalevi Trontti, Juho Väänänen, Tessa Sipilä, Dario Greco, Iiris Hovatta
Diversity in the structure and expression of microRNAs, important regulators of gene expression, arises from SNPs, duplications followed by divergence, production of isomiRs, and RNA editing. Inbred mouse strains and crosses using them are important reference populations for genetic mapping, and as models of human disease. We determined the nature and extent of interstrain miRNA variation by 1) identifying miRNA SNPs in whole genome sequence data from 36 strains, and 2) examining miRNA editing and expression in hippocampus (Hpc) and frontal cortex (FCx) of 6 strains, to facilitate the study of miRNAs in neurobehavioral phenotypes...
February 14, 2018: RNA
https://www.readbyqxmd.com/read/29445007/highly-efficient-and-versatile-plasmid-based-gene-editing-in-primary-t-cells
#8
Mara Kornete, Romina Marone, Lukas T Jeker
Adoptive cell transfer is an important approach for basic research and emerges as an effective treatment for various diseases, including infections and blood cancers. Direct genetic manipulation of primary immune cells opens up unprecedented research opportunities and could be applied to enhance cellular therapeutic products. In this article, we report highly efficient genome engineering in primary murine T cells using a plasmid-based RNA-guided CRISPR system. We developed a straightforward approach to ablate genes in up to 90% of cells and to introduce precisely targeted single nucleotide polymorphisms in up to 25% of the transfected primary T cells...
February 14, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29442507/functional-insights-revealed-by-the-kinetic-mechanism-of-crispr-cas9
#9
Austin T Raper, Anthony A Stephenson, Zucai Suo
The discovery of prokaryotic adaptive immunity prompted widespread use of the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) endonuclease Cas9 for genetic engineering. However, its kinetic mechanism remains undefined and details of DNA cleavage poorly characterized. Here, we establish a kinetic mechanism of Streptococcus pyogenes Cas9 from guide-RNA binding through DNA cleavage and product release. Association of DNA to the binary complex of Cas9 and guide-RNA is rate-limiting during the first catalytic turnover, while DNA cleavage from a pre-formed ternary complex of Cas9, guide-RNA, and DNA is rapid...
February 14, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29438517/genome-editing-in-kluyveromyces-and-ogataea-yeasts-using-a-broad-host-range-cas9-grna-co-expression-plasmid
#10
Hannes Juergens, Javier A Varela, Arthur R Gorter de Vries, Thomas Perli, Veronica J M Gast, Nikola Y Gyurchev, Arun S Rajkumar, Robert Mans, Jack T Pronk, John P Morrissey, Jean-Marc G Daran
While CRISPR-Cas9-mediated genome editing has transformed yeast research, current plasmids and cassettes for Cas9 and guide-RNA expression are species specific. CRISPR tools that function in multiple yeast species could contribute to the intensifying research on non-conventional yeasts. A plasmid carrying a pangenomic origin of replication and two constitutive expression cassettes, for Cas9 and a ribozyme-flanked gRNAs was constructed. Its functionality was tested by analyzing inactivation of the ADE2 gene in four yeast species...
February 9, 2018: FEMS Yeast Research
https://www.readbyqxmd.com/read/29434619/from-bioengineering-to-crispr-cas9-a-personal-retrospective-of-20-years-of-research-in-programmable-genome-targeting
#11
Albert Jeltsch
Genome targeting of restriction enzymes and DNA methyltransferases has many important applications including genome and epigenome editing. 15-20 years ago, my group was involved in the development of approaches for programmable genome targeting, aiming to connect enzymes with an oligodeoxynucleotide (ODN), which could form a sequence-specific triple helix at the genomic target site. Importantly, the target site of such enzyme-ODN conjugate could be varied simply by altering the ODN sequence promising great applicative values...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29433054/hallmarks-of-cancer-the-crispr-generation
#12
REVIEW
Colette Moses, Benjamin Garcia-Bloj, Alan R Harvey, Pilar Blancafort
The hallmarks of cancer were proposed as a logical framework to guide research efforts that aim to understand the molecular mechanisms and derive treatments for this highly complex disease. Recent technological advances, including comprehensive sequencing of different cancer subtypes, have illuminated how genetic and epigenetic alterations are associated with specific hallmarks of cancer. However, as these associations are purely descriptive, one particularly exciting development is the emergence of genome editing technologies, which enable rapid generation of precise genetic and epigenetic modifications to assess the consequences of these perturbations on the cancer phenotype...
February 9, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29432121/xrn2-accelerates-termination-by-rna-polymerase-ii-which-is-underpinned-by-cpsf73-activity
#13
Joshua D Eaton, Lee Davidson, David L V Bauer, Toyoaki Natsume, Masato T Kanemaki, Steven West
Termination is a ubiquitous phase in every transcription cycle but is incompletely understood and a subject of debate. We used gene editing as a new approach to address its mechanism through engineered conditional depletion of the 5' → 3' exonuclease Xrn2 or the polyadenylation signal (PAS) endonuclease CPSF73 (cleavage and polyadenylation specificity factor 73). The ability to rapidly control Xrn2 reveals a clear and general role for it in cotranscriptional degradation of 3' flanking region RNA and transcriptional termination...
February 8, 2018: Genes & Development
https://www.readbyqxmd.com/read/29427115/gene-therapies-for-polyglutamine-diseases
#14
Carlos A Matos, Vítor Carmona, Udaya-Geetha Vijayakumar, Sara Lopes, Patrícia Albuquerque, Mariana Conceição, Rui Jorge Nobre, Clévio Nóbrega, Luís Pereira de Almeida
Polyglutamine diseases are hereditary degenerative disorders of the nervous system that have remained, to this date, untreatable. Promisingly, investigation into their molecular etiology and the development of increasingly perfected tools have contributed to the design of novel strategies with therapeutic potential. Encouraging studies have explored gene therapy as a means to counteract cell demise and loss in this context. The current chapter addresses the two main focuses of research in the area: the characteristics of the systems used to deliver nucleic acids to cells and the molecular and cellular actions of the therapeutic agents...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29424307/new-developments-in-crispr-technology-improvements-in-specificity-and-efficiency
#15
Fatemeh Safari, Safar Farajnia, Younes Ghasemi, Nosratollah Zarghami
BACKGROUND: RNA-guided endonuclease as a versatile genome editing technology opened new windows in various fields of biology. The simplicity of this revolutionary technique provides a promising future for its application in a broad range of approaches from functional annotation of genes to diseases, to genetic manipulation and gene therapy. Besides the site-specific activity of Cas9 endonuclease, the unintended cleavage known as off-target effect is still a major challenge for this genome editing technique...
February 9, 2018: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/29424086/circadian-processes-in-the-rna-life-cycle
#16
REVIEW
Manon Torres, Denis Becquet, Jean-Louis Franc, Anne-Marie François-Bellan
The circadian clock drives daily rhythms of multiple physiological processes, allowing organisms to anticipate and adjust to periodic changes in environmental conditions. These physiological rhythms are associated with robust oscillations in the expression of at least 30% of expressed genes. While the ability for the endogenous timekeeping system to generate a 24-hr cycle is a cell-autonomous mechanism based on negative autoregulatory feedback loops of transcription and translation involving core-clock genes and their protein products, it is now increasingly evident that additional mechanisms also govern the circadian oscillations of clock-controlled genes...
February 9, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29421512/crispr-cas9-mediated-efficient-targeted-mutagenesis-of-ras-in-salvia-miltiorrhiza
#17
Zheng Zhou, Hexin Tan, Qing Li, Junfeng Chen, Shouhong Gao, Yun Wang, Wansheng Chen, Lei Zhang
The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 (CRISPR-associated) system is a powerful genome editing tool that has been used in many species. In this study, we focused on the phenolic acid metabolic pathway in the traditional Chinese medicinal herb Salvia miltiorrhiza, using the CRISPR/Cas9 system to edit the rosmarinic acid synthase gene (SmRAS) in the water-soluble phenolic acid biosynthetic pathway. The single guide RNA (sgRNA) was designed to precisely edit the most important SmRAS gene, which was selected from 11 family members through a bioinformatics analysis...
January 30, 2018: Phytochemistry
https://www.readbyqxmd.com/read/29420738/transcription-associated-mutation-promotes-rna-complexity-in-highly-expressed-genes-a-major-new-source-of-selectable-variation
#18
Shengkai Pan, Michael W Bruford, Yusong Wang, Zhenzhen Lin, Zhongru Gu, Xian Hou, Xuemei Deng, Andrew Dixon, Jennifer A Marshall Graves, Xiangjiang Zhan
Alternatively spliced transcript isoforms are thought to play a critical role for functional diversity. However, the mechanism generating the enormous diversity of spliced transcript isoforms remains unknown, and its biological significance remains unclear. We analyzed transcriptomes in saker falcons, chickens and mice to show that alternative splicing occurs more frequently, yielding more isoforms, in highly expressed genes. We focused on hemoglobin in the falcon, the most abundantly expressed genes in blood, finding that alternative splicing produces tenfold more isoforms than expected from the number of splice junctions in the genome...
February 6, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29420208/rna-editing-unexplored-opportunities-in-the-cardiovascular-system
#19
Shizuka Uchida, Steven P Jones
No abstract text is available yet for this article.
February 2, 2018: Circulation Research
https://www.readbyqxmd.com/read/29419780/differential-enzymatic-activity-of-rat-adar2-splicing-variants-is-due-to-altered-capability-to-interact-with-rna-in-the-deaminase-domain
#20
Alice Filippini, Daniela Bonini, Edoardo Giacopuzzi, Luca La Via, Fabrizio Gangemi, Marina Colombi, Alessandro Barbon
In mammals, adenosine (A) to inosine (I) RNA editing is performed by adenosine deaminases acting on RNA (ADAR), ADAR1 and ADAR2 enzymes, encoded by mRNAs that might undergo splicing process. In rat, two splicing events produce several isoforms of ADAR2, called ADAR2a, ADAR2b, ADAR2e, and ADAR2f, but only ADAR2a and ADAR2b are translated into an active protein. In particular, they differ for ten amino acids located in the catalytic domain of ADAR2b. Here, we focused on these two isoforms, analyzing the splicing pattern and their different function during rat neuronal maturation...
February 8, 2018: Genes
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