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Method: Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing
- Yanjun Zhang,
- Yin Tang,
- Zhongxing Sun,
- Junqi Jia,
- Yuan Fang,
- Xinyi Wan,
- and Dong Fang
Genome Res. March 2023 33: 412-426; Published in Advance March 23, 2023, doi:10.1101/gr.277213.122
...). Reads mapped to the sense strand were highly enriched on the gene transcription side, and reads mapped to the antisense strand were enriched on the opposite side, indicating that the sequencing results were highly strand specific. The read profile of unfragmented RNA showed a preference for distal sites...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
...III transcripts are not polyadenylated (Sisodia et al. 1987) and thereby were depleted in our sequenced data owing to poly(A) RNA pulldown step (Supplemental Fig. S1A). Also, antisense promoters in Alu elements have been reported to produce poly(A) RNAs (Jang et al. 2019; Shah et al. 2023). We suspect...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...of the transcript, which is essential to be able to detect new antisense transcripts. As we have recently shown in S. cerevisiae, antisense transcripts can originate rapidly during evolution, providing new functionalities (Blevins et al. 2021). No dRNA-seq of S. pombe has yet been produced, limiting our knowledge...
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Research: Sense–antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit
- Yulong Song,
- Lishi Li,
- Wenbing Yang,
- Qiang Fu,
- Wanying Chen,
- Zeng Fang,
- Wen Li,
- Nannan Gu,
- and Rui Zhang
Genome Res. May 2020 30: 661-672; Published in Advance May 18, 2020, doi:10.1101/gr.257121.119
...used to identify antisense transcripts. However, because of the overall weak expression of antisense transcripts (Pelechano and Steinmetz 2013), stranded RNA-seq has limited power to fully characterize the landscape of antisense transcription. Moreover, the strand specificity varies depending...
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Method: Strand-specific deep sequencing of the transcriptome
- Ana P. Vivancos,
- Marc Güell,
- Juliane C. Dohm,
- Luis Serrano,
- and Heinz Himmelbauer
Genome Res. July 2010 20: 989-999; Published in Advance June 2, 2010, doi:10.1101/gr.094318.109
...Several studies support that antisense-mediated regulation may affect a large proportion of genes. Using the Illumina next-generation sequencing platform, we developed DSSS ( d irect s trand s pecific s equencing), a strand-specific protocol for transcriptome sequencing. We tested DSSS with RNA from...
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Research: Antisense RNAs during early vertebrate development are divided in groups with distinct features
- Sanjana Pillay,
- Hazuki Takahashi,
- Piero Carninci,
- and Aditi Kanhere
Genome Res. June 2021 31: 995-1010; Published in Advance April 1, 2021, doi:10.1101/gr.262964.120
...on their expression pattern, cytosolic nature, and their higher complementarity to the overlapping developmental mRNAs, we speculate that Group 1 NATs function post-transcriptionally to silence spurious expression of developmental genes.Natural antisense transcripts (NATs) are noncoding RNAs that are transcribed...
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Resource: Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
- Alice S. Naftaly,
- Shana Pau,
- and Michael A. White
Genome Res. August 2021 31: 1486-1497; Published in Advance June 15, 2021, doi:10.1101/gr.274282.120
...contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made...
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Research: Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis
- Huan Wang,
- Pil Joong Chung,
- Jun Liu,
- In-Cheol Jang,
- Michelle J. Kean,
- Jun Xu,
- and Nam-Hai Chua
Genome Res. March 2014 24: 444-453; Published in Advance January 8, 2014, doi:10.1101/gr.165555.113
...transcripts in Arabidopsis. These lncNATs could be reproducibly detected by different technical platforms, including strand-specific tiling arrays, Agilent custom expression arrays, strand-specific RNA-seq, and qRT-PCR experiments. Moreover, we investigated the expression profiles of sense–antisense pairs...
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Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
- Kamal Ajit,
- Adele Alagia,
- Kaspar Burger,
- and Monika Gullerova
Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
...A,B). Furthermore, 60.4% of up-regulated Y1P lncRNAs are natural antisense transcripts that could trigger transcriptional interference of sense genes (Supplemental Fig. S3C; Modarresi et al. 2012). Nascent lncRNA transcripts associated with S2P RNA Pol II were mostly down-regulated (Supplemental Fig...
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Research: Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries
- Zubairul Islam,
- Bharath Saravanan,
- Kaivalya Walavalkar,
- Umer Farooq,
- Anurag Kumar Singh,
- Sabarinathan Radhakrishnan,
- Jitendra Thakur,
- Awadhesh Pandit,
- Steven Henikoff,
- and Dimple Notani
Genome Res. January 2023 33: 1-17; Published in Advance January 17, 2023, doi:10.1101/gr.276643.122
...-cycle regulators INK4A, ARF, and INK4B, respectively. Next, we asked if boundary RNAs play a direct role in transcriptional activity of genes within this TAD. Using shRNAs to sense and antisense B1 and B2 CTCF sites, we observed down-regulation of INK4, ARF, INK4b, and MTAP, whereas the transcription of DDX5...
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