In silico and experimental approaches for validating RNA editing events in transcriptomes DOI Creative Commons
Lai Wei

RNA Biology, Год журнала: 2024, Номер 21(1), С. 31 - 36

Опубликована: Ноя. 24, 2024

As a typical RNA virus, SARS-CoV-2 is subjected to editing in host cells. While some researchers believe that traditional variant calling pipeline retrieves all true-positive events from the transcriptome, others argue conventional methods identify many false-positive sites. Here, I describe several additional silico and experimental approaches validate authenticity of SARS-CoV-2. These include requiring strand-specific sequencing, analysis hyperedited reads, linkage analysis, orthogonal like mass spectrometry, use ADAR-deficient findings may improve future analyses on identification editing, especially viruses.

Язык: Английский

Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites DOI Creative Commons
Yuange Duan, Ling Ma, Tian-You Zhao

и другие.

Fly, Год журнала: 2024, Номер 18(1)

Опубликована: Июнь 18, 2024

Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for organisms to adapt environment. It is believed that recoding sites are well suited facilitating adaptive evolution by increasing proteomic diversity in a temporal-spatial manner. The function essentiality of few conserved recognized. However, experimentally discovered functional only make up small corner total sites, there still need expand repertoire such with bioinformatic approaches. In this study, we define new category termed 'conserved non-conserved recoding' systematically identify Drosophila editomes, figuring out their selection pressure signals adaptation at inter-species intra-species levels. Surprisingly, not suppressed even slightly overrepresented Drosophila. DNA mutations leading cases also favoured during evolution, suggesting those events different species might be diverged, specialized, maintained. Finally, structural prediction suggests potassium channel Shab increase ion permeability compensate effect low temperature. conclusion, as well. Our study provides novel aspects considering meanwhile expands candidates future validation.

Язык: Английский

Процитировано

6
Comparative genomic analyses on assassin bug Rhynocoris fuscipes (Hemiptera: Reduviidae) reveal genetic bases governing the diet-shift DOI Creative Commons
Ling Ma, Yuange Duan, Yunfei Wu

и другие.

iScience, Год журнала: 2024, Номер 27(8), С. 110411 - 110411

Опубликована: Июнь 28, 2024

Genetic basis underlying the biodiversity and phenotypic plasticity are fascinating questions in evolutionary biology. Such molecular diversity can be achieved at multi-omics levels. Here, we sequenced first chromosome-level genome of assassin bug Rhynocoris fuscipes, a polyphagous generalist predator for biological control agroecosystems. Compared to non-predatory true bugs Apolygus lucorum Riptortus pedestris, R. fuscipes-specific genes were enriched diet-related (e.g., serine proteinase, cytochrome P450) which had higher expression level more exons than non-diet genes. Extensive A-to-I RNA editing was identified all three species showed enrichment associated with diet diversifying transcriptome. An extended analysis between five predaceous 27 phytophagous hemipteran revealed an expansion fuscipes. Our findings bridge gap genotype phenotype, also advance our understanding on genetic epigenetic bases governing shifts ture bugs.

Язык: Английский

Процитировано

5
Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing DOI
Ling Ma,

Caiqing Zheng,

J. Liu

и другие.

Journal of Molecular Evolution, Год журнала: 2024, Номер 92(4), С. 488 - 504

Опубликована: Июль 16, 2024

Язык: Английский

Процитировано

5
Adaptive evolution of A-to-I auto-editing site in Adar of eusocial insects DOI Creative Commons

Caiqing Zheng,

J. Liu, Yuange Duan

и другие.

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Авг. 26, 2024

Adenosine-to-inosine (A-to-I) RNA editing is a co-/post-transcriptional modification introducing A-to-G variations in RNAs. There extensive discussion on whether the flexibility of exerts proteomic diversification role, or it just acts like hardwired mutations to correct genomic allele. Eusocial insects evolved ability generate phenotypically differentiated individuals with same genome, indicating involvement epigenetic/transcriptomic regulation. We obtained genomes 104 Hymenoptera and transcriptomes representative species. Comparative analysis was performed parse evolutionary trajectory regulatory Ile > Met auto-recoding site Adar gene. At genome level, pre-editing codon conserved across node containing all eusocial hymenopterans. events are confirmed species shows considerable condition-specificity. Compared random expectation, editable avoids substitutions uneditable codons, but does not avoid other unrelated amino acids. The selectively maintained, supporting flexible hypothesis. proposed new angle view adaptation editing, providing another layer explain great phenotypical plasticity insects.

Язык: Английский

Процитировано

3
An orthology-based methodology as a complementary approach to retrieve evolutionarily conserved A-to-I RNA editing sites DOI Creative Commons
J. Liu, Tian-You Zhao,

Caiqing Zheng

и другие.

RNA Biology, Год журнала: 2024, Номер 21(1), С. 29 - 45

Опубликована: Сен. 10, 2024

Adar-mediated adenosine-to-inosine (A-to-I) mRNA editing is a conserved mechanism that exerts diverse regulatory functions during the development, evolution, and adaptation of metazoans. The accurate detection RNA sites helps us understand their biological significance. In this work, with an improved genome assembly honeybee (

Язык: Английский

Процитировано

3
Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis DOI Open Access
Jipeng Cui, Qianhui Yang, Jiyue Zhang

и другие.

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(2), С. 546 - 546

Опубликована: Янв. 10, 2025

As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic environmental values. Here, we performed complete assembly annotation of the mitogenome P. using genomic data from PacBio BGI platforms. The is multibranched structure 501,134 bp, divided into two circular chromosomes 325,493 bp 175,641 respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which often translocated nuclear genome mitogenomes gramineous species. We also tissue-specific mitochondrial differentially expressed genes RNAseq data, providing new insights understanding energy allocation regulatory strategies long-term adaptive evolution mitochondria. In addition, studied features more detail, including repetitive sequences, Ka/Ks analyses, codon preferences, intracellular transfer, RNA editing, multispecies phylogenetic analyses. Our results provide an essential molecular resource for genetic characterisation research basis population genetics species Arundiaceae.

Язык: Английский

Процитировано

0
Systematic revelation and meditation on the significance of long exons using representative eukaryotic genomes DOI Creative Commons
Yuange Duan, Qi Cao

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Март 24, 2025

Long exons/introns are not evenly distributed in the genome, but biological significance of this phenomenon remains elusive. Exon properties were analyzed seven well-annotated reference genomes, including human and other representative model organisms: mouse, fruitfly, worm, mouse-ear cress, corn, rice. In all species, last exons genes tend to be longest. Additionally, we found that (1) canonical splicing motifs strongly underrepresented 3'UTR; (2) Last have low GC content; (3) Comparing with first D. melanogaster demonstrate lower content than internal exons. It cannot excluded exert essential regulatory roles is subjected natural selection, exhibiting differential tendency, compared parts gene body.

Язык: Английский

Процитировано

0
Bioinformatic approaches for accurate assessment of A to I editing in complete transcriptomes DOI
Eli Eisenberg

Methods in enzymology on CD-ROM/Methods in enzymology, Год журнала: 2024, Номер unknown, С. 241 - 265

Опубликована: Ноя. 23, 2024

Язык: Английский

Процитировано

1
Host-dependent C-to-U RNA editing in SARS-CoV-2 creates novel viral genes with optimized expressibility DOI Creative Commons

Pirun Zhang,

Wenli Zhang, Jiahuan Li

и другие.

Frontiers in Cellular and Infection Microbiology, Год журнала: 2024, Номер 14

Опубликована: Окт. 9, 2024

Rampant C-to-U RNA editing drives the mutation and evolution of SARS-CoV-2. While much attention has been paid to missense mutations, events leading A U G thus creating novel ORFs were uninvestigated. By utilizing public time-course data from worldwide SARS-CoV-2 population, we systematically identified “A G-gain mutations” caused by editing. Synonymous mutations special focus. total 58 synonymous sites are able create out-of-frame in coding sequence (CDS). These showed significantly higher allele frequency (AF) increasing rate ( d AF/ t) than other suggesting that these AUG-gain conferred additional benefits virus subjected positive selection. The predicted new created following advantages compared random expectation: they have longer lengths, codon adaptation index (CAI), Kozak scores, tRNA (tAI). putatively high expressibility very likely be functional, providing an explanation for selection on mutations. Our study proposed a possible mechanism emergence de novo genes This idea should helpful studying

Язык: Английский

Процитировано

0
In silico and experimental approaches for validating RNA editing events in transcriptomes DOI Creative Commons
Lai Wei

RNA Biology, Год журнала: 2024, Номер 21(1), С. 31 - 36

Опубликована: Ноя. 24, 2024

As a typical RNA virus, SARS-CoV-2 is subjected to editing in host cells. While some researchers believe that traditional variant calling pipeline retrieves all true-positive events from the transcriptome, others argue conventional methods identify many false-positive sites. Here, I describe several additional silico and experimental approaches validate authenticity of SARS-CoV-2. These include requiring strand-specific sequencing, analysis hyperedited reads, linkage analysis, orthogonal like mass spectrometry, use ADAR-deficient findings may improve future analyses on identification editing, especially viruses.

Язык: Английский

Процитировано

0