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Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
- Shruthi Rengarajan,
- Jason Derks,
- Daniel W. Bellott,
- Nikolai Slavov,
- and David C. Page
Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
...Biomedicals), MEM nonessential amino acids (GIBCO), and 100 IU/mL penicillin/streptomycin (Lonza).CRISPRiThree independent, unrelated 46,XY fibroblast cultures stably expressing a nuclease-dead Cas9 fused with a repressive KRAB domain (dCas9-KRAB) were obtained from Adrianna San Roman. gRNAs for control...
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Research: E4F1 and ZNF148 are transcriptional activators of the −57A > C and wild-type TERT promoter
- Boon Haow Chua,
- Nurkaiyisah Zaal Anuar,
- Laure Ferry,
- Cecilia Domrane,
- Anna Wittek,
- Vineeth T. Mukundan,
- Sudhakar Jha,
- Falk Butter,
- Daniel G. Tenen,
- Pierre-Antoine Defossez,
- and Dennis Kappei
Genome Res. November 2023 33: 1893-1905; Published in Advance November 2, 2023, doi:10.1101/gr.277724.123
...of a de novo E26-specific (ETS) site and have been shown to up-regulate promoter activity (Horn et al. 2013; Huang et al. 2013; Bell et al. 2015). Unlike other core components of the telomerase enzyme, telomerase RNA component (TERC) and dyskerin pseudouridine synthase 1 (DKC1), that are expressed...
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Research: Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
- Neelam Dabas Sen,
- Fujun Zhou,
- Nicholas T. Ingolia,
- and Alan G. Hinnebusch
Genome Res. August 2015 25: 1196-1205; Published in Advance June 29, 2015, doi:10.1101/gr.191601.115
...Biology, University of California, Berkeley, California 94720, USA Corresponding authors: nick@ingolia.org; ahinnebusch@nih.gov AbstractDEAD-box RNA helicases eIF4A and Ded1 are believed to promote translation initiation by resolving mRNA secondary structures that impede ribosome attachment at the mRNA 5...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...down, 3% of coding genes remain active. Furthermore, RNA polymerase II (RNAPII) accumulates at one-third of gene promoters. The corresponding genes are highly enriched among those showing a high level of transcription and high frequency of expression in individual cells, shortly after cells are refed...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...by the change in Adar activity which will be discussed in 181 subsequent sections. 182 Next, we identify individual RNA editing sites that show remarkable editing level 183 changes between GF and CV. Statistical significance was assessed using comparison of 184 editing levels in the 12 CV and 12 GF samples...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...by interacting with CD137 on activated T lymphocytes (Wang et al. 2016; Hashimoto 2021). The applicability of our ONT DRS method for ASM detection in human cells supports the wide-ranging utility of our approach in any system with known genetic information.RNA abundance is higher for the allele with higher m6A...
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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
...) pathway, leading to the production of interferons and pro-inflammatory cytokines(Feng et al. 2012; Brisse and Ly 2019; Hur 2019). While this antiviral defense mechanism is essential for combating infections, inappropriate activation by self-derived dsRNA can result in unnecessary immune activation...
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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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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...represent nascent transcripts adjacent to actively elongating RNAPII complexes. Therefore, the exon-exon junction reads in nascent samples likely represent more contaminating pre-existing spliced mRNAs than newly spliced nascent RNAs. Excluding exon-exon junction reads thus reduces background noise without...
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Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
- Leszek P. Pryszcz,
- Gregor Diensthuber,
- Laia Llovera,
- Rebeca Medina,
- Anna Delgado-Tejedor,
- Luca Cozzuto,
- Julia Ponomarenko,
- and Eva Maria Novoa
Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
...overview of the DRS and demultiplexing workflow. (A) Overview of the barcoded DRS workflow in which the standard RTA is replaced with a barcode-containing adapter. Following adapter ligation and reverse transcription, the RNA ligation adapter (RLA), containing the helicase enzyme, is ligated, making...
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