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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...-C, Kean MJ, Xu J, Chua N-H. 2014. Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res 24: 444–453. Werner A, Kanhere A, Wahlestedt C, Mattick JS. 2024. Natural antisense transcripts as versatile regulators of gene expression...
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Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
- Yang Liu,
- Qian Liu,
- Handong Su,
- Kunpeng Liu,
- Xue Xiao,
- Wei Li,
- Qianwen Sun,
- James A. Birchler,
- and Fangpu Han
Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
...characteristics of the R-loop pattern in the maize . We studied the relationships between R-loops and repetitive sequences in maize, such as tandem repeats and TEs. We also provide the first R-loop observation by atomic force microscopy (AFM) in plants.ResultsGenome-wide identification of R-loops in maize...
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Research: Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
- Chang Liu,
- Congmao Wang,
- George Wang,
- Claude Becker,
- Maricris Zaidem,
- and Detlef Weigel
Genome Res. August 2016 26: 1057-1068; Published in Advance May 25, 2016, doi:10.1101/gr.204032.116
...Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution Chang Liu 1 , 2 , Congmao Wang 1 , 3 , George Wang 1 , Claude Becker 1 , Maricris Zaidem 1 and Detlef Weigel 1 1...
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Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
- Stefan Oberlin,
- Alexis Sarazin,
- Clément Chevalier,
- Olivier Voinnet,
- and Arturo Marí-Ordóñez
Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
...and transcriptionally active transposons in A. thaliana is illustrated by our comprehensive analysis of the cotranscriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant s, and how such features impact their biology. Genome-wide transcript profiling revealed...
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Research: Genome-wide analysis of long noncoding RNA stability
- Michael B. Clark,
- Rebecca L. Johnston,
- Mario Inostroza-Ponta,
- Archa H. Fox,
- Ellen Fortini,
- Pablo Moscato,
- Marcel E. Dinger,
- and John S. Mattick
Genome Res. May 2012 22: 885-898; Published in Advance March 9, 2012, doi:10.1101/gr.131037.111
...that high turnover is not refractory to function and rather can promote the dynamic nature of lncRNAs and the cellular constituents with which they are associated. Results Genome-wide determination of RNA half-lives To examine the stability of lncRNAs, we inhibited transcription in mouse Neuro-2a (N2A...
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Research: Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
- Hai-Xi Sun,
- Yan Li,
- Qi-Wen Niu,
- and Nam-Hai Chua
Genome Res. August 2017 27: 1427-1436; Published in Advance May 18, 2017, doi:10.1101/gr.218669.116
..., a large group of long noncoding RNAs, including lincRNAs and long noncoding natural antisense transcripts (lncNATs), have been characterized in Arabidopsis (Liu et al. 2012; Zhu et al. 2013; Di et al. 2014; Wang et al. 2014). We found that the extended 3′ UTRs also had characteristics of long noncoding...
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Method: Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
- Song Li,
- Louisa M. Liberman,
- Neelanjan Mukherjee,
- Philip N. Benfey,
- and Uwe Ohler
Genome Res. October 2013 23: 1730-1739; Published in Advance July 1, 2013, doi:10.1101/gr.149310.112
...for further functional validation of cis-NAT pairs in Arabidopsis. Our statistical framework is general; it can be applied to any strand-specific protocol to facilitate the identification of natural antisense transcription in many biological systems. Methods Strand-specific RNA-seq protocol The A. thaliana...
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Research: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis
- Juncheng Lin,
- Fu-Yu Hung,
- Congting Ye,
- Liwei Hong,
- Yuan-Hsin Shih,
- Keqiang Wu,
- and Qingshun Q. Li
Genome Res. October 2020 30: 1407-1417; Published in Advance August 5, 2020, doi:10.1101/gr.255232.119
...that HDA6 regulates polyadenylation in a histone deacetylation–dependent manner in Arabidopsis.As one of the post-transcriptional modifications of mRNA, the polyadenylation process can critically regulate the gene expression in eukaryotes (Tian and Manley 2017). This universally required 3′ end processing...
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RESOURCE: Genome-wide assembly and analysis of alternative transcripts in mouse
- Alexei A. Sharov,
- Dawood B. Dudekula,
- and Minoru S.H. Ko
Genome Res. May 2005 15: 748-754; doi:10.1101/gr.3269805
...Genome-wide assembly and analysis of alternative transcripts in mouse Alexei A. Sharov , Dawood B. Dudekula , and Minoru S.H. Ko 1 Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, National Institutes...
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Resource: Long noncoding RNAs in C. elegans
- Jin-Wu Nam and
- David P. Bartel
Genome Res. December 2012 22: 2529-2540; Published in Advance June 15, 2012, doi:10.1101/gr.140475.112
...to thematuremRNA. lincRNAs are also called long intergenic RNAs, and ancRNAs are also called natural antisense transcripts (NATs). Most lncRNA gene models resemble those of protein-coding genes in terms of the CpG islands, multiexonic structures, and poly(A)-signals, but they have no more than chance potential...
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