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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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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...Lee SR, Pollard DA, Galati DF, Kelly ML, Miller B, Mong C, Morris MN, Roberts-519 Nygren K, Kapler GM, Zinkgraf M, et al. 2021. Disruption of a ∼23-24 nucleotide 520 small RNA pathway elevates DNA damage responses in Tetrahymena thermophila. 521 Mol Biol Cell 32: 1335–1346. 522 Lehoczký P, McHugh PJ...
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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
..., concentration measured by Qubit (DNA high sensitivity assay), and size distribution assessed using TapeStation (high sensitivity D5000 ScreenTape; Agilent, #5067-5592). For the DLD-1 experiment, 10 ng of purified 4sU-labeled RNA was used for high-throughput sequencing library preparation with the NEBNext Ultra...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...Figure 4. Effects of ICOP knockdowns (KDs) on DNA excision. (A) mRNA expression levels in fragments per kilobase per million mapped reads (FPKM) compared between ICOPa and ICOPb KDs for transcripts early in development (40% old MAC fragmentation) or asynchronous (asyn.) cultures (*) in which new MACs...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
..., Narayanan AK, et al. 2018. The Encyclopedia of DNA Elements (ENCODE): data portal update. Nucleic Acids Res 46: D794–D801. doi:10.1093/nar/gkx1081 ↵Di Persio S, Tekath T, Siebert-Kuss LM, Cremers J-F, Wistuba J, Li X, Meyer zu Hörste G, Drexler HCA, Wyrwoll MJ, Tüttelmann F, et al. 2021. Single-cell RNA...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...; Brennan et al. 2023). Prior studies have shown that repressed genes frequently contain nucleosomes within their promoter regions, preventing TFs and other DNA-binding factors from binding and subsequently inducing transcription (Schmid et al. 1992; Tran et al. 2021). On the other hand, activated genes...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...extraction and qPCRTotal RNA was isolated using TRIzol (Thermo Fisher Scientific) and Direct-zol RNA Kit (Zymo Research) according to the manufacturer's conditions. Samples were treated with DNase to remove genomic contamination. Five hundred nanograms of RNA was reverse-transcribed using 4 µL Q-Script cDNA...
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Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
- Emily Lowry,
- Yiqing Wang,
- Tal Dagan,
- and Amir Mitchell
Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
..., barcode amplification, and DNA sequencing (Fig. 1D). In these screens, barcode depletion in the pks+ condition relative to the pks− condition is indicative of a gene that mitigates colibactin-induced damage (Fig. 1D).Analysis of the DNA sequencing results identified at least 2.6 × 106 barcode sequences...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst...
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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
..., or 24 h.qPCRCells were washed once with PBS and collected 72 h post treatment. RNA was extracted with the RNeasy mini kit (Qiagen) and cDNAs prepared with SuperScript Vilo master mix (Thermo Fisher Scientific). DDX3X levels were quantified by qPCR using fast SYBR Green master mix (Thermo Fisher...
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