PRMdb: A Repository of Predicted RNA Modifications in Plants

2020 ◽  
Vol 61 (6) ◽  
pp. 1213-1222
Author(s):  
Xuan Ma ◽  
Fuyan Si ◽  
Xiaonan Liu ◽  
Weijiang Luan
Keyword(s):  
Plant Species ◽  
Posttranscriptional Regulation ◽  
Regulation Of Gene Expression ◽  
Rna Modification ◽  
Rna Seq ◽  
Rna Modifications ◽  
High Throughput Analysis ◽  
Functional Studies ◽  
Web Resource ◽  
Wide Range

Abstract Evidence is mounting that RNA modifications play essential roles in posttranscriptional regulation of gene expression. So far, over 150 RNA modifications catalyzed by distinct enzymes have been documented. In plants, genome-wide identification of RNA modifications is largely limited to the model species Arabidopsis thaliana, while lacking in diverse non-model plants. Here, we present PRMdb, a plant RNA modification database, based on the analysis of thousands of RNA-seq, degradome-seq and small RNA-seq data from a wide range of plant species using the well-documented tool HAMR (high-throughput analysis of modified ribonucleotide). PRMdb provides a user-friendly interface that enables easy browsing and searching of the tRNA and mRNA modification data. We show that PRMdb collects high-confidence RNA modifications including novel RNA modification sites that can be validated by genomic PCR and reverse transcription PCR. In summary, PRMdb provides a valuable web resource for deciphering the epitranscriptomes in diverse plant species and will facilitate functional studies of RNA modifications in plants. RPMdb is available via http://www.biosequencing.cn/PRMdb/.

scholarly journals RMVar: an updated database of functional variants involved in RNA modifications

2020 ◽  
Vol 49 (D1) ◽  
pp. D1405-D1412 ◽  
Author(s):  
Xiaotong Luo ◽  
Huiqin Li ◽  
Jiaqi Liang ◽  
Qi Zhao ◽  
Yubin Xie ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Posttranscriptional Regulation ◽  
Association Studies ◽  
Human Diseases ◽  
Rna Modification ◽  
Genome Wide Association Studies ◽  
Rna Modifications ◽  
Functional Studies ◽  
Functional Variants ◽  
New Perspective

Abstract Distinguishing the few disease-related variants from a massive number of passenger variants is a major challenge. Variants affecting RNA modifications that play critical roles in many aspects of RNA metabolism have recently been linked to many human diseases, such as cancers. Evaluating the effect of genetic variants on RNA modifications will provide a new perspective for understanding the pathogenic mechanism of human diseases. Previously, we developed a database called ‘m6AVar’ to host variants associated with m6A, one of the most prevalent RNA modifications in eukaryotes. To host all RNA modification (RM)-associated variants, here we present an updated version of m6AVar renamed RMVar (http://rmvar.renlab.org). In this update, RMVar contains 1 678 126 RM-associated variants for 9 kinds of RNA modifications, namely m6A, m6Am, m1A, pseudouridine, m5C, m5U, 2′-O-Me, A-to-I and m7G, at three confidence levels. Moreover, RBP binding regions, miRNA targets, splicing events and circRNAs were integrated to assist investigations of the effects of RM-associated variants on posttranscriptional regulation. In addition, disease-related information was integrated from ClinVar and other genome-wide association studies (GWAS) to investigate the relationship between RM-associated variants and diseases. We expect that RMVar may boost further functional studies on genetic variants affecting RNA modifications.

scholarly journals RNA Modification Level Estimation with pulseR

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 619
Author(s):  
Etienne Boileau ◽  
Christoph Dieterich
Keyword(s):  
Experimental Approach ◽  
High Efficiency ◽  
Rna Modification ◽  
Model Parameters ◽  
Metabolic Labeling ◽  
Rna Seq ◽  
Rna Modifications ◽  
Log Odds ◽  
Pros And Cons ◽  
Wide Scale

RNA modifications regulate the complex life of transcripts. An experimental approach called LAIC-seq was developed to characterize modification levels on a transcriptome-wide scale. In this method, the modified and unmodified molecules are separated using antibodies specific for a given RNA modification (e.g., m6A). In essence, the procedure of biochemical separation yields three fractions: Input, eluate, and supernatent, which are subjected to RNA-seq. In this work, we present a bioinformatics workflow, which starts from RNA-seq data to infer gene-specific modification levels by a statistical model on a transcriptome-wide scale. Our workflow centers around the pulseR package, which was originally developed for the analysis of metabolic labeling experiments. We demonstrate how to analyze data without external normalization (i.e., in the absence of spike-ins), given high efficiency of separation, and how, alternatively, scaling factors can be derived from unmodified spike-ins. Importantly, our workflow provides an estimate of uncertainty of modification levels in terms of confidence intervals for model parameters, such as gene expression and RNA modification levels. We also compare alternative model parametrizations, log-odds, or the proportion of the modified molecules and discuss the pros and cons of each representation. In summary, our workflow is a versatile approach to RNA modification level estimation, which is open to any read-count-based experimental approach.

scholarly journals AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Andrew J. Robinson ◽  
Muluneh Tamiru ◽  
Rachel Salby ◽  
Clayton Bolitho ◽  
Andrew Williams ◽  
...  
Keyword(s):  
Plant Species ◽  
Rna Seq ◽  
Functional Studies

scholarly journals The prevalent RNA modification on SARS-CoV-2 RNAs may confound the SNP profile and evolutionary patterns revealed by previous studies

2020 ◽  
Author(s):  
Yan Wang ◽  
Yanhong Gai ◽  
Yuefan Li ◽  
Chunxiao Li ◽  
Ziliang Li ◽  
...  
Keyword(s):  
Rna Virus ◽  
Variant Calling ◽  
Virus Genome ◽  
Rna Modification ◽  
High Signal ◽  
Rna Seq ◽  
Rna Modifications ◽  
Severe Damage ◽  
Evolutionary Patterns ◽  
Recent Outbreak

Abstract Background The recent outbreak of SARS-CoV-2 has caused severe damage to the world. The concomitant papers on the evolutionary patterns of SARS-CoV-2 is continuously emerging. Studies has utilized the publically available RNA-seq data to find out the so-called SNPs in the virus genome and analyzed their selection patterns. Methods We downloaded a set of RNA-seq data and performed a well-established but modified variant calling pipeline to allow the identification of multiple clustered mutations. Results We found prevalent “putative” but reliably detected A-to-G RNA modifications in the RNA-seq data of SARS-CoV-2 with high signal to noise ratios, presumably caused by the host’s deamination enzymes. Importantly, since SARS-CoV-2 is an RNA virus, it is technically impossible to truly distinguish SNPs and RNA modifications from the RNA-seq data alone. Conclusions The technically indistinguishable RNA modifications and SNPs of SARS-CoV-2 have complicated the situation where many researchers intend to unveil the evolutionary patterns behind the mutation spectrum. This is not a problem for DNA organisms but should be seriously considered when we are investigating the RNA viruses.

scholarly journals Identification of BvgA-Dependent and BvgA-Independent Small RNAs (sRNAs) in Bordetella pertussis Using the Prokaryotic sRNA Prediction Toolkit ANNOgesic

2021 ◽  
Author(s):  
Kyung Moon ◽  
Minji Sim ◽  
Chin-Hsien Tai ◽  
Kyungyoon Yoo ◽  
Charlotte Merzbacher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Posttranscriptional Regulation ◽  
Transcriptome Sequencing ◽  
Regulation Of Gene Expression ◽  
Bacterial Virulence ◽  
Human Pathogen ◽  
Rna Seq ◽  
Content Type ◽  
Search Program

Noncoding small RNAs (sRNAs) are crucial for posttranscriptional regulation of gene expression in all organisms and are known to be involved in the regulation of bacterial virulence. We have investigated the presence of sRNAs in the obligate human pathogen B. pertussis , using transcriptome sequencing (RNA-seq) and the recently developed prokaryotic sRNA search program ANNOgesic.

scholarly journals SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs

2018 ◽  
Author(s):  
Junchao Shi ◽  
Eun-A Ko ◽  
Kenton M. Sanders ◽  
Qi Chen ◽  
Tong Zhou
Keyword(s):  
Cell Types ◽  
Mouse Cell ◽  
Rapid Expansion ◽  
Rna Modification ◽  
Rna Seq ◽  
Additional Species ◽  
Wide Range ◽  
Non Coding Rnas ◽  
Nucleolar Rna ◽  
Mismatch Rate

AbstractHigh-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), Piwi-interacting RNA (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline optimized for rRNA- and tRNA- derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users’ input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0.

scholarly journals Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 35 ◽  
Author(s):  
Yuri Motorin ◽  
Mark Helm
Keyword(s):  
Deep Sequencing ◽  
Global Scale ◽  
High Rate ◽  
Rna Modification ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Rna Modifications ◽  
Accuracy And Precision ◽  
A Cell ◽  
Mapping Techniques

New analytics of post-transcriptional RNA modifications have paved the way for a tremendous upswing of the biological and biomedical research in this field. This especially applies to methods that included RNA-Seq techniques, and which typically result in what is termed global scale modification mapping. In this process, positions inside a cell`s transcriptome are receiving a status of potential modification sites (so called modification calling), typically based on a score of some kind that issues from the particular method applied. The resulting data are thought to represent information that goes beyond what is contained in typical transcriptome data, and hence the field has taken to use the term “epitranscriptome”. Due to the high rate of newly published mapping techniques, a significant number of chemically distinct RNA modifications have become amenable to mapping, albeit with variegated accuracy and precision, depending on the nature of the technique. This review gives a brief overview of known techniques, and how they were applied to modification calling.

scholarly journals The Airway Epithelium—A Central Player in Asthma Pathogenesis

2020 ◽  
Vol 21 (23) ◽  
pp. 8907
Author(s):  
Jenny Calvén ◽  
Elisabeth Ax ◽  
Madeleine Rådinger
Keyword(s):  
Airway Epithelium ◽  
Posttranscriptional Regulation ◽  
Inflammatory Responses ◽  
Regulation Of Gene Expression ◽  
Airflow Obstruction ◽  
Airway Disease ◽  
Airway Epithelial ◽  
Epithelial Barrier Function ◽  
Wide Range ◽  
External Stimuli

Asthma is a chronic inflammatory airway disease characterized by variable airflow obstruction in response to a wide range of exogenous stimuli. The airway epithelium is the first line of defense and plays an important role in initiating host defense and controlling immune responses. Indeed, increasing evidence indicates a range of abnormalities in various aspects of epithelial barrier function in asthma. A central part of this impairment is a disruption of the airway epithelial layer, allowing inhaled substances to pass more easily into the submucosa where they may interact with immune cells. Furthermore, many of the identified susceptibility genes for asthma are expressed in the airway epithelium. This review focuses on the biology of the airway epithelium in health and its pathobiology in asthma. We will specifically discuss external triggers such as allergens, viruses and alarmins and the effect of type 2 inflammatory responses on airway epithelial function in asthma. We will also discuss epigenetic mechanisms responding to external stimuli on the level of transcriptional and posttranscriptional regulation of gene expression, as well the airway epithelium as a potential treatment target in asthma.

scholarly journals Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists

2012 ◽  
Vol 2012 ◽  
pp. 1-21 ◽  
Author(s):  
Rosemary Jagus ◽  
Tsvetan R. Bachvaroff ◽  
Bhavesh Joshi ◽  
Allen R. Place
Keyword(s):  
Regulation Of Gene Expression ◽  
Babesia Bovis ◽  
Initiation Factor ◽  
Model Organisms ◽  
Text Book ◽  
Translational Initiation ◽  
Functional Studies ◽  
Wide Range ◽  
Genome Features ◽  
Multicellular Organisms

The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasiteBabesia bovisto 112,000-220,050 Mb in the dinoflagellateProrocentrum micans. Protists possess numerous cellular, molecular and biochemical traits not observed in “text-book” model organisms. These features challenge some of the concepts and assumptions about the regulation of gene expression in eukaryotes. Like multicellular eukaryotes, many protists encode multiple eIF4Es, but few functional studies have been undertaken except in parasitic species. An earlier phylogenetic analysis of protist eIF4Es indicated that they cannot be grouped within the three classes that describe eIF4E family members from multicellular organisms. Many more protist sequences are now available from which three clades can be recognized that are distinct from the plant/fungi/metazoan classes. Understanding of the protist eIF4Es will be facilitated as more sequences become available particularly for the under-represented opisthokonts and amoebozoa. Similarly, a better understanding of eIF4Es within each clade will develop as more functional studies of protist eIF4Es are completed.

scholarly journals Critical Roles of N6-Methyladenosine (m6A) in Cancer and Virus Infection

Biomolecules ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1071 ◽  
Author(s):  
Ken Asada ◽  
Amina Bolatkan ◽  
Ken Takasawa ◽  
Masaaki Komatsu ◽  
Syuzo Kaneko ◽  
...  
Keyword(s):  
Virus Infection ◽  
Cancer Biology ◽  
Viral Infections ◽  
Regulation Of Gene Expression ◽  
Rna Modification ◽  
Integrated Analysis ◽  
Biological Functions ◽  
Rna Modifications ◽  
Long Time ◽  
Epigenetic Analysis

Studies have shown that epigenetic abnormalities are involved in various diseases, including cancer. In particular, in order to realize precision medicine, the integrated analysis of genetics and epigenetics is considered to be important; detailed epigenetic analysis in the medical field has been becoming increasingly important. In the epigenetics analysis, DNA methylation and histone modification analyses have been actively studied for a long time, and many important findings were accumulated. On the other hand, recently, attention has also been focused on RNA modification in the field of epigenetics; now it is known that RNA modification is associated with various biological functions, such as regulation of gene expression. Among RNA modifications, functional analysis of N6-methyladenosine (m6A), the most abundant RNA modification found from humans to plants is actively progressing, and it has also been known that m6A abnormality is involved in cancer and other diseases. Importantly, recent studies have shown that m6A is related to viral infections. Considering the current world situation under threat of viral infections, it is important to deepen knowledge of RNA modification from the viewpoint of viral diseases. Hence, in this review, we have summarized the recent findings regarding the roles of RNA modifications in biological functions, cancer biology, and virus infection, particularly focusing on m6A in mRNA.

Sign in / Sign up

Export Citation Format

Share Document