Differential RNA Editing and Intron Splicing in Soybean Mitochondria during Nodulation

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.

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Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid

mBio ◽

10.1128/mbio.01498-15 ◽

2015 ◽

Vol 6 (6) ◽

Cited By ~ 15

Author(s):

Vojtěch David ◽

Pavel Flegontov ◽

Evgeny Gerasimov ◽

Goro Tanifuji ◽

Hassan Hashimi ◽

...

Keyword(s):

Rna Editing ◽

Deep Sequencing ◽

Gene Loss ◽

Mitochondrial Rna ◽

Evolutionary Perspective ◽

Rna Seq ◽

Protein Coding ◽

Mitochondrial Ribosomes ◽

Protein Coding Genes ◽

Mitochondrial Transcripts

ABSTRACT Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps12), despite the fact that the organelle itself contains more DNA than is present in either the host or endosymbiont nuclear genomes. An in silico analysis of two Perkinsela strains showed that mitochondrial RNA editing and processing machineries typical of kinetoplastid flagellates are generally conserved, and all mitochondrial transcripts undergo U-insertion/deletion editing. Canonical kinetoplastid mitochondrial ribosomes are also present. We have developed software tools for accurate and exhaustive mapping of transcriptome sequencing (RNA-seq) reads with extensive U-insertions/deletions, which allows detailed investigation of RNA editing via deep sequencing. With these methods, we show that up to 50% of reads for a given edited region contain errors of the editing system or, less likely, correspond to alternatively edited transcripts. IMPORTANCE Uridine insertion/deletion-type RNA editing, which occurs in the mitochondrion of kinetoplastid protists, has been well-studied in the model parasite genera Trypanosoma, Leishmania, and Crithidia. Perkinsela provides a unique opportunity to broaden our knowledge of RNA editing machinery from an evolutionary perspective, as it represents the earliest kinetoplastid branch and is an obligatory endosymbiont with extensive reductive trends. Interestingly, up to 50% of mitochondrial transcripts in Perkinsela contain errors. Our study was complemented by use of newly developed software designed for accurate mapping of extensively edited RNA-seq reads obtained by deep sequencing.

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SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency

BMC Bioinformatics ◽

10.1186/s12859-021-04282-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Verônica R. de Melo Costa ◽

Julianus Pfeuffer ◽

Annita Louloupi ◽

Ulf A. V. Ørom ◽

Rosario M. Piro

Keyword(s):

Gene Expression ◽

Cancer Progression ◽

Time Course ◽

Progressive Increase ◽

Rna Seq ◽

Transcript Processing ◽

Aberrant Transcript ◽

Genome Wide ◽

Splicing Efficiency ◽

Nascent Rna

Abstract Background Introns are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing. An efficient splicing of primary transcripts is an essential step in gene expression and its misregulation is related to numerous human diseases. Thus, to better understand the dynamics of this process and the perturbations that might be caused by aberrant transcript processing it is important to quantify splicing efficiency. Results Here, we introduce SPLICE-q, a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification. It supports studies focusing on the implications of splicing efficiency in transcript processing dynamics. SPLICE-q uses aligned reads from strand-specific RNA-seq to quantify splicing efficiency for each intron individually and allows the user to select different levels of restrictiveness concerning the introns’ overlap with other genomic elements such as exons of other genes. We applied SPLICE-q to globally assess the dynamics of intron excision in yeast and human nascent RNA-seq. We also show its application using total RNA-seq from a patient-matched prostate cancer sample. Conclusions Our analyses illustrate that SPLICE-q is suitable to detect a progressive increase of splicing efficiency throughout a time course of nascent RNA-seq and it might be useful when it comes to understanding cancer progression beyond mere gene expression levels. SPLICE-q is available at: https://github.com/vrmelo/SPLICE-q

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Comparative RNA editing profile of mitochondrial transcripts in cytoplasmic male sterile and fertile pigeonpea reveal significant changes at the protein level

Molecular Biology Reports ◽

10.1007/s11033-019-04657-2 ◽

2019 ◽

Vol 46 (2) ◽

pp. 2067-2084

Author(s):

Tanvi Kaila ◽

Swati Saxena ◽

G. Ramakrishna ◽

Anshika Tyagi ◽

Kishor U. Tribhuvan ◽

...

Keyword(s):

Rna Editing ◽

Protein Level ◽

Male Sterile ◽

Cytoplasmic Male Sterile ◽

Mitochondrial Transcripts

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Abstract 2168: Multi-regional RNA-Seq reveals pattern of RNA-editing in brain tumor

10.1158/1538-7445.am2021-2168 ◽

2021 ◽

Author(s):

Cheng Yan ◽

Jun Wu ◽

Dan Wang ◽

Lan Su ◽

Yufei Yang

Keyword(s):

Brain Tumor ◽

Rna Editing ◽

Rna Seq

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Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing

PeerJ ◽

10.7717/peerj.9309 ◽

2020 ◽

Vol 8 ◽

pp. e9309

Author(s):

Viktoria Yu Shtratnikova ◽

Mikhail I. Schelkunov ◽

Aleksey A. Penin ◽

Maria D. Logacheva

Keyword(s):

Mitochondrial Genome ◽

Rna Editing ◽

Transcriptome Sequencing ◽

Unique Feature ◽

Genetic Material ◽

Mitochondrial Genes ◽

Vaccinium Macrocarpon ◽

Mitochondrial Genomes ◽

Plastid Genomes ◽

Trans Splicing

Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.

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Automated Isoform Diversity Detector (AIDD): A pipeline for investigating transcriptome diversity of RNA-seq data

10.1101/2020.01.22.915348 ◽

2020 ◽

Author(s):

Noel-Marie Plonski ◽

Emily Johnson ◽

Madeline Frederick ◽

Heather Mercer ◽

Gail Fraizer ◽

...

Keyword(s):

Rna Editing ◽

Large Scale ◽

Neural Progenitor Cells ◽

Viral Infections ◽

Variant Calling ◽

Rna Seq ◽

Major Mechanism ◽

Isoform Diversity ◽

Adar Editing ◽

Transcriptome Diversity

AbstractBackgroundAs the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. Many available tools facilitate analyses of one of the two major mechanisms of transcriptome diversity, namely, differential expression of isoforms due to alternative splicing, while the second major mechanism - RNA editing due to post-transcriptional changes of individual nucleotides – remains under-appreciated. Both these mechanisms play an essential role in physiological and diseases processes, including cancer and neurological disorders. However, elucidation of RNA editing events at transcriptome-wide level requires increasingly complex computational tools, in turn resulting in a steep entrance barrier for labs who are interested in high-throughput variant calling applications on a large scale but lack the manpower and/or computational expertise.ResultsHere we present an easy-to-use, fully automated, computational pipeline (Automated Isoform Diversity Detector, AIDD) that contains open source tools for various tasks needed to map transcriptome diversity, including RNA editing events. To facilitate reproducibility and avoid system dependencies, the pipeline is contained within a pre-configured VirtualBox environment. The analytical tasks and format conversions are accomplished via a set of automated scripts that enable the user to go from a set of raw data, such as fastq files, to publication-ready results and figures in one step. A publicly available dataset of Zika virus-infected neural progenitor cells is used to illustrate AIDD’s capabilities.ConclusionsAIDD pipeline offers a user-friendly interface for comprehensive and reproducible RNA-seq analyses. Among unique features of AIDD are its ability to infer RNA editing patterns, including ADAR editing, and inclusion of Guttman scale patterns for time series analysis of such editing landscapes. AIDD-based results show importance of diversity of ADAR isoforms, key RNA editing enzymes linked with the innate immune system and viral infections. These findings offer insights into the potential role of ADAR editing dysregulation in the disease mechanisms, including those of congenital Zika syndrome. Because of its automated all-inclusive features, AIDD pipeline enables even a novice user to easily explore common mechanisms of transcriptome diversity, including RNA editing landscapes.

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Genome-Wide Analysis of Multiple Organellar RNA Editing Factor (MORF) Family in Kiwifruit (Actinidia chinensis) Reveals Its Roles in Chloroplast RNA Editing and Pathogens Stress

Plants ◽

10.3390/plants11020146 ◽

2022 ◽

Vol 11 (2) ◽

pp. 146

Author(s):

Yuhong Xiong ◽

Jing Fang ◽

Xiaohan Jiang ◽

Tengfei Wang ◽

Kangchen Liu ◽

...

Keyword(s):

Rna Editing ◽

Chloroplast Development ◽

Structural Features ◽

Resistance Mechanisms ◽

Actinidia Chinensis ◽

Rna Seq ◽

Good Taste ◽

Genome Wide ◽

Solid Foundation ◽

Chloroplast Rna

Kiwifruit (Actinidia chinensis) is well known for its high vitamin C content and good taste. Various diseases, especially bacterial canker, are a serious threat to the yield of kiwifruit. Multiple organellar RNA editing factor (MORF) genes are pivotal factors in the RNA editosome that mediates Cytosine-to-Uracil RNA editing, and they are also indispensable for the regulation of chloroplast development, plant growth, and response to stresses. Although the kiwifruit genome has been released, little is known about MORF genes in kiwifruit at the genome-wide level, especially those involved in the response to pathogens stress. In this study, we identified ten MORF genes in the kiwifruit genome. The genomic structures and chromosomal locations analysis indicated that all the MORF genes consisted of three conserved motifs, and they were distributed widely across the seven linkage groups and one contig of the kiwifruit genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the kiwifruit MORF gene family members were classified into six groups (Groups A–F). A synteny analysis indicated that two pairs of MORF genes were tandemly duplicated and five pairs of MORF genes were segmentally duplicated. Moreover, based on analysis of RNA-seq data from five tissues of kiwifruit, we found that both expressions of MORF genes and chloroplast RNA editing exhibited tissue-specific patterns. MORF2 and MORF9 were highly expressed in leaf and shoot, and may be responsible for chloroplast RNA editing, especially the ndhB genes. We also observed different MORF expression and chloroplast RNA editing profiles between resistant and susceptible kiwifruits after pathogen infection, indicating the roles of MORF genes in stress response by modulating the editing extend of mRNA. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes, in particular, for clarifying the resistance mechanisms in kiwifruits and breeding new cultivars with high resistance.

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LeafCutter: annotation-free quantification of RNA splicing

10.1101/044107 ◽

2016 ◽

Cited By ~ 21

Author(s):

Yang I Li ◽

David A Knowles ◽

Jack Humphrey ◽

Alvaro N. Barbeira ◽

Scott P. Dickinson ◽

...

Keyword(s):

Complex Traits ◽

Rna Splicing ◽

Population Variation ◽

Disease Genes ◽

Intron Splicing ◽

Rna Seq ◽

Exon Usage ◽

Molecular Effects ◽

Free Quantification ◽

Gene Expression Levels

AbstractThe excision of introns from pre-mRNA is an essential step in mRNA processing. We developed LeafCutter to study sample and population variation in intron splicing. LeafCutter identifies variable intron splicing events from short-read RNA-seq data and finds alternative splicing events of high complexity. Our approach obviates the need for transcript annotations and circumvents the challenges in estimating relative isoform or exon usage in complex splicing events. LeafCutter can be used both for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). Compared to contemporary methods, we find 1.4–2.1 times more sQTLs, many of which help us ascribe molecular effects to disease-associated variants. Strikingly, transcriptome-wide associations between LeafCutter intron quantifications and 40 complex traits increased the number of associated disease genes at 5% FDR by an average of 2.1-fold as compared to using gene expression levels alone. LeafCutter is fast, scalable, easy to use, and available at https://github.com/davidaknowles/leafcutter.

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Genome-Wide Characterization of RNA Editing Sites in Primary Gastric Adenocarcinoma through RNA-seq Data Analysis

International Journal of Genomics ◽

10.1155/2020/6493963 ◽

2020 ◽

Vol 2020 ◽

pp. 1-16

Author(s):

Javad Behroozi ◽

Shirin Shahbazi ◽

Mohammad Reza Bakhtiarizadeh ◽

Habibollah Mahmoodzadeh

Keyword(s):

Gastric Cancer ◽

Rna Editing ◽

Gastric Adenocarcinoma ◽

Cancer Progression ◽

Variant Calling ◽

Distinct Pattern ◽

Rna Seq ◽

Comprehensive Overview ◽

Protein Coding ◽

Cancer Tissues

RNA editing is a posttranscriptional nucleotide modification in humans. Of the various types of RNA editing, the adenosine to inosine substitution is the most widespread in higher eukaryotes, which is mediated by the ADAR family enzymes. Inosine is recognized by the biological machinery as guanosine; therefore, editing could have substantial functional effects throughout the genome. RNA editing could contribute to cancer either by exclusive editing of tumor suppressor/promoting genes or by introducing transcriptomic diversity to promote cancer progression. Here, we provided a comprehensive overview of the RNA editing sites in gastric adenocarcinoma and highlighted some of their possible contributions to gastric cancer. RNA-seq data corresponding to 8 gastric adenocarcinoma and their paired nontumor counterparts were retrieved from the GEO database. After preprocessing and variant calling steps, a stringent filtering pipeline was employed to distinguish potential RNA editing sites from SNPs. The identified potential editing sites were annotated and compared with those in the DARNED database. Totally, 12362 high-confidence adenosine to inosine RNA editing sites were detected across all samples. Of these, 12105 and 257 were known and novel editing events, respectively. These editing sites were unevenly distributed across genomic regions, and nearly half of them were located in 3 ′ UTR. Our results revealed that 4868 editing sites were common in both normal and cancer tissues. From the remaining sites, 3985 and 3509 were exclusive to normal and cancer tissues, respectively. Further analysis revealed a significant number of differentially edited events among these sites, which were located in protein coding genes and microRNAs. Given the distinct pattern of RNA editing in gastric adenocarcinoma and adjacent normal tissue, edited sites have the potential to serve as the diagnostic biomarkers and therapeutic targets in gastric cancer.

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Genome sequences of both organelles of the grapevine rootstock cultivar 'Börner'

10.1101/2020.03.18.996405 ◽

2020 ◽

Author(s):

Bianca Frommer ◽

Daniela Luise Holtgräwe ◽

Ludger Hausmann ◽

Prisca Viehöver ◽

Bruno Hüttel ◽

...

Keyword(s):

Rna Editing ◽

Mitochondrial Genes ◽

Genome Sequences ◽

Vitis Riparia ◽

Organellar Genomes ◽

Long Reads

Genomic long reads of the interspecific grapevine rootstock cultivar 'Börner' (Vitis riparia GM183 x 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 organellar genomes were maternally inherited to 'Börner' from Vitis riparia.

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