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Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
- Brigitta Szabo,
- Therese C. Mandl,
- Bernhard Woldrich,
- Gregor Diensthuber,
- David Martin,
- Michael F. Jantsch,
- and Konstantin Licht
Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
...RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels Brigitta Szabo, Therese C. Mandl, Bernhard Woldrich, Gregor Diensthuber, David Martin, Michael F. Jantsch and Konstantin Licht Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...(Pol II) -wide. These approaches provide a high-resolution view of transcription initiation, pausing, and elongation, enabling rapid detection of transcriptional changes following TF perturbation.Other methods survey Pol II–associated chromatin-bound RNAs, such as chromatin-associated RNA-seq (Chr...
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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
.... Whereas much research has focused on the initiation of transcription, regulation of elongation plays an important role not only in transcription dynamics but also in cotranscriptional RNA processing and stability. Despite advances in high-throughput approaches for global quantification of RNA polymerase...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...(Figs. 1A,D, 2), our analyses of the gar mobilome demonstrate that, across multiple levels of genomic organization, gars have maintained genomic stability over the 100 million year evolutionary history of their crown clade that exceeds the levels of stasis observed even in other living fossil lineages...
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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
...(R = 0.19, P = 0.0046), which could suggest that Pol II and other machinery disrupt well-phased nucleosomes in order for transcription to occur (Fig. 5C). Although the strongest nucleosome changes were observed within the first three nucleosomes (500 bp downstream from the TSS), we also investigated...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...integrated analyses of single-cell RNA-seq data from multiple human tissues and organs. Single-cell epigenomic data further indicate that the expression is likely driven by an alternative promoter at the end of the first exon, resulting in at least one shorter transcript (referred to as sXIST) that is active...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...; Agilent 600559).The endogenous MYC, DNAJC9, RPL30, and POL2RA mRNA expression levels were measured by quantitative RT-PCR using EvaGreen dye (Biotium) on a Bio-Rad CFX real-time system. A standard curve was generated for each primer set with thermal cycle conditions for 40 PCR cycles (12 min at 95°C, 15...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...the process of transcription as the nascent RNA strand exits RNA polymerase II (Pol II) and hybridizes to the template DNA strand (Ginno et al. 2012; Sanz et al. 2016). In addition, recent studies showed that some long noncoding RNAs (lncRNAs) can associate to distant genomic regions through the formation...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...-specific gDNA, new predictions in N2-shared gDNA are possibly but not certainly real.Transcription of long tandem repeat regionsIn C. elegans, TRs could be transcriptionally active either because they fall inside regions of transcribed genes that harbor them or because the TRs are themselves actively...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...enriched for genomic regions that contained bivalent domains, similar to prior findings (Thudium et al. 2022). These findings suggest that instances of specific genomic features identified in ASD risk genes (King et al. 2013; Zhao et al. 2018) are also common features of transcriptional disruptions...

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