DNA and RNA editing of retrotransposons accelerate mammalian genome evolution

2015 ◽  
Vol 1341 (1) ◽  
pp. 115-125 ◽  
Author(s):  
Binyamin A. Knisbacher ◽  
Erez Y. Levanon
Keyword(s):  
Genome Evolution ◽  
Rna Editing ◽  
Mammalian Genome ◽  
Dna And Rna

scholarly journals Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids

2017 ◽  
Vol 9 (5) ◽  
pp. 1161-1174 ◽  
Author(s):  
Jiwon Yang ◽  
Tommy Harding ◽  
Ryoma Kamikawa ◽  
Alastair G.B. Simpson ◽  
Andrew J. Roger
Keyword(s):  
Mitochondrial Genome ◽  
Genome Evolution ◽  
Rna Editing ◽  
Mitochondrial Genome Evolution

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 A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals

2020 ◽  
Vol 12 (4) ◽  
pp. 345-357 ◽  
Author(s):  
Niko Popitsch ◽  
Christian D Huber ◽  
Ilana Buchumenski ◽  
Eli Eisenberg ◽  
Michael Jantsch ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Single Nucleotide Polymorphisms ◽  
Genome Evolution ◽  
Rna Editing ◽  
Adaptive Evolution ◽  
Population Genomics ◽  
Common Type ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cellular Machinery

Abstract In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.

scholarly journals Linkage of A-to-I RNA Editing in Metazoans and the Impact on Genome Evolution

2017 ◽  
Vol 35 (1) ◽  
pp. 132-148 ◽  
Author(s):  
Yuange Duan ◽  
Shengqian Dou ◽  
Hong Zhang ◽  
Changcheng Wu ◽  
Mingming Wu ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Rna Editing ◽  
The Impact

scholarly journals Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution

2011 ◽  
Vol 2 (1) ◽  
Author(s):  
Shai Carmi ◽  
George M. Church ◽  
Erez Y. Levanon
Keyword(s):  
Genome Evolution ◽  
Large Scale ◽  
Mammalian Genome ◽  
Dna Editing

Mobile elements and mammalian genome evolution

2003 ◽  
Vol 13 (6) ◽  
pp. 651-658 ◽  
Author(s):  
Prescott L Deininger ◽  
John V Moran ◽  
Mark A Batzer ◽  
Haig H Kazazian
Keyword(s):  
Genome Evolution ◽  
Mobile Elements ◽  
Mammalian Genome

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 Asymmetric Divergence in Transmitted SNPs of DNA Replication/Transcription and Their Impact on Gene Expression in Polyploid Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Minqiang Tang ◽  
Juanling Li ◽  
Xu Hu ◽  
Lu Sun ◽  
MMU Helal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Replication ◽  
Brassica Napus ◽  
Genome Evolution ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expression Levels ◽  
Dna And Rna ◽  
Polyploid Genome ◽  
Gene Expression Levels

The marked increase in plant genomic data has provided valuable resources for investigating the dynamic evolution of duplicate genes in polyploidy. Brassica napus is an ideal model species for investigating polyploid genome evolution. The present study comprehensively analyzed DNA and RNA variation of two representative B. napus inbredlines, Zhongshuang11 and Zhongyou821, and we investigated gene expression levels of An and Cn subgenomes in multiple tissues of the two lines. The distribution of transmitted single nucleotide polymorphisms (SNPs) was significantly different in two subgenomes of B. napus. Gene expression levels were significantly negatively correlated with number of variations in replication and transcription of the corresponding genes, but were positively correlated with the ratios of transmitted SNPs from DNA to RNA. We found a higher density of SNP variation in An than that in Cn during DNA replication and more SNPs were transmitted to RNA during transcription, which may contribute to An expression dominance. These activities resulted in asymmetrical gene expression in polyploid B. napus. The SNPs transmitted from DNA to RNA could be an important complement feature in comparative genomics, and they may play important roles in asymmetrical genome evolution in polyploidy.

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