scholarly journals Computational analysis of DNA and RNA editing in human cells

2019 ◽  
Author(s):  
◽  
Harini Srinivasan
Keyword(s):  
Rna Editing ◽  
Computational Analysis ◽  
Human Cells ◽  
Dna And Rna

scholarly journals DNA and RNA editing without sequence limitation using the flap endonuclease 1 guided by hairpin DNA probes

2020 ◽  
Vol 48 (20) ◽  
pp. e117-e117
Author(s):  
Kun Tian ◽  
Yongjian Guo ◽  
Bingjie Zou ◽  
Liang Wang ◽  
Yun Zhang ◽  
...  
Keyword(s):  
Rna Editing ◽  
Human Cells ◽  
Hairpin Dna ◽  
Flap Endonuclease 1 ◽  
Dna And Rna ◽  
Rna Targets ◽  
Single Base Mismatch ◽  
Compact Size

Abstract Here, we characterized a flap endonuclease 1 (FEN1) plus hairpin DNA probe (hpDNA) system, designated the HpSGN system, for both DNA and RNA editing without sequence limitation. The compact size of the HpSGN system make it an ideal candidate for in vivo delivery applications. In vitro biochemical studies showed that the HpSGN system required less nuclease to cleave ssDNA substrates than the SGN system we reported previously by a factor of ∼40. Also, we proved that the HpSGN system can efficiently cleave different RNA targets in vitro. The HpSGN system cleaved genomic DNA at an efficiency of ∼40% and ∼20% in bacterial and human cells, respectively, and knocked down specific mRNAs in human cells at a level of ∼25%. Furthermore, the HpSGN system was sensitive to the single base mismatch at the position next to the hairpin both in vitro and in vivo. Collectively, this study demonstrated the potential of developing the HpSGN system as a small, effective, and specific editing tool for manipulating both DNA and RNA without sequence limitation.

scholarly journals Evidence for Transcriptome-wide RNA Editing Among Sus scrofa PRE-1 SINE Elements

2017 ◽  
Author(s):  
Scott A. Funkhouser ◽  
Juan P. Steibel ◽  
Ronald O. Bates ◽  
Nancy E. Raney ◽  
Darius Schenk ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Transcriptional Regulation ◽  
Rna Editing ◽  
High Throughput ◽  
Sus Scrofa ◽  
Sequence Data ◽  
Rna Sequences ◽  
Editing Event ◽  
Coding Regions ◽  
Dna And Rna

AbstractBackgroundRNA editing by ADAR (adenosine deaminase acting on RNA) proteins is a form of transcriptional regulation that is widespread among humans and other primates. Based on high-throughput scans used to identify putative RNA editing sites, ADAR appears to catalyze a substantial number of adenosine to inosine transitions within repetitive regions of the primate transcriptome, thereby dramatically enhancing genetic variation beyond what is encoded in the genome.ResultsHere, we demonstrate the editing potential of the pig transcriptome by utilizing DNA and RNA sequence data from the same pig. We identified a total of 8550 mismatches between DNA and RNA sequences across three tissues, with 75% of these exhibiting an A-to-G (DNA to RNA) discrepancy, indicative of a canonical ADAR-catalyzed RNA editing event. When we consider only mismatches within repetitive regions of the genome, the A-to-G percentage increases to 94%, with the majority of these located within the swine specific SINE retrotransposon PRE-1. We also observe evidence of A-to-G editing within coding regions that were previously verified in primates.ConclusionsThus, our high-throughput evidence suggests that pervasive RNA editing by ADAR can exist outside of the primate lineage to dramatically enhance genetic variation in pigs.

scholarly journals Dimerisation of APOBEC1 is dispensable for its RNA editing activity

2018 ◽  
Author(s):  
Martina Chieca ◽  
Marco Montini ◽  
Francesco Severi ◽  
Riccardo Pecori ◽  
Silvestro G. Conticello
Keyword(s):  
Rna Editing ◽  
Stop Codon ◽  
Dominant Negative ◽  
Dominant Negative Effect ◽  
Main Determinant ◽  
Apob Mrna ◽  
Dna And Rna ◽  
Negative Effect ◽  
Editing Activity ◽  
Nuclear Degradation

ABSTRACTAmong the AID/APOBECs -a family of DNA and RNA deaminases-APOBEC1 physiologically partakes into a complex that edits a CAA codon into UAA Stop codon in the transcript of Apolipoprotein B (ApoB), a protein crucial in the transport of lipids in the blood. Catalytically inactive mutants of APOBEC1 have a dominant negative effect on its activity, as they compete for the targeting to the ApoB mRNA. Here we show that catalytically inactive chimeras of APOBEC1 restricted to different compartments of the cell present different abilities to titrate APOBEC1-mediated RNA editing, and that the ability of APOBEC1 to interact with these mutants is the main determinant for its activity. Our results demonstrate that dimerisation, a feature common to other APOBECs targeting DNA, is not required for APOBEC1 activity on mRNA. Furthermore, APOBEC1-mediated RNA editing is a dynamic process where interplay among the components of the editing complex is regulated through the balance between availability of A1CF, one of APOBEC1 cofactors, and nuclear degradation of APOBEC1.

scholarly journals The First Successful Observation of in-cell NMR Signals of DNA and RNA in Living Human Cells

2019 ◽  
Vol 59 (1) ◽  
pp. 018-020 ◽  
Author(s):  
Yudai YAMAOKI ◽  
Takashi NAGATA ◽  
Masato KATAHIRA
Keyword(s):  
Human Cells ◽  
Dna And Rna ◽  
Nmr Signals ◽  
Successful Observation

scholarly journals Highly efficient and specific genome editing in human cells with paired CRISPR-Cas9 nickase ribonucleoproteins

2019 ◽  
Author(s):  
Jacob Lamberth ◽  
Laura Daley ◽  
Pachai Natarajan ◽  
Stanislav Khoruzhenko ◽  
Nurit Becker ◽  
...  
Keyword(s):  
Cell Culture ◽  
Genome Editing ◽  
Plasmid Dna ◽  
High Efficiency ◽  
High Specificity ◽  
Human Cells ◽  
Dna And Rna ◽  
Genome Modification ◽  
Delivery Technology ◽  
Target Effects

ABSTRACTCRISPR technology has opened up many diverse genome editing possibilities in human somatic cells, but has been limited in the therapeutic realm by both potential off-target effects and low genome modification efficiencies. Recent advancements to combat these limitations include delivering Cas9 nucleases directly to cells as highly purified ribonucleoproteins (RNPs) instead of the conventional plasmid DNA and RNA-based approaches. Here, we extend RNP-based delivery in cell culture to a less characterized CRISPR format which implements paired Cas9 nickases. The use of paired nickase Cas9 RNP system, combined with a GMP-compliant non-viral delivery technology, enables editing in human cells with high specificity and high efficiency, a development that opens up the technology for further exploration into a more therapeutic role.

scholarly journals Genopo: a nanopore sequencing analysis toolkit for portable Android devices

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Hiruna Samarakoon ◽  
Sanoj Punchihewa ◽  
Anjana Senanayake ◽  
Jillian M. Hammond ◽  
Igor Stevanovski ◽  
...  
Keyword(s):  
Computational Analysis ◽  
Smartphone Application ◽  
Sequencing Analysis ◽  
Nanopore Sequencing ◽  
Android Application ◽  
Sequencing Data ◽  
Human Coronavirus ◽  
Dna And Rna ◽  
Bioinformatics Tools

Abstract The advent of portable nanopore sequencing devices has enabled DNA and RNA sequencing to be performed in the field or the clinic. However, advances in in situ genomics require parallel development of portable, offline solutions for the computational analysis of sequencing data. Here we introduce Genopo, a mobile toolkit for nanopore sequencing analysis. Genopo compacts popular bioinformatics tools to an Android application, enabling fully portable computation. To demonstrate its utility for in situ genome analysis, we use Genopo to determine the complete genome sequence of the human coronavirus SARS-CoV-2 in nine patient isolates sequenced on a nanopore device, with Genopo executing this workflow in less than 30 min per sample on a range of popular smartphones. We further show how Genopo can be used to profile DNA methylation in a human genome sample, illustrating a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes. As the first ever smartphone application for nanopore sequencing analysis, Genopo enables the genomics community to harness this cheap, ubiquitous computational resource.

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