Rna Editing
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2021 ◽  
Author(s):  
Yan Zheng ◽  
Yuan Jiang ◽  
Yujing Miao ◽  
Zhan Feng ◽  
Min Zhang ◽  
...  

Abstract The Taihangia is a native endangered cliff species that grows in the Taihang Mountains in China. The cp genomes with a whole length of 155,558 bp and 155,479 bp for Taihangia rupestris and Taihangia rupestris var. rupestris. They have 131 genes in total, covering 79 protein-coding genes, 29 tRNA, and 4 rRNA. Analyses of codon usage, RNA-editing sites, repeat sequences, and comparison of cp genomes showed a high degree of conservation. Phylogenetic analysis indicated that the Taihangia are closed to the Geum. Taihangia genus was inferred to have originated at 0.2057 Mya, and Geum rupestre was inferred to have originated at 1.4431 Mya. Overall, the gene contents, gene arrangements, the types, and frequency of codon usage, repeat sequences, and SSRs are similar and highly conserved in the species of T. rupestris and T. rupestris var. ciliate. It is found that based on bioprospecting, T. rupestris and T. rupestris var. rupestris are potential medicinal resources. This study provides a scientific basis for the conservation and sustainable use of endangered medicinal resources..


Author(s):  
Youyeon Go ◽  
Hye-Bin Ahn ◽  
Byeong-Seon Kim ◽  
Ae-Ree Lee ◽  
Kwang-Im Oh ◽  
...  

QJM ◽  
2021 ◽  
Vol 114 (Supplement_1) ◽  
Author(s):  
Islam A Desoky ◽  
Kamelia Ahmed Zaki ◽  
Magda I Mohamad ◽  
Samar Kamal Kassim

Abstract Background A-to-I RNA editing represents a new player in the pathogenesis of cancer. However, the knowledge of RNA editing process in cancer is still limited and represents only the tip of the iceberg. The ADAR gene family regulate the dynamic landscape of RNA editing. Aberrant RNA editing status played a vital role in the pathogenesis of hepatocellular carcinoma (HCC). The nutri-epigenomic agent- pterostilbene- exhibits anti-inflammatory, antioxidative and antiproliferative activities. However, the effect of pterostilbene on ADAR(s) expression in HCC was not studied before. Aim of the work to evaluate the potential effect of pterostilbene administration on Adar(s) expression in HCC rats. Materials and methods Twenty four adult male rats were randomly divided into 4 groups: the control group, untreated HCC group received diethylnitrosamine (DENA) for 14 weeks, HCC group take received pterostilbene and DENA for 14 weeks, and non-HCC rats were given pterostilbene for 14 weeks. These groups were subjected to histological examination of liver tissues, laboratory measures (serum albumin, ALT, AST, and α fetoprotein), and Adar(s) expression by real time-PCR. Results liver enzymes (ALT, AST) and α fetoprotein levels in treated HCC group were significantly lower than untreated HCC group (p<0.05). Serum albumin levels were significantly higher in treated HCC rats than untreated HCC group (P<0.05). Adar1 was highly expressed in untreated HCC rats in comparison to the control group (p<0.05). Meanwhile, treated HCC group had lower expression levels of Adar1 in comparison to untreated HCC rats. Conclusions pterostilbene had a beneficial effect on HCC and it may alleviate the aberrant expression of Adar1 in HCC rats. Key words HCC, ADARs, pterostilbene, RNA editing enzymes. Acknowledgments: No finical support was present Conflict of interest: the authors declared that no conflicts of interest concerning the article. Authors’ contributions: The authors contributed to the design and implementation of the research, to the analysis of the results and to the writing of the manuscript


RNA Biology ◽  
2021 ◽  
pp. 1-10
Author(s):  
Hamid Mansouri Khosravi ◽  
Michael F. Jantsch
Keyword(s):  

2021 ◽  
Vol 35 (10) ◽  
Author(s):  
Ke‐Yun Xie ◽  
Shao‐Ju Chien ◽  
Bertrand Chin‐Ming Tan ◽  
Yun‐Wen Chen

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
N. M. Prashant ◽  
Nawaf Alomran ◽  
Yu Chen ◽  
Hongyu Liu ◽  
Pavlos Bousounis ◽  
...  

Abstract Background Recent studies have demonstrated the utility of scRNA-seq SNVs to distinguish tumor from normal cells, characterize intra-tumoral heterogeneity, and define mutation-associated expression signatures. In addition to cancer studies, SNVs from single cells have been useful in studies of transcriptional burst kinetics, allelic expression, chromosome X inactivation, ploidy estimations, and haplotype inference. Results To aid these types of studies, we have developed a tool, SCReadCounts, for cell-level tabulation of the sequencing read counts bearing SNV reference and variant alleles from barcoded scRNA-seq alignments. Provided genomic loci and expected alleles, SCReadCounts generates cell-SNV matrices with the absolute variant- and reference-harboring read counts, as well as cell-SNV matrices of expressed Variant Allele Fraction (VAFRNA) suitable for a variety of downstream applications. We demonstrate three different SCReadCounts applications on 59,884 cells from seven neuroblastoma samples: (1) estimation of cell-level expression of known somatic mutations and RNA-editing sites, (2) estimation of cell- level allele expression of biallelic SNVs, and (3) a discovery mode assessment of the reference and each of the three alternative nucleotides at genomic positions of interest that does not require prior SNV information. For the later, we applied SCReadCounts on the coding regions of KRAS, where it identified known and novel somatic mutations in a low-to-moderate proportion of cells. The SCReadCounts read counts module is benchmarked against the analogous modules of GATK and Samtools. SCReadCounts is freely available (https://github.com/HorvathLab/NGS) as 64-bit self-contained binary distributions for Linux and MacOS, in addition to Python source. Conclusions SCReadCounts supplies a fast and efficient solution for estimation of cell-level SNV expression from scRNA-seq data. SCReadCounts enables distinguishing cells with monoallelic reference expression from those with no gene expression and is applicable to assess SNVs present in only a small proportion of the cells, such as somatic mutations in cancer.


Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1980
Author(s):  
Ji-Young Yang ◽  
Mi-Jung Choi ◽  
Seon-Hee Kim ◽  
Hyeok-Jae Choi ◽  
Seung-Chul Kim

The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically challenging owing to insufficient diagnostic features, continuous morphological variation, and the process of hybridization and introgression, making species circumscription and phylogenetic inference difficult. In this study, we sequenced 11 accessions of Hosta plastomes, including members of three geographically defined subgenera, Hosta, Bryocles, and Giboshi, determined the characteristics of plastomes, and inferred their phylogenetic relationships. We found highly conserved plastomes among the three subgenera, identified several mutation hotspots that can be used as barcodes, and revealed the patterns of codon usage bias and RNA editing sites. Five positively selected plastome genes (rbcL, rpoB, rpoC2, rpl16, and rpl20) were identified. Phylogenetic analysis suggested (1) the earliest divergence of subg. Hosta, (2) non-monophyly of subg. Bryocles and its two sections (Lamellatae and Stoloniferae), (3) a sister relationship between H. sieboldiana (subg. Giboshi) and H. ventricosa (subg. Bryocles), and (4) reciprocally monophyletic and divergent lineages of H. capitata in Korea and Japan, requiring further studies of their taxonomic distinction.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sonia Jimeno ◽  
Rosario Prados-Carvajal ◽  
María Jesús Fernández-Ávila ◽  
Sonia Silva ◽  
Domenico Alessandro Silvestris ◽  
...  

AbstractThe maintenance of genomic stability requires the coordination of multiple cellular tasks upon the appearance of DNA lesions. RNA editing, the post-transcriptional sequence alteration of RNA, has a profound effect on cell homeostasis, but its implication in the response to DNA damage was not previously explored. Here we show that, in response to DNA breaks, an overall change of the Adenosine-to-Inosine RNA editing is observed, a phenomenon we call the RNA Editing DAmage Response (REDAR). REDAR relies on the checkpoint kinase ATR and the recombination factor CtIP. Moreover, depletion of the RNA editing enzyme ADAR2 renders cells hypersensitive to genotoxic agents, increases genomic instability and hampers homologous recombination by impairing DNA resection. Such a role of ADAR2 in DNA repair goes beyond the recoding of specific transcripts, but depends on ADAR2 editing DNA:RNA hybrids to ease their dissolution.


RNA ◽  
2021 ◽  
pp. rna.078804.121
Author(s):  
Brendan Robert E. Ansell ◽  
Simon N Thomas ◽  
Roberto Bonelli ◽  
Jacob E Munro ◽  
Saskia Freytag ◽  
...  

BACKGROUND: Conversion of adenosine to inosine in RNA by ADAR enzymes occurs at thousands of sites in the human transcriptome, and is essential for healthy brain development. This editing process is dysregulated in many neuropsychiatric diseases, but has not yet been investigated at the level of individual neurons. METHODS: We quantified RNA editing sites in full-length capture nuclear transcriptomes of 3055 neurons from six cortical regions of a neurotypical post-mortem female donor. Putative editing sites were intersected with sites in bulk human tissue transcriptomes including healthy and neuropsychiatric brain tissue, and sites identified in single nuclei from unrelated brain donors. Differential editing between cell types and cortical regions, and individual sites and genes therein, was quantified using linear models. Associations between gene abundance and editing were also tested. RESULTS: We identified 41,930 RNA editing sites with robust read coverage in at least ten neuronal nuclei. Most sites were located within Alu repeats in introns or 3’ UTRs, and approximately 80% were catalogued in published RNA editing databases. We identified 9285 putative novel RNA editing sites, 29% of which were also detectable in neuronal transcriptomes from unrelated donors. Among the strongest correlates of global editing rates were snoRNAs from the SNORD115 and SNORD116 cluster (15q11), known to modulate serotonin receptor processing and to colocalize with ADAR2. Autism related genes were enriched with editing sites predicted to modify RNA structure. Inhibitory neurons showed higher overall transcriptome editing than excitatory neurons. Additionally, we identified 29 genes preferentially edited in excitatory neurons and 43 genes edited more heavily in inhibitory neurons including RBFOX1, its target genes, and small nucleolar RNA-associated genes in the autism-associated Prader-Willi locus 15q11. These results provide cell-type and spatial context for 1730 sites that are differentially edited in the brains of schizophrenic patients, and 910 sites in autistic patients. CONCLUSIONS: RNA editing, including thousands of previously unreported sites, is robustly detectable in single neuronal nuclei, where gene editing differences are stronger between cell subtypes than between cortical regions. Insufficient editing of autism-related genes in inhibitory neurons may manifest in the specific perturbation of these cells in autism.


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