Η αλληλεπίδραση των ενδογενών ρετροϊών και της μεταγωγικής οδού των ιντερφερονών με την υπομεθυλιωτική θεραπεία στα Μυελοδυσπλαστικά Σύνδρομα.

2021 ◽  
Author(s):  
Χρυσούλα Κορδελλά
Keyword(s):  
Rna Sequencing ◽  
De Novo ◽  
Rna Seq

Τα μυελοδυσπλαστικά σύνδρομα (ΜΔΣ) και η οξεία μυελογενής λευχαιμία (ΟΜΛ) χαρακτηρίζονται από μη φυσιολογικά πρότυπα μεθυλίωσης του DNA, τα οποία συμβάλλουν στη παθοφυσιολογία της νόσου, με αποτέλεσμα τη μη φυσιολογική επιγενετική καταστολή και διαφοροποίηση των αιμοποιητικών βλαστικών κυττάρων του μυελού των οστών (HSCs). Οι υπομεθυλιωτικοί παράγοντες (ΥΜΠ), οι οποία αντιστρέφουν αυτή την επιγενετική καταστολή, όπως είναι η 5-αζακυτιδίνη (AZA) και η 5-αζα-2'-δεοξυκυτιδίνη (DAC), παραμένουν η κύρια θεραπεία επιλογής για τους ασθενείς με ΜΔΣ υψηλού κινδύνου και ΟΜΛ. Παρόλο αυτά, ο ακριβής μηχανισμός δράσης των ΥΜΠ παραμένει αδιευκρίνιστος, ενώ απουσιάσουν και προγνωστικοί παράγοντες απόκρισης στους ΥΜΠ. Πρόσφατα δεδομένα σε καρκινικές κυτταρικές σειρές δείχνουν ότι η επανενεργοποίηση ενδογενών ρετροϊικών στοιχείων και η επακόλουθη επαγωγή κυτταρικής ενδογενούς αντιϊικής απόκρισης ενδέχεται να αποτελούν το υπόβαθρο της αντικαρκινικής δραστηριότητας των ΥΜΠ. Χρησιμοποιώντας την τεχνική RNA sequencing (RNA-seq), πραγματοποιήθηκε σύγκριση των επιπέδων μεταγραφής των ενδογενών ρετροϊικών στοιχείων σε HSC απομονωμένα από το μυελό των οστών ασθενών με ΜΔΣ και χρόνιας μυελομονοκυτταρική λευχαιμία (CMML) πριν και μετά τη θεραπεία με AZA και σε HSC μυελού των οστών προερχόμενα από υγιείς δότες και ασθενείς με πρωτοπαθή ΟΜΛ. Σε συμφωνία και με προηγούμενες βιβλιογραφικές αναφορές, διαπιστώθηκε ότι η θεραπεία με ΑZA αύξησε τη μεταγραφή των ενδογενών ρετροϊικών στοιχείων. Ωστόσο, η αύξηση αυτή δε συσχετίστηκε με το αποτέλεσμα της θεραπείας με ΑΖΑ, καθώς παρατηρήθηκε τόσο στους αποκρινόμενους όσο καις τους μη αποκρινόμενους ασθενείς. Η παρατήρηση αυτή επιβεβαιώθηκε και με τη τεχνική της de novo συναρμολόγησης του μεταγραφώματος, αποκαλύπτοντας ότι οι, αποκρινόμενοι στην ΑΖΑ, ενδογενείς ρετροϊοί δεν αποτελούν καθοριστικό παράγοντα για το αποτέλεσμα της θεραπείας με ΥΜΠ. Επίσης, παρατηρήθηκε έλλειψη επαγωγής μίας αντιϊικής απόκρισης των ιντερφερονών η οποία να σχετίζεται με την απόκριση στη θεραπεία με ΑΖΑ. Αντίθετα, αποκαλύφθηκε ότι η προθεραπευτική έκφραση και η διαδικασία του εναλλακτικού ματίσματος συγκεκριμένων, αναπτυξιακά ρυθμιζόμενων, γονιδίων μπορεί να αποτελούν προγνωστικούς παράγοντες για την ανταπόκριση των ασθενών με ΜΔΣ και CMML-ΙΙ στη θεραπεία με AZA. Συμπερασματικά, η παρούσα διδακτορική διατριβή αναδεικνύει τη μη συμμετοχή των ενδογενών ρετροϊικών στοιχείων στην αποτελεσματικότητα δράσης των ΥΜΠ. Προσδιορίζει ταυτόχρονα τις αναπτυξιακά ρυθμιζόμενες μεταγραφικές υπογραφές συγκεκριμένων γονιδίων, που είτε κωδικοποιούν την αντίστοιχη πρωτεΐνη είτε όχι, ως συσχετίζομενα με μια ευνοϊκή ανταπόκριση των ασθενών με ΜΔΣ και CMML-ΙΙ στη θεραπεία με AZA, προσφέροντας νέους υποψηφίους δείκτες για περαιτέρω αξιολόγηση.

scholarly journals Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9588 ◽  
Author(s):  
Yeonhwa Jo ◽  
Hoseong Choi ◽  
Sen Lian ◽  
Jin Kyong Cho ◽  
Hyosub Chu ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
De Novo ◽  
Reference Database ◽  
Rna Seq ◽  
Rt Pcr ◽  
Virus Identification ◽  
Hop Stunt Viroid ◽  
Chlorotic Leaf ◽  
Peach Trees ◽  
Next Generation Sequencing Ngs

Background Plums are a kind of stone fruit, a category that includes peaches, cherries, apricots, and almonds. In Korea, Japanese plum trees are usually cultivated as they best suit the climate. To date, there have been few studies in Korea on viruses infecting plum trees compared to those infecting peach trees. Methods To identify viruses and viroids infecting plum trees, we collected leaf samples from six different plum cultivars and subjected them to RNA-sequencing (RNA-seq). Six different plum transcriptomes were de novo assembled using the Trinity assembler followed by BLAST searching against a viral reference database. Results We identified hop stunt viroid (HSVd) and six viruses, including apple chlorotic leaf spot virus (ACLSV), little cherry virus-1 (LChV-1), peach virus D (PeVD), peach leaf pitting-associated virus (PLPaV), plum bark necrosis stem pitting-associated virus (PBNSPaV), and prunus necrotic ringspot virus (PNRSV), from six plum cultivars by RNA-seq. RT-PCR confirmed the infection of HSVd and three viruses—ACLSV, PBNSPaV, and PNRSV—in plum trees. However, RT-PCR demonstrated that plum trees in this study were not infected by LChV-1, PeVD, or PLPaV. It is likely that the three viruses LChV-1, PeVD, and PLPaV as identified by RNA-seq were contaminants from other peach libraries caused by index misassignment, which suggests that careful confirmation by other methods should be carried out in next-generation sequencing (NGS)-based virus identification. Taken together, we identified a viroid and three viruses infecting plum trees in Korea.

scholarly journals Rare Variant Phasing and Haplotypic Expression from RNA-Sequencing with phASER

2016 ◽  
Author(s):  
Stephane E. Castel ◽  
Pejman Mohammadi ◽  
Wendy K. Chung ◽  
Yufeng Shen ◽  
Tuuli Lappalainen
Keyword(s):  
Rna Sequencing ◽  
De Novo ◽  
Genomic Analysis ◽  
Population Based ◽  
Rna Seq ◽  
High Confidence ◽  
Population Genetic Analysis ◽  
Haplotype Phasing ◽  
Functional Genomic Analysis ◽  
Expression Studies

Haplotype phasing of genetic variants is important for clinical interpretation of the genome, population genetic analysis, and functional genomic analysis of allelic activity. Here we present phASER, a fast and accurate approach for phasing variants that are overlapped by sequencing reads, including those from RNA-sequencing (RNA-seq), which often span multiple exons due to splicing. This provides 1) dramatically more accurate phasing of rare and de novo variants compared to population-based phasing; 2) phasing of variants in the same gene up to hundreds of kilobases away which cannot be obtained from DNA-sequencing reads; 3) high confidence measures of haplotypic expression, greatly improving power for allelic expression studies.

scholarly journals rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Elena Bushmanova ◽  
Dmitry Antipov ◽  
Alla Lapidus ◽  
Andrey D Prjibelski
Keyword(s):  
Rna Sequencing ◽  
De Novo ◽  
Transcriptome Assembly ◽  
The Novel ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Weak Points ◽  
Transcriptome Reconstruction ◽  
Evaluation Approaches ◽  
Genome Assembler

Abstract Background The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing, and paralogous genes. Results Herein we describe the novel transcriptome assembler rnaSPAdes, which has been developed on top of the SPAdes genome assembler and explores computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-sequencing datasets, and briefly highlight strong and weak points of different assemblers. Conclusions Based on the performed comparison between different assembly methods, we infer that it is not possible to detect the absolute leader according to all quality metrics and all used datasets. However, rnaSPAdes typically outperforms other assemblers by such important property as the number of assembled genes and isoforms, and at the same time has higher accuracy statistics on average comparing to the closest competitors.

scholarly journals RNA-Sequencing Based Assessment of Targets, Risk and Long Term Survival for Personalized Treatment of Multiple Myeloma

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1801-1801
Author(s):  
Martina Emde ◽  
Susanne Beck ◽  
Vladimir Benes ◽  
Jerome Moreaux ◽  
Anja Seckinger ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Rna Sequencing ◽  
De Novo ◽  
Proliferation Index ◽  
High Dose ◽  
Rna Seq ◽  
Term Survival ◽  
Malignant Plasma Cell

Aim of our study is to implement RNA-sequencing as basis for risk adapted and targeted treatment-strategies in multiple myeloma. We establish assessment of malignant plasma cell proliferation and risk-stratification de novo (HDHRS) by RNA-sequencing, transfer microarray-based risk scores to RNA-sequencing, and report expression of actionable including immune-oncological targets. Methods. Transcriptome profiling was performed on CD138 purified malignant plasma cell samples from previously untreated symptomatic multiple myeloma patients undergoing high-dose melphalan treatment and autologous stem cell transplantation. RNA-sequencing was performed on an Illumina NextSeq500-platform using 5ng of total RNA (n=535), and, in the same cohort, by gene expression profiling using Affymetrix U133 2.0 DNA-microarrays (n=534). iFISH was performed using a ten-probe panel (n=535). Clinical data and survival of patients treated with high-dose therapy and autologous stem cell transplantation were assessed (n=534/533/534 for RNA-seq/GEP/iFISH) with median follow up of 64 months. Data were validated using the independent COMPASS cohort (n=767 pts., median follow up of 31 months). Results. RNA-sequencing is feasible in more than 90% of myeloma patients. It allows assessment of proliferation (RPI) and risk, both de novo (HDHRS) and regarding microarray-based scores (UAMS GEP70-, EMC92-, Rs-score). All scores are significantly predictive for overall and event-free survival in GEP are likewise in RNA-seq with hazard ratio for high risk to low risk group of 3.06, 4.3, 2.84, 3.93 and 3.30 in overall survival of test group. (See as example gene expression based proliferation index / RNA-seq based proliferation index, Fig. 1). The de novo RNA-seq risk stratification (HDHRS) superiorly delineates three significantly different groups of 40%, 38%, and 22% of patients with 5-year survival rates of 84%, 67%, and 32%, respectively (Fig.2). It likewise discerns a group of long term surviving patients with a survival rate of 57% and 49%, at 10 and 12 years, respectively. Targets expressed in normal plasma cells with varying expression height in malignant include BCMA and CD38, those aberrantly expressed CSF1, CD20 and HGF. Mutated actionable transcripts include BRAF V600E/K (target), the proteasome and cereblon (resistance). In conclusion, RNA-seq allows assessment of risk, long term survival and targets in multiple myeloma both in phase III multicenter trials as well as in clinical Routine. Disclosures Moreaux: Diag2Tec: Other: Co-founder of Diag2Tec company.

scholarly journals Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 620
Author(s):  
Leticia Botella ◽  
Thomas Jung
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Viral Infections ◽  
De Novo ◽  
Phytophthora Species ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Rt Pcr ◽  
Total Rna ◽  
Southern Portugal

Marine oomycetes have recently been shown to be concurrently infected by (−)ssRNA viruses of the order Bunyavirales. In this work, even higher virus variability was found in a single isolate of Phytophthora condilina, a recently described member of Phytophthora phylogenetic Clade 6a, which was isolated from brackish estuarine waters in southern Portugal. Using total and small RNA-seq the full RdRp of 13 different potential novel bunya-like viruses and two complete toti-like viruses were detected. All these viruses were successfully confirmed by reverse transcription polymerase chain reaction (RT-PCR) using total RNA as template, but complementarily one of the toti-like and five of the bunya-like viruses were confirmed when dsRNA was purified for RT-PCR. In our study, total RNA-seq was by far more efficient for de novo assembling of the virus sequencing but small RNA-seq showed higher read numbers for most viruses. Two main populations of small RNAs (21 nts and 25 nts-long) were identified, which were in accordance with other Phytophthora species. To the best of our knowledge, this is the first study using small RNA sequencing to identify viruses in Phytophthora spp.

scholarly journals nanotatoR: a tool for enhanced annotation of genomic structural variants

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Surajit Bhattacharya ◽  
Hayk Barseghyan ◽  
Emmanuèle C. Délot ◽  
Eric Vilain
Keyword(s):  
De Novo ◽  
Genome Mapping ◽  
Gene List ◽  
Sufficient Information ◽  
Rna Seq ◽  
Structural Variants ◽  
De Novo Genome Assembly ◽  
Pathogenic Variants ◽  
Increased Sensitivity

Abstract Background Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity. Results We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient’s phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.). nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR’s annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM. Conclusions The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.

scholarly journals Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1465
Author(s):  
Ramon de Koning ◽  
Raphaël Kiekens ◽  
Mary Esther Muyoka Toili ◽  
Geert Angenon
Keyword(s):  
Common Bean ◽  
Seed Development ◽  
Expression Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Raffinose Family Oligosaccharides ◽  
Specific Expression ◽  
Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

scholarly journals RNA-Seq reveals divergent gene expression between larvae with contrasting trophic modes in the poecilogonous polychaete Boccardia wellingtonensis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Álvaro Figueroa ◽  
Antonio Brante ◽  
Leyla Cárdenas
Keyword(s):  
De Novo ◽  
Juvenile Stage ◽  
Type I ◽  
Rna Seq ◽  
Mrna Synthesis ◽  
De Novo Transcriptome ◽  
Larval Stages ◽  
Divergent Gene ◽  
Genetic Mechanisms ◽  
Planktotrophic Larvae

AbstractThe polychaete Boccardia wellingtonensis is a poecilogonous species that produces different larval types. Females may lay Type I capsules, in which only planktotrophic larvae are present, or Type III capsules that contain planktotrophic and adelphophagic larvae as well as nurse eggs. While planktotrophic larvae do not feed during encapsulation, adelphophagic larvae develop by feeding on nurse eggs and on other larvae inside the capsules and hatch at the juvenile stage. Previous works have not found differences in the morphology between the two larval types; thus, the factors explaining contrasting feeding abilities in larvae of this species are still unknown. In this paper, we use a transcriptomic approach to study the cellular and genetic mechanisms underlying the different larval trophic modes of B. wellingtonensis. By using approximately 624 million high-quality reads, we assemble the de novo transcriptome with 133,314 contigs, coding 32,390 putative proteins. We identify 5221 genes that are up-regulated in larval stages compared to their expression in adult individuals. The genetic expression profile differed between larval trophic modes, with genes involved in lipid metabolism and chaetogenesis over expressed in planktotrophic larvae. In contrast, up-regulated genes in adelphophagic larvae were associated with DNA replication and mRNA synthesis.

scholarly journals Identification of New Transcription Factors that Can Promote Pluripotent Reprogramming

2021 ◽  
Author(s):  
Ping Huang ◽  
Jieying Zhu ◽  
Yu Liu ◽  
Guihuan Liu ◽  
Ran Zhang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Embryonic Stem Cells ◽  
Rna Sequencing ◽  
Human Urine ◽  
Embryonic Stem ◽  
Rna Seq ◽  
Reprogramming Efficiency ◽  
Yamanaka Factors ◽  
Urine Cells

Abstract Background Four transcription factors, Oct4, Sox2, Klf4, and c-Myc (the Yamanka factors), can reprogram somatic cells to induced pluripotent stem cells (iPSCs). Many studies have provided a number of alternative combinations to the non-Yamanaka factors. However, it is clear that many additional transcription factors that can generate iPSCs remain to be discovered. Methods The chromatin accessibility and transcriptional level of human embryonic stem cells and human urine cells were compared by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to identify potential reprogramming factors. Selected transcription factors were employed to reprogram urine cells, and the reprogramming efficiency was measured. Urine-derived iPSCs were detected for pluripotency by Immunofluorescence, quantitative polymerase chain reaction, RNA sequencing and teratoma formation test. Finally, we assessed the differentiation potential of the new iPSCs to cardiomyocytes in vitro. Results ATAC-seq and RNA-seq datasets predicted TEAD2, TEAD4 and ZIC3 as potential factors involved in urine cell reprogramming. Transfection of TEAD2, TEAD4 and ZIC3 (in the presence of Yamanaka factors) significantly improved the reprogramming efficiency of urine cells. We confirmed that the newly generated iPSCs possessed pluripotency characteristics similar to normal H1 embryonic stem cells. We also confirmed that the new iPSCs could differentiate to functional cardiomyocytes. Conclusions In conclusion, TEAD2, TEAD4 and ZIC3 can increase the efficiency of reprogramming human urine cells into iPSCs, and provides a new stem cell sources for the clinical application and modeling of cardiovascular disease. Graphical abstract

scholarly journals Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAs

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Milda Mickutė ◽  
Kotryna Kvederavičiūtė ◽  
Aleksandr Osipenko ◽  
Raminta Mineikaitė ◽  
Saulius Klimašauskas ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Regulatory Networks ◽  
Library Preparation ◽  
Rna Seq ◽  
Basic Principles ◽  
Cofactor Binding ◽  
Sequencing Library ◽  
Sequencing Library Preparation ◽  
Target Rna

Abstract Background Targeted installation of designer chemical moieties on biopolymers provides an orthogonal means for their visualisation, manipulation and sequence analysis. Although high-throughput RNA sequencing is a widely used method for transcriptome analysis, certain steps, such as 3′ adapter ligation in strand-specific RNA sequencing, remain challenging due to structure- and sequence-related biases introduced by RNA ligases, leading to misrepresentation of particular RNA species. Here, we remedy this limitation by adapting two RNA 2′-O-methyltransferases from the Hen1 family for orthogonal chemo-enzymatic click tethering of a 3′ sequencing adapter that supports cDNA production by reverse transcription of the tagged RNA. Results We showed that the ssRNA-specific DmHen1 and dsRNA-specific AtHEN1 can be used to efficiently append an oligonucleotide adapter to the 3′ end of target RNA for sequencing library preparation. Using this new chemo-enzymatic approach, we identified miRNAs and prokaryotic small non-coding sRNAs in probiotic Lactobacillus casei BL23. We found that compared to a reference conventional RNA library preparation, methyltransferase-Directed Orthogonal Tagging and RNA sequencing, mDOT-seq, avoids misdetection of unspecific highly-structured RNA species, thus providing better accuracy in identifying the groups of transcripts analysed. Our results suggest that mDOT-seq has the potential to advance analysis of eukaryotic and prokaryotic ssRNAs. Conclusions Our findings provide a valuable resource for studies of the RNA-centred regulatory networks in Lactobacilli and pave the way to developing novel transcriptome and epitranscriptome profiling approaches in vitro and inside living cells. As RNA methyltransferases share the structure of the AdoMet-binding domain and several specific cofactor binding features, the basic principles of our approach could be easily translated to other AdoMet-dependent enzymes for the development of modification-specific RNA-seq techniques.

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