scholarly journals Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events

2014 ◽  
Author(s):  
Laure Frésard ◽  
Sophie Leroux ◽  
Pierre-François Roux ◽  
C Klopp ◽  
Stéphane Fabre ◽  
...  
Keyword(s):  
Rna Editing ◽  
High Throughput Sequencing ◽  
Nucleotide Substitutions ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Level Increase ◽  
Functional Consequences ◽  
Genome Screening ◽  
Editing Level

RNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating an alternative nucleotide, not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is more and more described in mammals, notably since the availability of next generation sequencing technologies allowing a whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken are still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, to understand to what extent this phenomenon is conserved in vertebrates. We performed RNA and DNA sequencing from 8 embryos. Being aware of common pitfalls inherent to sequence analyses leading to false positive discovery, we stringently filtered our datasets and found less than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual editing level increase with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, and provide support of an absence of non A-to-I events from the chicken transcriptome.

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

scholarly journals Adenosine-to-inosine RNA editing may be implicated in human pathogenesis

2019 ◽  
pp. 22-25
Author(s):  
AA Kliuchnikova ◽  
SA Moshkovskii
Keyword(s):  
Immune Responses ◽  
Rna Editing ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Common Mechanism ◽  
Adenosine Deaminases ◽  
Human Transcriptome ◽  
Sequencing Technologies

Adenosine-to-inosine (A-to-I) RNA editing is a common mechanism of post-transcriptional modification in many metazoans including vertebrates; the process is catalyzed by adenosine deaminases acting on RNA (ADARs). Using high-throughput sequencing technologies resulted in finding thousands of RNA editing sites throughout the human transcriptome however, their functions are still poorly understood. The aim of this brief review is to draw attention of clinicians and biomedical researchers to ADAR-mediated RNA editing phenomenon and its possible implication in development of neuropathologies, antiviral immune responses and cancer.

Genome wide quantification of A-to-I RNA editing activity

2019 ◽  
Author(s):  
Shalom Hillel Roth ◽  
Erez Y. Levanon ◽  
Eli Eisenberg
Keyword(s):  
Rna Editing ◽  
Innate Immune ◽  
Rna Modification ◽  
Immune Disorders ◽  
Computational Tool ◽  
Genome Wide ◽  
Editing Activity ◽  
Single Number ◽  
Editing Level

Abstract Adenosine to inosine (A-to-I) RNA editing by the ADAR enzymes is a common RNA modification, preventing false activation of the innate immune system by endogenous dsRNAs. Methods for quantification of ADAR activity are sought after, due to an increasing interest in the role of ADARs in cancer and auto-immune disorders, as well as attempts to harness the ADAR enzymes for RNA engineering. Here we present the Alu Editing Index (AEI), a robust and simple-to-use computational tool devised for this purpose that produces a single number representing the global editing level from BAM files. The AEI tool is available at https://github.com/a2iEditing/RNAEditingIndexer

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.

scholarly journals Integrated computational and experimental methods for the characterization of the frequency and functional consequences of RNA editing in microRNAs

2020 ◽  
Author(s):  
Σπυρίδων Ταστσόγλου
Keyword(s):  
Rna Editing ◽  
Small Rna Sequencing ◽  
Messenger Rnas ◽  
Non Coding Rna ◽  
Functional Consequences ◽  
Recognition Elements ◽  
Next Generation Sequencing Ngs ◽  
High Throughput Experiments ◽  
Long Non Coding Rna

Η ανακάλυψη των μικρών RNAs (microRNAs, miRNAs) τη δεκαετία του 1990 και άλλων κλάσεων μη-κωδικοποιών RNAs (non-coding RNAs, ncRNAs), δημιούργησε ένα πεδίο εντατικής έρευνας. Στο χώρο αυτό αναδείχτηκε η σημασία της μελέτης των αλληλεπιδράσεων των ncRNAs, τόσο μεταξύ τους όσο και με κωδικοποιά μετάγραφα (messenger RNAs, mRNAs). Η βιοπληροφορική ανάλυση αποτελεί κύριο μέσο για τη χαρτογράφηση και σύγκριση της αφθονίας των κωδικοποιών και μη-κωδικοποιών RNAs και των αλληλεπιδράσεων μεταξύ τους, τόσο σε παθολογικές όσο και σε φυσιολογικές καταστάσεις. Η πρόοδος της βιοτεχνολογίας επέτρεψε την ανάπτυξη πληθώρας πειραμάτων αλληλούχησης υψηλής διεκπεραιωτικής ικανότητας (high-throughput experiments), τα οποία αποφέρουν τεράστιο όγκο βιολογικών δεδομένων. Η ανάλυση και αξιοποίηση των δεδομένων αυτών βασίζεται εξ' ολοκλήρου σε αλγορίθμους και υπολογιστικές μεθοδολογίες αιχμής. Η αξιοποίηση και ενσωμάτωση (integration) συνόλων δεδομένων από πειράματα Αλληλούχησης Επόμενης Γενιάς (Next Generation Sequencing, NGS) επιτρέπει την ανάπτυξη μεθόδων/μοντέλων που αναπαριστούν ή καταγράφουν με πιστότητα τη βιογένεση, το μηχανισμό δράσης, καθώς και τις τροποποιήσεις των ncRNAs και επιτρέπουν τη μελέτη βιολογικών μηχανισμών, την ανάδειξη θεραπευτικών στόχων και διαγνωστικών βιοδεικτών. Η παρούσα διατριβή επικεντρώνεται στην πιο εντατικά μελετούμενη κατηγορία ncRNAs, τα miRNAs. Πρόκειται για RNAs μήκους περίπου 22 νουκλεοτιδίων που δρουν ως ισχυροί μετα-μεταγραφικοί ρυθμιστές της γονιδιακής έκφρασης, στοχεύοντας κωδικοποιά (mRNA) και μακρά μη-κωδικοποιά (π.χ. long non-coding RNA, lncRNA) μετάγραφα σε μικρές ακολουθίες τους που αποκαλούνται Στοιχεία Αναγνώρισης από miRNAs (miRNA Recognition Elements, MREs). Κατά τη στόχευση, τα miRNAs προσδένονται στα MREs με βάση σύνθετους κανόνες τέλειας ή ατελούς συμπληρωματικότητας του RNA, επάγοντας την καταστολή της μετάφρασης και/ή την αποικοδόμησή του. Η πλειοψηφία των βιολογικών διεργασιών στα ανώτερα θηλαστικά ρυθμίζεται από τη δράση των miRNAs.Η μετα-μεταγραφική τροποποίηση (RNA editing) των miRNAs από εξειδικευμένα ένζυμα αποτελεί μια φυσιολογική βιολογική διεργασία που μεταβάλλει το ρεπερτόριο στόχευσής τους. Η μεταβολή αυτή δύναται να είναι ήπια ή δραστική, ανάλογα με τη θέση στην οποία λαμβάνει χώρα η τροποποίηση. Τα πειράματα NGS επιτρέπουν την ταυτόχρονη μελέτη του RNA editing σε όλα τα μεταγραφθέντα RNAs, όμως η αναγνώριση συμβάντων τροποποίησης μέσα από αυτά αποτελεί πρόκληση· οι παρατηρούμενες αλλαγές στη γνωστή ακολουθία των RNAs ενδέχεται εναλλακτικά να οφείλονται στην παρουσία μεταλλαγών στο επίπεδο του DNA ή σε σφάλματα κατά την αλληλούχηση.Κατά τη διατριβή αυτή σχεδιάστηκε αλγόριθμος ταυτοποίησης περιστατικών RNA editing στα miRNAs, ο οποίος συνδυάζει σύνολα δεδομένων Αλληλούχησης των Μικρών RNAs (small RNA Sequencing) με πληροφορίες για την παρουσία μεταλλαγών, προερχόμενες από Βάσεις Δεδομένων αναφοράς ή πειράματα Αλληλούχησης του Γονιδιώματος (Whole Genome Sequencing) του ίδιου ατόμου, ιστού, ή της ίδιας πειραματικής συνθήκης. Ο αλγόριθμος αξιοποιήθηκε για την ταυτοποίηση συμβάντων RNA τροποποίησης στην ακολουθία των miRNAs σε υγιείς/καρκινικούς ιστούς και κυτταρικές σειρές. Πέραν της καταγραφής των πιο επιφανών περιπτώσεων τροποποίησης, τα miRNAs που βρέθηκαν τροποποιημένα υποβλήθηκαν σε ανάλυση για να αναδειχθεί η μεταβολή στο ρεπερτόριο στόχευσής τους, χρησιμοποιώντας αλγορίθμους αιχμής για την εύρεση των στόχων τους. Επίσης, μελετήθηκαν συγκριτικά χαρακτηριστικά της εξελικτικής συντήρησης και της θερμοδυναμικής ευστάθειας των ακολουθιών των miRNAs στα οποία παρατηρούνται φαινόμενα RNA τροποποίησης. Κατά την εκπόνηση του διδακτορικού μου, συμμετείχα σε 7 δημοσιευμένες εργασίες σε επιστημονικά περιοδικά υψηλού κύρους (μία παρουσίαση εργαλείου ποσοτικοποίησης των μικρών RNAs, τρεις εργασίες σχετικές με τη μελέτη της στόχευσης mRNAs/lncRNAs από miRNAs, μία παρουσίαση Βάσης Δεδομένων με συσχετίσεις της αφθονίας μικροβίων με ασθένειες και δύο μεταγραφωματικές μελέτες δράσης εμβολίων ενάντια στη λεϊσμάνια), καθώς και στη συγγραφή ενός κεφαλαίου βιβλίου αναφορικά με τις υπολογιστικές μεθόδους μελέτης των miRNAs. Έχω παρουσιάσει ερευνητικά ευρήματα συνολικά σε 7 επιστημονικά συνέδρια-ημερίδες (4 εθνικά, 3 διεθνή), και έχω συμβάλει στη διοργάνωση του Πανευρωπαϊκού Συνεδρίου Βιοπληροφορικής ECCB’18 και της 5ης Ημερίδας Μεταπτυχιακών και Μεταδιδακτόρων του Ελληνικού Ινστιτούτου Παστέρ, το 2019. Σύμφωνα με το Google Scholar οι εργασίες στις οποίες μετέχω έχουν μέχρι στιγμής λάβει 356 αναφορές. Στις 7/12/2016 έγινε δεκτή η αίτησή μου στο Ίδρυμα Κρατικών Υποτροφιών για χρηματοδότηση διατριβής με αντικείμενο την υπολογιστική και πειραματική μελέτη του RNA editing φαινομένου στα microRNAs, μέσα από μια υποτροφία διάρκειας 36 μηνών.

scholarly journals Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 436 ◽  
Author(s):  
Varvara Maliogka ◽  
Angelantonio Minafra ◽  
Pasquale Saldarelli ◽  
Ana Ruiz-García ◽  
Miroslav Glasa ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Infected Plant ◽  
Fruit Trees ◽  
Plant Viruses ◽  
Fruit Tree ◽  
Advantages And Disadvantages ◽  
Sequencing Technologies ◽  
Recent Advances

Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed.

scholarly journals Identification and characterization of salt-tolerance relative miRNAs in Procambarus clarkii by high-throughput sequencing

ExRNA ◽  
2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Fangfang Jin ◽  
Yuling Sun
Keyword(s):  
Salt Tolerance ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Procambarus Clarkii ◽  
Economic Losses ◽  
Srna Library ◽  
Genome Wide ◽  
A Genome

Abstract Procambarus clarkii is one of the important economic species in China and has been served as tasty food in recent years after being introduced to Nanjing. Significant problems of environment factors, such as salinity, pH and temperature, especially salinity, has the potential to result in significant economic losses in many crayfish-producing farms in China. miRNAs are a kind of ~ 22 nucleotide small non coding RNAs which were encoded by plants, animals and some viruses with functions in RNA silencing or post-transcription regulation. We constructed four sRNA library of P. clarkia from different tissues and treatments by using high-throughput sequencing technology. A total of 101 conserved miRNAs and two novel pre-miRNAs were identified and RT-qPCR were further performed to confirm existence of part of identified miRNAs. A genome wide expression profile of salt-tolerance miRNAs was proved and three miRNAs were further validated by RT-qPCR with dynamic response to different salinity stages. The study of miRNAs in P. clarkia can help us better understanding the role of miRNAs in salt-tolerance in P. clarkia.

scholarly journals A porcine brain-wide RNA editing landscape

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jinrong Huang ◽  
Lin Lin ◽  
Zhanying Dong ◽  
Ling Yang ◽  
Tianyu Zheng ◽  
...  
Keyword(s):  
Rna Editing ◽  
Repetitive Sequences ◽  
Brain Regions ◽  
Mammalian Brain ◽  
Protein Coding ◽  
Coding Regions ◽  
Pig Brain ◽  
Genome Wide ◽  
A Genome ◽  
Editing Level

AbstractAdenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is an essential post-transcriptional modification. Although hundreds of thousands of RNA editing sites have been reported in mammals, brain-wide analysis of the RNA editing in the mammalian brain remains rare. Here, a genome-wide RNA-editing investigation is performed in 119 samples, representing 30 anatomically defined subregions in the pig brain. We identify a total of 682,037 A-to-I RNA editing sites of which 97% are not identified before. Within the pig brain, cerebellum and olfactory bulb are regions with most edited transcripts. The editing level of sites residing in protein-coding regions are similar across brain regions, whereas region-distinct editing is observed in repetitive sequences. Highly edited conserved recoding events in pig and human brain are found in neurotransmitter receptors, demonstrating the evolutionary importance of RNA editing in neurotransmission functions. Although potential data biases caused by age, sex or health status are not considered, this study provides a rich resource to better understand the evolutionary importance of post-transcriptional RNA editing.

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