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JACUSA: site-specific identification of RNA editing events from replicate sequencing data

Michael Piechotta, Emanuel Wyler, Uwe Ohler, Markus Landthaler, Christoph Dieterich
2017 BMC Bioinformatics  
However, a method for robust detection of site-specific editing events from replicate RNA-seq data has not been published so far.  ...  Intriguingly, JACUSA captures most A → I events from RRD comparisons of RNA sequencing data derived from Drosophila and HEK-293 data sets.  ...  Acknowledgments All authors would like thank all members of the Dieterich and Landthaler Labs for numerous valuable discussions. Funding  ... 
doi:10.1186/s12859-016-1432-8 pmid:28049429 pmcid:PMC5210316 fatcat:txo23tnmbvdeldlfmp7shnx33a

Quantifying RNA Editing in Deep Transcriptome Datasets

Claudio Lo Giudice, Domenico Alessandro Silvestris, Shalom Hillel Roth, Eli Eisenberg, Graziano Pesole, Angela Gallo, Ernesto Picardi
2020 Frontiers in Genetics  
Using real RNAseq data, we demonstrate the impact of different bioinformatics steps on RNA editing detection and describe the main metrics to quantify its level of activity.  ...  Accurate profiling of RNA editing using deep transcriptome data is still a challenge, and the results depend strongly on processing and alignment steps taken.  ...  Deep transcriptome sequencing, through the RNAseq technology, has greatly promoted identification of RNA editing events at genomic scale, revealing the extent of A-to-I editing in humans, with more than  ... 
doi:10.3389/fgene.2020.00194 pmid:32211029 pmcid:PMC7069340 fatcat:llr3eco3yjfk7cbasjljtrxp2y

RNA modification mapping with JACUSA2 [article]

Michael Piechotta, Qi Wang, Janine Altmueller, Christoph Dieterich
2021 bioRxiv   pre-print
A whole series of high-throughput antibody-free methods for RNA modification detection from sequencing data emerged lately.  ...  Importantly, JACUSA2 can integrate information from multiple experiments (e.g. replicates and different conditions) and different library types (e.g. first- or secondstrand libraries).  ...  We thank Volker Boehm for discussing an early attempt of the MazF digest with us.  ... 
doi:10.1101/2021.07.02.450888 fatcat:fxmtji7drrgrlaswus2uhyaheq

RESIC: A Tool for Comprehensive Adenosine to Inosine RNA Editing Site Identification and Classification

Dean Light, Roni Haas, Mahmoud Yazbak, Tal Elfand, Tal Blau, Ayelet T. Lamm
2021 Frontiers in Genetics  
Several computational approaches have been recently developed to identify A-to-I RNA editing sites from sequencing data, each addressing a particular issue.  ...  Here, we present RNA Editing Sites Identification and Classification (RESIC), an efficient pipeline that combines several approaches for the detection and classification of RNA editing sites.  ...  JACUSA: site-specific identification of RNA editing events from replicate sequencing data.  ... 
doi:10.3389/fgene.2021.686851 fatcat:nxdki7grgfhaha75d7bxdipk7a

Mapping the dsRNA World

Daniel P. Reich, Brenda L. Bass
2019 Cold Spring Harbor Perspectives in Biology  
the detection of editing sites and dsRNAs.  ...  In this review, we detail approaches to map ADAR editing sites and dsRNAs genome-wide, with particular focus on high-throughput sequencing methods and considerations for their successful application to  ...  The nonselective editing observed in early studies was put aside by most. Sanger sequencing of cloned cDNAs was instrumental in the identification of the first ADAR editing sites.  ... 
doi:10.1101/cshperspect.a035352 pmid:30824577 pmcid:PMC6396333 fatcat:ra76l2y47rdqfgjmtr6rerjjdm

RESIC: A tool for comprehensive adenosine to inosine RNA Editing Site Identification and Classification [article]

Dean Light, Roni Haas, Mahmoud Yazbak, Tal Helfand, Tal Blau, Ayelet Lamm
2021 bioRxiv   pre-print
Several computational approaches have been recently developed to identify A-to-I RNA editing sites from sequencing data, each addressing a particular issue.  ...  The detection of editing sites in both repetitive and non-repetitive genomic regions; 2. The identification of hyper-edited regions; 3.  ...  ., and Dieterich, C. (2017). 570 JACUSA: site-specific identification of RNA editing events from replicate 571 sequencing data. BMC Bioinformatics 18(1), 7. doi: 10., Y., and Levanon, E.Y. (2019).  ... 
doi:10.1101/2021.04.11.439401 fatcat:linckwxmu5ae7hgjn27dthmj7q

Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi

Baojun Wu, Jill Gaskell, Jiwei Zhang, Christina Toapanta, Steven Ahrendt, Igor V. Grigoriev, Robert A. Blanchette, Jonathan S. Schilling, Emma Master, Daniel Cullen, David S. Hibbett
2019 The ISME Journal  
We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the 'Antrodia clade' (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce  ...  We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment.  ...  Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.  ... 
doi:10.1038/s41396-019-0359-2 pmid:30718807 pmcid:PMC6776062 fatcat:fw4n6un4bndqngmr3oljcazczu

APOBEC2 binds Chromatin and Represses Transcription during Myoblast Differentiation [article]

Jose Paulo Lorenzo, Linda Molla, Ignacio L. Ibarra, Sandra Ruf, Poorani Ganesh Subramani, Jonathan Boulais, Dewi Harjanto, Alin Vonica, Javier M. Di Noia, Christoph Dieterich, Judith B. Zaugg, F. Nina Papavasiliou
2020 bioRxiv   pre-print
This family of nucleic acid editors has diverse molecular roles ranging from antibody diversification to RNA transcript editing.  ...  APOBEC2 is a member of the prolific activation induced cytidine deaminase/ apolipoprotein B editing complex (AID/APOBEC) family of DNA or RNA editors.  ...  DH performed RNA editing analysis.  ... 
doi:10.1101/2020.07.29.223594 fatcat:6vqxouqvorfmnlpkejsyg4zjbu

Recognition of Z-RNA by ADAR1 limits interferon responses [article]

Qiannan Tang, Rachel E Rigby, George R Young, Astrid Korning-Hvidt, Tiong Kit Tang, Anne Bridgeman, Alain R Townsend, George Kassiotis, Jan Rehwinkel
2020 bioRxiv   pre-print
Finally, analysis of A-to-I changes revealed a specific requirement of ADAR1's Zα domain in editing of a subset of RNAs.  ...  The p150 isoform of adenosine deaminase acting on RNA 1 (ADAR1) prevents aberrant interferon (IFN) induction and contains a Z-nucleic acid binding (Zα) domain.  ...  ., and Dieterich, C. (2017). 923 JACUSA: site-specific identification of RNA editing events from replicate 924 to-I RNA editing is common across the Metazoa and correlates with 927 dsRNA abundance.  ... 
doi:10.1101/2020.12.04.411793 fatcat:nvqbmu2juvgi7eoiyaarkfijii

Maximizing the Utility of Transcriptomics Data in Inflammatory Skin Diseases

Jingni Wu, Zhixiao Fang, Teng Liu, Wei Hu, Yangjun Wu, Shengli Li
2021 Frontiers in Immunology  
Here, we will summarize discoveries from transcriptomics data and discuss how to maximize the transcriptomics data to propel the development of diagnostic biomarkers and therapeutic targets in inflammatory  ...  Additionally, single-cell RNA sequencing (scRNA-seq) as well as spatial transcriptomic profiling have revealed multiple potential translational targets and offered guides to improve diagnosis and treatment  ...  Multiple tools have been developed to identify RNA editing sites, such as RNAEditor (67) , REDItools (68) , JACUSA (69) , and RES-Scanner (70) .  ... 
doi:10.3389/fimmu.2021.761890 pmid:34777377 pmcid:PMC8586455 fatcat:eistnlxwjbhn5cs2e2vngx5cia

MePMe-seq: Antibody-free simultaneous m6A and m5C mapping in mRNA by metabolic propargyl labeling and sequencing [article]

Katja Hartstock, Anna Ovcharenko, Nadine A Kueck, Petr Spacek, Nicolas Vincent Cornelissen, Sabine Huewel, Christoph Dieterich, Andrea Rentmeister
2022 bioRxiv   pre-print
The joint evaluation of m6A and m5C sites opens the door to study their interconnectivity and improve our understanding of mechanisms and functions of the RNA methylome.  ...  MePMe-seq overcomes the problems of antibodies for enrichment and sequence-motifs for evaluation, limiting previous methodologies.  ...  At the WWU Münster, we would like to thank Ann-Marie Lawrence Dörner and the analytical facilities of the Organic Chemistry Institute for excellent technical assistance.  ... 
doi:10.1101/2022.03.16.484494 fatcat:bkwpsmhmcjbs5p36a5ns3op3oe

Evolution of resilience against heat stress in a red-tide dinoflagellate [article]

Katherine Elisabeth Dougan, Zhi-Luo Deng, Lars Woehlbrand, Carsten Reuse, Boyke Bunk, Yibi Chen, Juliane Hartlich, Karsten Hiller, Uwe John, Jana Kalvelage, Johannes Mansky, Meina Neumann-Schaal (+13 others)
2022 bioRxiv   pre-print
The transcriptome data show that 25% of genes are differentially expressed under heat stress, with concomittant extensive RNA editing and alternative exon usage.  ...  To understand this response, we integrated transcriptome, proteome and metabolome data and identified both a global and a temperature specific heat-stress response.  ...  Acknowledgements The authors want to thank Nicole Heyer and Simone Schrader for technical assistance regarding genome sequencing.  ... 
doi:10.1101/2022.07.25.501386 fatcat:azezxuuacrft5cjj5kl4exgfsa

Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola

Baojun Wu, Jill Gaskell, Benjamin W. Held, Cristina Toapanta, Thu Vuong, Steven Ahrendt, Anna Lipzen, Jiwei Zhang, Jonathan S. Schilling, Emma Master, Igor V. Grigoriev, Robert A. Blanchette (+3 others)
2018 Applied and Environmental Microbiology  
We examined both gene expression (transcription levels) and RNA editing (posttranscriptional modification of RNA, which can potentially yield different proteins from the same gene).  ...  We analyzed the gene expression levels and RNA editing profiles of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using  ...  For instance, the spruce-specific RNA editing sites in 10-day cultures 423 can be up to 41% of total RNA editing events relative to that on pine (Fig. 6A) .  ... 
doi:10.1128/aem.00991-18 pmid:29884757 fatcat:lrxu6opw2jevfeswabizuo6uea

Variants in RNA-Seq data show a continued mutation rate during strain preservation of Schizophyllum commune [article]

Thies Gehrmann, Jordi F Pelkmans, Luis G Lugones, Han A B Wösten, Thomas Abeel, Marcel J T Reinders
2017 bioRxiv   pre-print
We designed a methodology to detect SNPs from the RNA-seq data, and found a mutation rate of 1.923 10-8 per haploid genome per base per generation, highly similar to the previously described mutation rate  ...  Therefore, we recommend labs to ensure that biological replicates originate from different parental plates, as much as possible.  ...  With the exception of JACUSA (Piechotta et al., 2017) , which was designed for the identification of RNA editing events, other approaches generally rely on GATK (McKenna et al., 2010) , which was primarily  ... 
doi:10.1101/201012 fatcat:yv3nrgbhyfe3baxb5m76pmgqwi

Molecular Mechanisms Of Hamiltonian Traits In Hymenoptera

Alun R.C. Jones
To understand how altruistic behaviour is controlled in social insects I conducted a comparative analysis exploring RNA editing and its relation to reproductive phenotypic plasticity in Hymenoptera.  ...  While there is a strong theoretical understanding of these types of interactions, how they manifest molecularly is poorly understood.  ...  Your patience with me as I test the boundaries of written English has been really appreciated. As a role model and mentor I could not have asked for better. Thank you.  ... 
doi:10.25392/ fatcat:bankg2p5arbozncf2o7kb7qqnm
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