scholarly journals Detection and Analysis of C-to-U RNA Editing in Rice Mitochondria-Encoded ORFs

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1277
Author(s):  
Peng Zheng ◽  
Dongxin Wang ◽  
Yuqing Huang ◽  
Hao Chen ◽  
Hao Du ◽  
...  
Keyword(s):  
Rna Editing ◽  
Sanger Sequencing ◽  
Open Reading Frames ◽  
Rna Modification ◽  
Rna Seq ◽  
Functional Consequence ◽  
Precise Information ◽  
Conserved Amino Acids ◽  
Reading Frames ◽  
Biological Context

Cytidine to uridine (C-to-U) RNA editing is an important type of substitutional RNA modification and is almost omnipresent in plant chloroplasts and mitochondria. In rice mitochondria, 491 C-to-U editing sites have been identified previously, and case studies have elucidated the function of several C-to-U editing sites in rice, but the functional consequence of most C-to-U alterations needs to be investigated further. Here, by means of Sanger sequencing and publicly available RNA-seq data, we identified a total of 569 C-to-U editing sites in rice mitochondria-encoded open reading frames (ORFs), 85.41% of these editing sites were observed on the first or the second base of a codon, resulting in the alteration of encoded amino acid. Moreover, we found some novel editing sites and several inaccurately annotated sites which may be functionally important, based on the highly conserved amino acids encoded by these edited codons. Finally, we annotated all 569 C-to-U RNA editing sites in their biological context. More precise information about C-to-U editing sites in rice mitochondria-encoded ORFs will facilitate our investigation on the function of C-to-U editing events in rice and also provide a valid benchmark from rice for the analysis of mitochondria C-to-U editing in other plant species.

scholarly journals Site to site detection and analysis of C-to-U RNA editing in rice mitochondria-encoded ORFs

2020 ◽  
Author(s):  
Peng Zheng ◽  
Yuqing Huang ◽  
Hao Chen ◽  
Hao Du ◽  
Jumin Tu
Keyword(s):  
Signal Transduction ◽  
Amino Acids ◽  
Rna Editing ◽  
Environmental Changes ◽  
Organelle Biogenesis ◽  
Functional Consequence ◽  
Precise Information ◽  
Evolutionarily Conserved ◽  
Conserved Amino Acids ◽  
Biological Context

Abstract Background Cytidine to uridine (C-to-U) RNA editing is an important type of substitutional RNA editing. In plants, C-to-U modification is almost omnipresent in chloroplasts and mitochondria, where it mainly serves to restore evolutionarily conserved amino acids by changing the codon information. The important roles that C-to-U RNA editing plays in organelle biogenesis, adaptation to environmental changes, and signal transduction have been confirmed in different plant species. In rice mitochondria, 491 C-to-U editing sites have been identified previously, and case studies have elucidated the function of several C-to-U editing sites in rice, but the functional consequence of most C-to-U alteration need to be investigated further. Results Here, we totally identified 539 C-to-U editing sites in rice mitochondria-encoded ORFs, 87.2% of these editing sites were observed on the first or the second base of a codon, resulting in the alteration of encoded amino acid. Moreover, we found some novel editing sites and several inaccurately annotated sites which may be functionally important, with the support of the highly conserved amino acids encoded by these edited codons. Finally, we annotated all 539 C-to-U RNA editing sites in their biological context. Conclusions We detected 539 C-to-U editing sites in rice mitochondria-encoded ORFs and annotated them with more precise information, which will facilitate our investigation on the function of C-to-U editing events in rice.

scholarly journals The Functions of the Multiproduct and Rapidly Evolving dec-1 Eggshell Gene Are Conserved Between Evolutionarily Distant Species of Drosophila

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1089-1102
Author(s):  
James C Badciong ◽  
Jeffery M Otto ◽  
Gail L Waring
Keyword(s):  
Biological Significance ◽  
Extracellular Proteins ◽  
Female Fertility ◽  
Open Reading Frames ◽  
Amino Acid Variability ◽  
Normal Expression ◽  
Evolutionary Comparison ◽  
Phenotypic Rescue ◽  
Conserved Amino Acids ◽  
Reading Frames

Abstract The Drosophila dec-1 gene encodes multiple proteins that are required for female fertility and proper eggshell morphogenesis. Genetic and immunolocalization data suggest that the different DEC-1 proteins are functionally distinct. To identify regions within the proteins with potential biological significance, we cloned and sequenced the D. yakuba and D. virilis dec-1 homologs. Interspecies comparisons of the predicted translation products revealed rapidly evolving sequences punctuated by blocks of conserved amino acids. Despite extensive amino acid variability, the proteins produced by the different dec-1 homologs were functionally interchangeable. The introduction of transgenes containing either the D. yakuba or the D. virilis dec-1 open reading frames into a D. melanogaster DEC-1 protein null mutant was sufficient to restore female fertility and wild-type eggshell morphology. Normal expression and extracellular processing of the DEC-1 proteins was correlated with the phenotypic rescue. The nature of the conserved features highlighted by the evolutionary comparison and the molecular resemblance of some of these features to those found in other extracellular proteins suggests functional correlates for some of the multiple DEC-1 derivatives.

scholarly journals YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 155 ◽  
Author(s):  
Sandeep Chakraborty ◽  
Monica Britton ◽  
Jill Wegrzyn ◽  
Timothy Butterfield ◽  
Pedro José Martínez-García ◽  
...  
Keyword(s):  
Transition Zone ◽  
Transcript Abundance ◽  
Black Walnut ◽  
Open Reading Frames ◽  
Rna Seq ◽  
Reading Frame ◽  
Homologous Genes ◽  
Associated Proteins ◽  
Molecular Components ◽  
Reading Frames

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software.

scholarly journals Intrinsic and regulated properties of minimally edited trypanosome mRNAs

2019 ◽  
Vol 47 (7) ◽  
pp. 3640-3657 ◽  
Author(s):  
Brianna L Tylec ◽  
Rachel M Simpson ◽  
Laura E Kirby ◽  
Runpu Chen ◽  
Yijun Sun ◽  
...  
Keyword(s):  
Rna Editing ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Substrate Binding ◽  
Open Reading Frames ◽  
Mrna Editing ◽  
Accessory Factors ◽  
Reading Frames ◽  
Complex Components

Abstract Most mitochondrial mRNAs in kinetoplastids require extensive uridine insertion/deletion editing to generate translatable open reading frames. Editing is specified by trans-acting gRNAs and involves a complex machinery including basal and accessory factors. Here, we utilize high-throughput sequencing to analyze editing progression in two minimally edited mRNAs that provide a simplified system due their requiring only two gRNAs each for complete editing. We show that CYb and MURF2 mRNAs exhibit barriers to editing progression that differ from those previously identified for pan-edited mRNAs, primarily at initial gRNA usage and gRNA exchange. We demonstrate that mis-edited junctions arise through multiple pathways including mis-alignment of cognate gRNA, incorrect and sometimes promiscuous gRNA utilization and inefficient gRNA anchoring. We then examined the roles of accessory factors RBP16 and MRP1/2 in maintaining edited CYb and MURF2 populations. RBP16 is essential for initiation of CYb and MURF2 editing, as well as MURF2 editing progression. In contrast, MRP1/2 stabilizes both edited mRNA populations, while further promoting progression of MURF2 mRNA editing. We also analyzed the effects of RNA Editing Substrate Binding Complex components, TbRGG2 and GAP1, and show that both proteins modestly impact progression of editing on minimally edited mRNAs, suggesting a novel function for GAP1.

scholarly journals MultiEditR: An easy validation method for detecting and quantifying RNA editing from Sanger sequencing

2019 ◽  
Author(s):  
Mitchell Kluesner ◽  
Annette Arnold ◽  
Taga Lerner ◽  
Rafail Nikolaos Tasakis ◽  
Sandra Wüst ◽  
...  
Keyword(s):  
Rna Editing ◽  
Sanger Sequencing ◽  
Tumour Progression ◽  
Cost Effective ◽  
Base Change ◽  
Rna Seq ◽  
Multiple Sources ◽  
Base Editing ◽  
Cost Effective Method ◽  
Apobec Family

ABSTRACTRNA editing is the base change that results from RNA deamination by two predominant classes of deaminases; the APOBEC family and the ADAR family. Respectively, deamination of nucleobases by these enzymes are responsible for endogenous editing of cytosine to uracil (C-to-U) and adenosine to inosine (A-to-I). RNA editing is known to play an essential role both in maintaining normal cellular function, as well as altered cellular physiology during oncogenesis and tumour progression. Analysis of RNA editing in these important processes, largely relies on RNA-seq technology for the detection and quantification of RNA editing sites. Despite the power of these technologies, multiple sources of error in detecting and measuring base editing still exist, therefore additional validation and quantification of editing through Sanger sequencing is still required for confirmation of editing. Depending on the number of RNA editing sites that are of interest, this validation step can be both expensive and time-consuming. To address this need we developed the tool MultiEditR which provides a simple, and cost-effective method of detecting and quantifying RNA editing form Sanger sequencing. We expect that MultiEditR will foster further discoveries in this rapidly expanding field.

scholarly journals Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Li ◽  
Urminder Singh ◽  
Zebulun Arendsee ◽  
Eve Syrkin Wurtele
Keyword(s):  
Open Reading Frames ◽  
Rna Seq ◽  
Protein Coding ◽  
Interactive Analysis ◽  
Yeast Data ◽  
Specific Proteins ◽  
Species Specific ◽  
Developmental Conditions ◽  
Reading Frames ◽  
Expression Matrix

The “dark transcriptome” can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression of 6,692 annotated genes and 29,354 unannotated open reading frames (ORFs) in the Saccharomyces cerevisiae genome across diverse environmental, genetic and developmental conditions (3,457 RNA-Seq samples). Over 30% of the highly transcribed ORFs have translation evidence. Phylostratigraphic analysis infers most of these transcribed ORFs would encode species-specific proteins (“orphan-ORFs”); hundreds have mean expression comparable to annotated genes. These data reveal unannotated ORFs most likely to be protein-coding genes. We partitioned a co-expression matrix by Markov Chain Clustering; the resultant clusters contain 2,468 orphan-ORFs. We provide the aggregated RNA-Seq yeast data with extensive metadata as a project in MetaOmGraph (MOG), a tool designed for interactive analysis and visualization. This approach enables reuse of public RNA-Seq data for exploratory discovery, providing a rich context for experimentalists to make novel, experimentally testable hypotheses about candidate genes.

CNCTDISCRIMINATOR: CODING AND NONCODING TRANSCRIPT DISCRIMINATOR — AN EXCURSION THROUGH HYPOTHESIS LEARNING AND ENSEMBLE LEARNING APPROACHES

2013 ◽  
Vol 11 (05) ◽  
pp. 1342002 ◽  
Author(s):  
ASHIS KUMER BISWAS ◽  
BAOJU ZHANG ◽  
XIAOYONG WU ◽  
JEAN X. GAO
Keyword(s):  
Ensemble Learning ◽  
Expression Profiles ◽  
Open Reading Frames ◽  
Learning Approaches ◽  
Rna Seq ◽  
Sequencing Platform ◽  
Noncoding Transcript ◽  
Comparable Performance ◽  
Generation Sequencing ◽  
Reading Frames

The statistics about the open reading frames, the base compositions and the properties of the predicted secondary structures have potential to address the problem of discriminating coding and noncoding transcripts. Again, the Next Generation Sequencing platform, RNA-seq, provides us bounty of data from which expression profiles of the transcripts can be extracted which urged us adding a new set of dimension in this classification task. In this paper, we proposed CNCTDiscriminator — a coding and noncoding transcript discriminating system where we applied the integration of these four categories of features about the transcripts. The feature integration was done using both hypothesis learning and feature specific ensemble learning approaches. The CNCTDiscriminator model which was trained with composition and ORF features outperforms (precision 83.86%, recall 82.01%) other three popular methods — CPC (precision 98.31%, recall 25.95%), CPAT (precision 97.74%, recall 52.50%) and PORTRAIT (precision 84.37%, recall 73.2%) when applied to an independent benchmark dataset. However, the CNCTDiscriminator model that was trained using the ensemble approach shows comparable performance (precision 89.85%, recall 71.08%).

scholarly journals orfipy: a fast and flexible tool for extracting ORFs

2020 ◽  
Author(s):  
Urminder Singh ◽  
Eve Syrkin Wurtele
Keyword(s):  
Open Reading Frames ◽  
Supplementary Information ◽  
Rna Seq ◽  
Flexible Tool ◽  
Coding Regions ◽  
Link Type ◽  
Alternative Reading Frames ◽  
Downstream Analysis ◽  
Fine Tune ◽  
Reading Frames

SummarySearching for ORFs in transcripts is a critical step prior to annotating coding regions in newly-sequenced genomes and to search for alternative reading frames within known genes. With the tremendous increase in RNA-Seq data, faster tools are needed to handle large input datasets. These tools should be versatile enough to fine-tune search criteria and allow efficient downstream analysis. Here we present a new python based tool, orfipy, which allows the user to flexibly search for open reading frames in fasta sequences. The search is rapid and is fully customizable, with a choice of Fasta and BED output formats.Availability and implementationorfipy is implemented in python and is compatible with python v3.6 and higher. Source code: https://github.com/urmi-21/orfipy. Installation: from the source, or via PyPi (https://pypi.org/project/orfipy) or bioconda (https://anaconda.org/bioconda/orfipy)[email protected], [email protected] informationSupplementary data are available at https://github.com/urmi-21/orfipy

scholarly journals RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria

2021 ◽  
Author(s):  
Rick Gelhausen ◽  
Teresa Müller ◽  
Sarah Svensson ◽  
Omer S. Alkhnbashi ◽  
Cynthia M. Sharma ◽  
...  
Keyword(s):  
High Sensitivity ◽  
Predictive Performance ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Rna Seq ◽  
E Coli ◽  
Prediction Tools ◽  
Small Proteins ◽  
Significant Difference ◽  
Reading Frames

Small proteins, those encoded by open reading frames, with less than or equal to 50 codons, are emerging as an important class of cellular macromolecules in all kingdoms of life. However, they are recalcitrant to detection by proteomics or in silico methods. Ribosome profiling (Ribo-seq) has revealed widespread translation of sORFs in diverse species, and this has driven the development of ORF detection tools using Ribo-seq read signals. However, only a handful of tools have been designed for bacterial data, and have not yet been systematically compared. Here, we have performed a comprehensive benchmark of ORF prediction tools which handle bacterial Ribo-seq data. For this, we created a novel Ribo-seq dataset for E. coli, and based on this plus three publicly available datasets for different bacteria, we created a benchmark set by manual labeling of translated ORFs using their Ribo-seq expression profile. This was then used to investigate the predictive performance of four Ribo-seq-based ORF detection tools we found are compatible with bacterial data (REPARATION_blast, DeepRibo, Ribo-TISH and SPECtre). The tool IRSOM was also included as a comparison for tools using coding potential and RNA-seq coverage only. DeepRibo and REPARATION_blast robustly predicted translated ORFs, including sORFs, with no significant difference for those inside or outside of operons. However, none of the tools was able to predict a set of recently identified, novel, experimentally-verified sORFs with high sensitivity. Overall, we find there is potential for improving the performance, applicability, usability, and reproducibility of prokaryotic ORF prediction tools that use Ribo-Seq as input.

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