scholarly journals Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing

2021 ◽  
Vol 22 (18) ◽  
pp. 9842
Author(s):  
Zheng-Shan He ◽  
Andan Zhu ◽  
Jun-Bo Yang ◽  
Weishu Fan ◽  
De-Zhu Li
Keyword(s):  
Rna Editing ◽  
Regulation Of Gene Expression ◽  
Basal Angiosperm ◽  
Intron Splicing ◽  
Sequencing Data ◽  
Full Spectrum ◽  
Short Reads ◽  
Codon Preference ◽  
Organelle Genomes ◽  
Cis And Trans

Posttranscriptional modifications, including intron splicing and RNA editing, are common processes during regulation of gene expression in plant organelle genomes. However, the intermediate products of intron-splicing, and the interplay between intron-splicing and RNA-editing were not well studied. Most organelle transcriptome analyses were based on the Illumina short reads which were unable to capture the full spectrum of transcript intermediates within an organelle. To fully investigate the intermediates during intron splicing and the underlying relationships with RNA editing, we used PacBio DNA-seq and Iso-seq, together with Illumina short reads genome and transcriptome sequencing data to assemble the chloroplast and mitochondrial genomes of Nymphaea ‘Joey Tomocik’ and analyze their posttranscriptional features. With the direct evidence from Iso-seq, multiple intermediates partially or fully intron-spliced were observed, and we also found that both cis- and trans-splicing introns were spliced randomly. Moreover, by using rRNA-depleted and non-Oligo(dT)-enrichment strand-specific RNA-seq data and combining direct SNP-calling and transcript-mapping methods, we identified 98 and 865 RNA-editing sites in the plastome and mitogenome of N. ‘Joey Tomocik’, respectively. The target codon preference, the tendency of increasing protein hydrophobicity, and the bias distribution of editing sites are similar in both organelles, suggesting their common evolutionary origin and shared editing machinery. The distribution of RNA editing sites also implies that the RNA editing sites in the intron and exon regions may splice synchronously, except those exonic sites adjacent to intron which could only be edited after being intron-spliced. Our study provides solid evidence for the multiple intermediates co-existing during intron-splicing and their interplay with RNA editing in organelle genomes of a basal angiosperm.

Evolutionary Model of Plastidial RNA Editing in Angiosperms Presumed from Genome-Wide Analysis of Amborella trichopoda

2019 ◽  
Vol 60 (10) ◽  
pp. 2141-2151 ◽  
Author(s):  
Kota Ishibashi ◽  
Ian Small ◽  
Toshiharu Shikanai
Keyword(s):  
Phylogenetic Tree ◽  
Rna Editing ◽  
Nuclear Genome ◽  
Evolutionary Model ◽  
Basal Angiosperm ◽  
Pentatricopeptide Repeat ◽  
Protein Coding ◽  
Codon Preference ◽  
Genome Wide ◽  
Branching Points

Abstract Amborella trichopoda is placed close to the base of the angiosperm lineage (basal angiosperm). By genome-wide RNA sequencing, we identified 184C-to-U RNA editing sites in the plastid genome of Amborella. This number is much higher than that observed in other angiosperms including maize (44 sites), rice (39 sites) and grape (115 sites). Despite the high frequency of RNA editing, the biased distribution of RNA editing sites in the genome, target codon preference and nucleotide preference adjacent to the edited cytidine are similar to that in other angiosperms, suggesting a common editing machinery. Consistent with this idea, the Amborella nuclear genome encodes 2–3 times more of the E- and DYW-subclass members of pentatricopeptide repeat proteins responsible for RNA editing site recognition in plant organelles. Among 165 editing sites in plastid protein coding sequences in Amborella, 100 sites were conserved at least in one out of 38 species selected to represent key branching points of the angiosperm phylogenetic tree. We assume these 100 sites represent at least a subset of the sites in the plastid editotype of ancestral angiosperms. We then mapped the loss and gain of editing sites on the phylogenetic tree of angiosperms. Our results support the idea that the evolution of angiosperms has led to the loss of RNA editing sites in plastids.

scholarly journals Genome Sequences of Both Organelles of the Grapevine Rootstock Cultivar ‘Börner’

2020 ◽  
Vol 9 (15) ◽  
Author(s):  
Bianca Frommer ◽  
Daniela Holtgräwe ◽  
Ludger Hausmann ◽  
Prisca Viehöver ◽  
Bruno Huettel ◽  
...  
Keyword(s):  
Rna Editing ◽  
Mitochondrial Genes ◽  
Genome Sequences ◽  
Content Type ◽  
Vitis Riparia ◽  
Long Reads ◽  
Organelle Genomes

Genomic long reads of the interspecific grapevine rootstock cultivar ‘Börner’ (Vitis riparia GM183 × Vitis cinerea Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes, including the RNA editing sites. The organelle genomes in ‘Börner’ were maternally inherited from Vitis riparia.

scholarly journals Developmental atlas of the RNA editome in Sus scrofa skeletal muscle

DNA Research ◽  
2019 ◽  
Vol 26 (3) ◽  
pp. 261-272 ◽  
Author(s):  
Yalan Yang ◽  
Min Zhu ◽  
Xinhao Fan ◽  
Yilong Yao ◽  
Junyu Yan ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Rna Editing ◽  
Sus Scrofa ◽  
Muscle Development ◽  
Rna Seq ◽  
Sequencing Data ◽  
Adenosine Deaminases ◽  
Bisulphite Sequencing ◽  
Highly Correlated ◽  
Gain Loss

AbstractAdenosine-to-inosine (A-to-I) RNA editing meditated by adenosine deaminases acting on RNA (ADARs) enzymes is a widespread post-transcriptional event in mammals. However, A-to-I editing in skeletal muscle remains poorly understood. By integrating strand-specific RNA-seq, whole genome bisulphite sequencing, and genome sequencing data, we comprehensively profiled the A-to-I editome in developing skeletal muscles across 27 prenatal and postnatal stages in pig, an important farm animal and biomedical model. We detected 198,892 A-to-I editing sites and found that they occurred more frequently at prenatal stages and showed low conservation among pig, human, and mouse. Both the editing level and frequency decreased during development and were positively correlated with ADAR enzymes expression. The hyper-edited genes were functionally related to the cell cycle and cell division. A co-editing module associated with myogenesis was identified. The developmentally differential editing sites were functionally enriched in genes associated with muscle development, their editing levels were highly correlated with expression of their host mRNAs, and they potentially influenced the gain/loss of miRNA binding sites. Finally, we developed a database to visualize the Sus scrofa RNA editome. Our study presents the first profile of the dynamic A-to-I editome in developing animal skeletal muscle and provides evidences that RNA editing is a vital regulator of myogenesis.

PERHAPS: Paired-End short Reads-based HAPlotyping from next-generation Sequencing data

2020 ◽  
Author(s):  
Jie Huang ◽  
Stefano Pallotti ◽  
Qianling Zhou ◽  
Marcus Kleber ◽  
Xiaomeng Xin ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Snp Array ◽  
Simple Approach ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Short Read ◽  
Array Data ◽  
Short Reads ◽  
Generation Sequencing

Abstract The identification of rare haplotypes may greatly expand our knowledge in the genetic architecture of both complex and monogenic traits. To this aim, we developed PERHAPS (Paired-End short Reads-based HAPlotyping from next-generation Sequencing data), a new and simple approach to directly call haplotypes from short-read, paired-end Next Generation Sequencing (NGS) data. To benchmark this method, we considered the APOE classic polymorphism (*1/*2/*3/*4), since it represents one of the best examples of functional polymorphism arising from the haplotype combination of two Single Nucleotide Polymorphisms (SNPs). We leveraged the big Whole Exome Sequencing (WES) and SNP-array data obtained from the multi-ethnic UK BioBank (UKBB, N=48,855). By applying PERHAPS, based on piecing together the paired-end reads according to their FASTQ-labels, we extracted the haplotype data, along with their frequencies and the individual diplotype. Concordance rates between WES directly called diplotypes and the ones generated through statistical pre-phasing and imputation of SNP-array data are extremely high (>99%), either when stratifying the sample by SNP-array genotyping batch or self-reported ethnic group. Hardy-Weinberg Equilibrium tests and the comparison of obtained haplotype frequencies with the ones available from the 1000 Genome Project further supported the reliability of PERHAPS. Notably, we were able to determine the existence of the rare APOE*1 haplotype in two unrelated African subjects from UKBB, supporting its presence at appreciable frequency (approximatively 0.5%) in the African Yoruba population. Despite acknowledging some technical shortcomings, PERHAPS represents a novel and simple approach that will partly overcome the limitations in direct haplotype calling from short read-based sequencing.

scholarly journals ADAR1 Interacts with NF90 through Double-Stranded RNA and Regulates NF90-Mediated Gene Expression Independently of RNA Editing

2005 ◽  
Vol 25 (16) ◽  
pp. 6956-6963 ◽  
Author(s):  
Yongzhan Nie ◽  
Li Ding ◽  
Peter N. Kao ◽  
Robert Braun ◽  
Jing-Hua Yang
Keyword(s):  
Gene Expression ◽  
Rna Editing ◽  
Nuclear Export ◽  
Fetal Liver ◽  
Regulation Of Gene Expression ◽  
Nuclear Export Signal ◽  
Binding Domain ◽  
Double Stranded Rna ◽  
Recognition Element ◽  
Dsrna Binding

ABSTRACT The RNA-editing enzyme ADAR1 modifies adenosines by deamination and produces A-to-I mutations in mRNA. ADAR1 was recently demonstrated to function in host defense and in embryonic erythropoiesis during fetal liver development. The mechanisms for these phenotypic effects are not yet known. Here we report a novel function of ADAR1 in the regulation of gene expression by interacting with the nuclear factor 90 (NF90) proteins, known regulators that bind the antigen response recognition element (ARRE-2) and have been demonstrated to stimulate transcription and translation. ADAR1 upregulates NF90-mediated gene expression by interacting with the NF90 proteins, including NF110, NF90, and NF45. A knockdown of NF90 with small interfering RNA suppresses this function of ADAR1. Coimmunoprecipitation and double-stranded RNA (dsRNA) digestion demonstrate that ADAR1 is associated with NF110, NF90, and NF45 through the bridge of cellular dsRNA. Studies with ADAR1 deletions demonstrate that the dsRNA binding domain and a region covering the Z-DNA binding domain and the nuclear export signal comprise the complete function of ADAR1 in upregulating NF90-mediated gene expression. These data suggest that ADAR1 has the potential both to change information content through editing of mRNA and to regulate gene expression through interacting with the NF90 family proteins.

scholarly journals APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival

2019 ◽  
Vol 20 (22) ◽  
pp. 5621 ◽  
Author(s):  
Mariko Asaoka ◽  
Takashi Ishikawa ◽  
Kazuaki Takabe ◽  
Santosh K. Patnaik
Keyword(s):  
Breast Cancer ◽  
T Cell ◽  
Rna Editing ◽  
Cell Receptor ◽  
Cytolytic Activity ◽  
Sequencing Data ◽  
Immune Activity ◽  
Normal Tissues ◽  
Gene Sets ◽  
M1 Macrophage

APOBEC3 enzymes contribute significantly to DNA mutagenesis in cancer. These enzymes are also capable of converting C bases at specific positions of RNAs to U. However, the prevalence and significance of this C-to-U RNA editing in any cancer is currently unknown. We developed a bioinformatics workflow to determine RNA editing levels at known APOBEC3-mediated RNA editing sites using exome and mRNA sequencing data of 1040 breast cancer tumors. Although reliable editing determinations were limited due to sequencing depth, editing was observed in both tumor and adjacent normal tissues. For 440 sites (411 genes), editing was determinable for ≥5 tumors, with editing occurring in 0.6%–100% of tumors (mean 20%, SD 14%) at an average level of 0.6%–20% (mean 7%, SD 4%). Compared to tumors with low RNA editing, editing-high tumors had enriched expression of immune-related gene sets, and higher T cell and M1 macrophage infiltration, B and T cell receptor diversity, and immune cytolytic activity. Concordant with this, patients with increased RNA editing in tumors had better disease- and progression-free survivals (hazard ratio = 1.67–1.75, p < 0.05). Our study identifies that APOBEC3-mediated RNA editing occurs in breast cancer tumors and is positively associated with elevated immune activity and improved survival.

scholarly journals REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

2020 ◽  
Vol 49 (D1) ◽  
pp. D1012-D1019 ◽  
Author(s):  
Luigi Mansi ◽  
Marco Antonio Tangaro ◽  
Claudio Lo Giudice ◽  
Tiziano Flati ◽  
Eli Kopel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Comparative Genomics ◽  
Rna Editing ◽  
Innate Immune Response ◽  
Transcriptome Sequencing ◽  
Regulation Of Gene Expression ◽  
Innate Immune ◽  
Neurotransmitter Receptors ◽  
Eukaryotic Organisms

Abstract RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of the innate immune response or functioning of several neurotransmitter receptors. Massive transcriptome sequencing has fostered the research in this field. Nonetheless, different aspects of the RNA editing biology are still unknown and need to be elucidated. To support the study of A-to-I RNA editing we have updated our REDIportal catalogue raising its content to about 16 millions of events detected in 9642 human RNAseq samples from the GTEx project by using a dedicated pipeline based on the HPC version of the REDItools software. REDIportal now allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context and hosts the CLAIRE database. Starting from this novel version, REDIportal will start collecting non-human RNA editing changes for comparative genomics investigations. The database is freely available at http://srv00.recas.ba.infn.it/atlas/index.html.

scholarly journals Differential RNA Editing and Intron Splicing in Soybean Mitochondria during Nodulation

2020 ◽  
Vol 21 (24) ◽  
pp. 9378
Author(s):  
Yuzhe Sun ◽  
Min Xie ◽  
Zhou Xu ◽  
Koon Chuen Chan ◽  
Jia Yi Zhong ◽  
...  
Keyword(s):  
Rna Editing ◽  
Mitochondrial Genes ◽  
Protein Abundance ◽  
Intron Splicing ◽  
Rna Seq ◽  
Intron 1 ◽  
Tremendous Amount ◽  
Mitochondrial Transcripts ◽  
Splicing Efficiency ◽  
Transcript Profiles

Nitrogen fixation in soybean consumes a tremendous amount of energy, leading to substantial differences in energy metabolism and mitochondrial activities between nodules and uninoculated roots. While C-to-U RNA editing and intron splicing of mitochondrial transcripts are common in plant species, their roles in relation to nodule functions are still elusive. In this study, we performed RNA-seq to compare transcript profiles and RNA editing of mitochondrial genes in soybean nodules and roots. A total of 631 RNA editing sites were identified on mitochondrial transcripts, with 12% or 74 sites differentially edited among the transcripts isolated from nodules, stripped roots, and uninoculated roots. Eight out of these 74 differentially edited sites are located on the matR transcript, of which the degrees of RNA editing were the highest in the nodule sample. The degree of mitochondrial intron splicing was also examined. The splicing efficiencies of several introns in nodules and stripped roots were higher than in uninoculated roots. These include nad1 introns 2/3/4, nad4 intron 3, nad5 introns 2/3, cox2 intron 1, and ccmFc intron 1. A greater splicing efficiency of nad4 intron 1, a higher NAD4 protein abundance, and a reduction in supercomplex I + III2 were also observed in nodules, although the causal relationship between these observations requires further investigation.

scholarly journals RNA Editing Alters miRNA Function in Chronic Lymphocytic Leukemia

Cancers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1159 ◽  
Author(s):  
Franz J. Gassner ◽  
Nadja Zaborsky ◽  
Daniel Feldbacher ◽  
Richard Greil ◽  
Roland Geisberger
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Rna Editing ◽  
Treatment Resistance ◽  
Lymphocytic Leukemia ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Survival Times ◽  
Specific Expression ◽  
B Cell Leukemia ◽  
Specific Expression Pattern

Chronic lymphocytic leukemia (CLL) is a high incidence B cell leukemia with a highly variable clinical course, leading to survival times ranging from months to several decades. MicroRNAs (miRNAs) are small non-coding RNAs that regulate the expression levels of genes by binding to the untranslated regions of transcripts. Although miRNAs have been previously shown to play a crucial role in CLL development, progression and treatment resistance, their further processing and diversification by RNA editing (specifically adenosine to inosine or cytosine to uracil deamination) has not been addressed so far. In this study, we analyzed next generation sequencing data to provide a detailed map of adenosine to inosine and cytosine to uracil changes in miRNAs from CLL and normal B cells. Our results reveal that in addition to a CLL-specific expression pattern, there is also specific RNA editing of many miRNAs, particularly miR-3157 and miR-6503, in CLL. Our data draw further light on how miRNAs and miRNA editing might be implicated in the pathogenesis of the disease.

scholarly journals Genome-Wide Investigation and Functional Analysis of Sus scrofa RNA Editing Sites across Eleven Tissues

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 327 ◽  
Author(s):  
Zishuai Wang ◽  
Xikang Feng ◽  
Zhonglin Tang ◽  
Shuai Cheng Li
Keyword(s):  
Rna Editing ◽  
Sus Scrofa ◽  
Sequencing Data ◽  
Coding Regions ◽  
Genome Wide ◽  
Model Animal ◽  
High Enrichment ◽  
The Impact ◽  
Sequence Characteristics ◽  
Editing Level

Recently, the prevalence and importance of RNA editing have been illuminated in mammals. However, studies on RNA editing of pigs, a widely used biomedical model animal, are rare. Here we collected RNA sequencing data across 11 tissues and identified more than 490,000 RNA editing sites. We annotated their biological features, detected flank sequence characteristics of A-to-I editing sites and the impact of A-to-I editing on miRNA–mRNA interactions, and identified RNA editing quantitative trait loci (edQTL). Sus scrofa RNA editing sites showed high enrichment in repetitive regions with a median editing level as 15.38%. Expectedly, 96.3% of the editing sites located in non-coding regions including intron, 3′ UTRs, intergenic, and gene proximal regions. There were 2233 editing sites located in the coding regions and 980 of them caused missense mutation. Our results indicated that to an A-to-I editing site, the adjacent four nucleotides, two before it and two after it, have a high impact on the editing occurrences. A commonly observed editing motif is CCAGG. We found that 4552 A-to-I RNA editing sites could disturb the original binding efficiencies of miRNAs and 4176 A-to-I RNA editing sites created new potential miRNA target sites. In addition, we performed edQTL analysis and found that 1134 edQTLs that significantly affected the editing levels of 137 RNA editing sites. Finally, we constructed PRESDB, the first pig RNA editing sites database. The site provides necessary functions associated with Sus scrofa RNA editing study.

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