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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...-Loeffler-Institut, 17493 Greifswald, Germany; 3School of Health Sciences-Biomedical Sciences Program, Missouri State University, Springfield, Missouri 65897, USA A tightly regulated DNA damage response is critical to the overall integrity of the . Here, we combine transcriptomics and proteomics to study DNA damage...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...contexts (Wood et al. 2008; Cowley et al. 2012; Nanavaty et al. 2020). However, the extent to 70 which DNA methylation contributes to cell-type specific regulation of IPA remains unclear. 71 72 4 In this study, we investigate the dynamics of IPA across hematopoietic lineages using -73 wide transcriptomic...
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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. April 2026 36: 684-694; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
...is also present in the nucleus where it participates in the regulation of RNA processing and export. Its roles also extend to the regulation of transcription and DNA repair (Hurst et al. 2019). ACTB associates with both RNA polymerase II (Pol II) (Pestic-Dragovich et al. 2000) and RNA polymerase III (Pol...
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Research: A 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 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...and editing on both strands. In addition, the GENCODE database, a well-regarded repositoryof gene annotations, was utilized to search for cis-NAT regions. We identified 12,793 genomic regions annotated as being expressed from both the positive and negative DNA strands (regardless of whether they are expressed...
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Research: Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation
- Joanna Delimata-Raczek,
- Natalia Koralewska,
- Bart Krist,
- Magdalena Rakoczy,
- Marek Figlerowicz,
- and Ireneusz Stolarek
Genome Res. April 3, 2026 ; Published in Advance April 3, 2026, doi:10.1101/gr.281150.125
...of differentiation efficiency. All cells in culture were maintained at 37°C in incubators with 5% CO2. RNA extraction and cDNA synthesis The RNA was extracted from the iCMs on day 4 and day 30. Cells were first washedwith PBS and dissociated from the plate either by 3 min incubation in 37°C with PBS with EDTA (4 day...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...sought to systematically identify additional genes exhibiting similar patterns of dynamic epigenetic regulation across the OPC-to-OL trajectory. Specifically, we performed a regression analysis using pseudotime as the independent variable and DNA methylation levels at gene promoter regions...
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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
...higher differentially expressed genes (DEGs) in the GSC-like cell cluster. The GSC-like transcriptome is differentially enriched for protein complexes involved in chromatin regulation, such as DNA replication, heterochromatin maintenance, and chromatin accessibility (Fig. 2F,G; Supplemental Fig. S3B...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...MHC in newts illuminates the evolutionary dynamics of complex regions in giant s Wiesław Babik1, Katarzyna Dudek1, Gemma Palomar1,2, Marzena Marszałek1,3, Grzegorz Dubin4, Maximina H. Yun5,6 and Magdalena Migalska1 1Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University...
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Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
...isoforms varied significantly among cell classes. For example, Pcbp4 is a gene predicted to facilitate mRNA 3′-UTR-binding activity. It acts upstream of or within the negative regulation of the DNA damage response and mRNA splicing via the spliceosome. Although all isoforms of Pcbp4 were expressed in all...
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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
...was inhibited, the repression of gene expression is impaired, highlighting the active regulation of this process by DDR signaling pathways (Iannelli et al. 2017).A mechanism for global transcriptional shutdown through degradation of ubiquitinated RNA Pol II has been shown upon UV-induced DNA damage. However, UV...
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