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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...splicing (AS) and alternative cleavage and polyadenylation (APA) in humans. Yet, these studies are generally performed with mature mRNA, so they report on the outcome rather than the processes of RNA maturation and thus may overlook how variants directly modulate pre-mRNA processing. The order in which...
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Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
- Konstantin Licht,
- Utkarsh Kapoor,
- Fabian Amman,
- Ernesto Picardi,
- David Martin,
- Prajakta Bajad,
- and Michael F. Jantsch
Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
...authors: Michael.Jantsch@meduniwien.ac.at, Konstantin.Licht@meduniwien.ac.atAbstractPre-mRNA-splicing and adenosine to inosine (A-to-I) RNA-editing occur mostly cotranscriptionally. During A-to-I editing, a genomically encoded adenosine is deaminated to inosine by adenosine deaminases acting on RNA (ADARs...
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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
...that are suppressed upon MYC activation. Moreover, low pre-mRNA synthesis rates and low pre-mRNA expression levels support high levels of editing. We also show that editing levels greatly differ between nascent pre-mRNA and mRNA in a cellular system, as well as in mouse tissues. Editing levels can increase...
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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
..., this analysis detected differentially expressed circRNAs in Adar KO tissues, suggesting that ADAR may affect a few selected circRNAs in their biogenesis.DiscussionThe cotranscriptional nature of mRNA processing has permitted evolution of various coupling mechanisms such as RNA editing and pre-mRNA splicing...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
...modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev 31: 990–1006. doi:10.1101/gad.301036.117 ↵Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, et al. 2016. Enrichr...
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Resource: The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting
- Lishi Li,
- Yulong Song,
- Xinrui Shi,
- Jianheng Liu,
- Shaolei Xiong,
- Wanying Chen,
- Qiang Fu,
- Zichao Huang,
- Nannan Gu,
- and Rui Zhang
Genome Res. January 2018 28: 132-143; Published in Advance December 12, 2017, doi:10.1101/gr.224386.117
.... 2009) can map spliced or unspliced RNA-seq reads to the at the same time. To simplify the pipeline, we used TopHat2 to quantify RNA editing level for both miR-mmPCR-seq and nascent RNA-seq data. For miR-mmPCR-seq data, we mapped the paired-end reads via TopHat2 (tophat2 --library-type fr-unstranded -N...
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Method: Identification and dynamic quantification of regulatory elements using total RNA
- Sascha H. Duttke,
- Max W. Chang,
- Sven Heinz,
- and Christopher Benner
Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
...the molecular complexes necessary to start transcription. Annotation of genes and regulatory elements and the analysis of the underlying molecular mechanisms regulating transcription therefore depend on the identification of TSSs and the measurement of their activity -wide.The advent of nascent RNA sequencing...
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Perspective: Linking RNA biology to lncRNAs
- Loyal A. Goff and
- John L. Rinn
Genome Res. October 2015 25: 1456-1465; doi:10.1101/gr.191122.115
...activity to degrade an RNA (A) or occlude putative functional regions (B). Recently, strategies have used the flexible CRISPR/Cas9 system to positively or negatively affect the transcription of a lncRNA gene (C) or the incorporation of an auto-catalytic regulatory RNA element to destabilize the nascent lncRNA...
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Method: Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
- Shilin Zhang,
- Yichen Wang,
- Lin Jia,
- Xue Wen,
- Zhonghua Du,
- Cong Wang,
- Yajing Hao,
- Dehai Yu,
- Lei Zhou,
- Naifei Chen,
- Jingcheng Chen,
- Huiling Chen,
- Hui Zhang,
- Ilkay Celik,
- Günhan Gülsoy,
- Jianjun Luo,
- Baoming Qin,
- Xueling Cui,
- Zhonghui Liu,
- Songling Zhang,
- Miguel A. Esteban,
- Ferhat Ay,
- Wei Xu,
- Runsheng Chen,
- Wei Li,
- Andrew R. Hoffman,
- Ji-Fan Hu,
- and Jiuwei Cui
Genome Res. September 2019 29: 1521-1532; Published in Advance July 17, 2019, doi:10.1101/gr.244996.118
...promoter interacting mRNA Snurf in both the cytoplasm and the nucleus. The qPCR primers were designed to cover the intron splicing site. Thus, the RNAs detected should be the mature mRNAs, and not pre-mRNAs. It is not clear why and how these coding mRNAs participate in the formation of the Sox2-promoter...
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Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
- Tim R. Mercer,
- Marcel E. Dinger,
- Cameron P. Bracken,
- Gabriel Kolle,
- Jan M. Szubert,
- Darren J. Korbie,
- Marjan E. Askarian-Amiri,
- Brooke B. Gardiner,
- Gregory J. Goodall,
- Sean M. Grimmond,
- and John S. Mattick
Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
..., termination, alternative splicing, and editing, plays a significant part in the diversification of both the coding and noncoding transcriptional repertoire of the . Results Evidence of widespread intraexonic post-transcriptional cleavage To identify likely sites of post-transcriptional RNA cleavage, we mapped...

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