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Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
- Brigitta Szabo,
- Therese C. Mandl,
- Bernhard Woldrich,
- Gregor Diensthuber,
- David Martin,
- Michael F. Jantsch,
- and Konstantin Licht
Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
...al. 2018).The bulk of exonic A-to-I editing occurs cotranscriptionally before pre-mRNA splicing, as recoding-editing frequently depends on an intronic editing-complementary site (Rodriguez et al. 2012; Hsiao et al. 2018). Here, we systematically study regulation and fine-tuning of editing levels...
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Research: RNA editing in nascent RNA affects pre-mRNA splicing
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Yun Yang,
- Xianzhi Lin,
- Stephen Tran,
- Ei-Wen Yang,
- Giovanni Quinones-Valdez,
- and Xinshu Xiao
Genome Res. June 2018 28: 812-823; Published in Advance May 3, 2018, doi:10.1101/gr.231209.117
...impact on exons undergoing post-transcriptional splicing.Editing sites located in the splice site regions often disrupt 3′ splice sitesNext, we hypothesized that A-to-I editing may affect pre-mRNA splicing by altering splice site sequences. To this end, we searched for editing sites identified in the Ch...
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Method: Accurate identification of A-to-I RNA editing in human by transcriptome sequencing
- Jae Hoon Bahn,
- Jae-Hyung Lee,
- Gang Li,
- Christopher Greer,
- Guangdun Peng,
- and Xinshu Xiao
Genome Res. January 2012 22: 142-150; Published in Advance September 29, 2011, doi:10.1101/gr.124107.111
...is indeed the main enzyme involved in A-to-I editing in the studied cell line. It also suggests that the other types of differences, if being bona fide editing events, are not likely affected by ADAR. Among the A-to-G differences identified in the control and knockdown samples (5965 and 938, respectively...
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Research: ADAR-deficiency perturbs the global splicing landscape in mouse tissues
- Utkarsh Kapoor,
- Konstantin Licht,
- Fabian Amman,
- Tobias Jakobi,
- David Martin,
- Christoph Dieterich,
- and Michael F. Jantsch
Genome Res. August 2020 30: 1107-1118; Published in Advance July 29, 2020, doi:10.1101/gr.256933.119
...(Fig. 3E). The two targets Mcts1 and Neil1 predicted to have insignificant co-occurrence were found to be significant by qPCR (Fig. 3E). Overall, this led us to conclude that a co-occurrence analysis is a reliable strategy to identify splicing events that are affected by A-to-I RNA editing events near...
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Research: Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development
- Suba Rajendren,
- Alfa Dhakal,
- Pranathi Vadlamani,
- Jack Townsend,
- Sarah N. Deffit,
- and Heather A. Hundley
Genome Res. January 2021 31: 27-39; Published in Advance December 18, 2020, doi:10.1101/gr.267575.120
...), the previous studies used whole-worm lysates to identify editing sites. Many of these studies performed control experiments, in which sites were also computationally predicted for adr-2(-) worms (that lack all A-to-I editing) and any false-positive sites were removed. This list also includes edited sites from...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
..., RNA methylation, specifically N6-methyladenosine (m6A), can alter translation efficiency. Pseudouridylation can affect translation dynamics by influencing ribosome stalling and pausing during protein synthesis. RNA editing events, such as adenosine-to-inosine (A-to-I) editing, can modify regulatory...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
.... 2018). In the same vein, Zhou et al. (2020) identified an edited neoantigen (arising from an A-to-I editing site in the OSBPL9 gene) that was complexed to MHC I based on high-resolution mass-spectrometry in an ovarian cancer sample.m6A has also been found to regulate antigen presentation. In dendritic...
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Research: Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation
- Amanda J. Price,
- Taeyoung Hwang,
- Ran Tao,
- Emily E. Burke,
- Anandita Rajpurohit,
- Joo Heon Shin,
- Thomas M. Hyde,
- Joel E. Kleinman,
- Andrew E. Jaffe,
- and Daniel R. Weinberger
Genome Res. January 2020 30: 1-11; Published in Advance December 18, 2019, doi:10.1101/gr.250217.119
....Assessment of RNA editing and nuclear pore components by fraction across cortical developmentWe next profiled RNA editing across fractions and ages, identifying 3064–5840 editing sites per sample and 25,051 unique sites (Supplemental Fig. S7A–E). Of these unique sites, 75.5% were A-to-I edited sites (appears as A...
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Research: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
- Claire Vandiedonck,
- Martin S. Taylor,
- Helen E. Lockstone,
- Katharine Plant,
- Jennifer M. Taylor,
- Caroline Durrant,
- John Broxholme,
- Benjamin P. Fairfax,
- and Julian C. Knight
Genome Res. July 2011 21: 1042-1054; Published in Advance May 31, 2011, doi:10.1101/gr.116681.110
...found that only 0.1% of probes present in these distant intergenic TARs matched the A-to-I or C-to-U edited RNA sequences cataloged in the comprehensive DAtabase of RNa EDiting (Kiran and Baranov 2010). Altogether, our data support an abundant transcriptional activity from Alu sequences...
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Research: Profiling the RNA editomes of wild-type C. elegans and ADAR mutants
- Han-Qing Zhao,
- Pan Zhang,
- Hua Gao,
- Xiandong He,
- Yanmei Dou,
- August Y. Huang,
- Xi-Ming Liu,
- Adam Y. Ye,
- Meng-Qiu Dong,
- and Liping Wei
Genome Res. January 2015 25: 66-75; Published in Advance November 4, 2014, doi:10.1101/gr.176107.114
...in the mouse is determined by the genomic repeat repertoire. RNA 12: 1802–1809. Nishikura K, Yoo C, Kim U, Murray JM, Estes PA, Cash FE, Liebhaber SA. 1991. Substrate specificity of the dsRNA unwinding/modifying activity. EMBO J 10: 3523–3532. PalladinoMJ, Keegan LP, O’Connell MA, Reenan RA. 2000. A-to-I pre-mRNA...
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