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Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...involving the coordinated action of transcription factors, chromatin remodelers, and RNA polymerase, which determine where and when transcription begins. Accurately mapping and quantifying transcription start sites (TSSs) from nascently transcribed RNAs remains a key area of interest, as it provides...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Johannes Hiltunen1,3, Laura Helminen1,3, Niina Aaltonen1,3, Kaisa-Mari Launonen1, Hanna Laakso1, Marjo Malinen2, Einari A. Niskanen1, Jorma J. Palvimo1 and Ville...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...of euchromatic regions and facilitates transcription elongation. In contrast, Ash1-mediated H3K36me3 localizes to promoters within facultative heterochromatin and represses transcription. Notably, Ash1-mediated H3K36me3 cooperates with Polycomb repressive complex 2 (PRC2)-dependent H3K27me3 to silence secondary...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...conditions. In response to upstream stimuli, such as the pro-inflammatory cytokine tumor necrosis factor (TNF), the IKB inhibitors are degraded and NF-kB rapidly translocates into the nucleus where it binds promoter-proximal and promoter-distal CREs that drive the expression of multiple innate immunity...
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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
...) demonstrated that introns are not always removed in the order in which they appear in the nascent transcript. Our recent work extended these results by studying posttranscriptional splicing order for three to six consecutive introns (Choquet et al. 2023) using long-read direct RNA nanopore sequencing (Garalde...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...progenitor programs. Our study provides in vitro and in vivo molecular evidence that paired-class HD cooperative dimerization regulates neuronal development and that dysregulation of cooperative binding contributes to severe dominant blinding retinopathies.Homeodomain (HD) transcription factors (TFs...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...). As nascent RNAs emerge from the RNAPII exit channel, a seven-methyl-guanosine cap is added to protect the 5′ end (Galloway and Cowling 2019). Splice sites on the pre-mRNA are recognized by spliceosomal complexes to excise introns, often as the molecule is actively being elongated (Carrocci and Neugebauer...
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Research: Acute depletion of METTL3 implicates N⁶-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome
- Guifeng Wei,
- Mafalda Almeida,
- Greta Pintacuda,
- Heather Coker,
- Joseph S. Bowness,
- Jernej Ule,
- and Neil Brockdorff
Genome Res. August 2021 31: 1395-1408; Published in Advance June 15, 2021, doi:10.1101/gr.271635.120
...depletion of METTL3 on nascent RNA splicing.ResultsMapping m6A in the nascent mESC transcriptomeChromatin-associated RNA (ChrRNA) is substantially enriched for nascent transcripts (Nesterova et al. 2019). Thus, to investigate the roles of m6A in nascent RNA processing in mouse embryonic stem cells, we...
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Research: Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
- Anushka Gupta,
- Farnaz Shamsi,
- Nicolas Altemose,
- Gabriel F. Dorlhiac,
- Aaron M. Cypess,
- Andrew P. White,
- Nir Yosef,
- Mary Elizabeth Patti,
- Yu-Hua Tseng,
- and Aaron Streets
Genome Res. February 2022 32: 242-257; Published in Advance January 18, 2022, doi:10.1101/gr.275509.121
...that intronic reads originate from nascent transcripts (Ameur et al. 2011; Gray et al. 2014; Hendriks et al. 2014) and, hence, are informative about expression levels in single-cell data. Furthermore, the additional read counts improve gene detection sensitivity and can improve cell-cluster resolution (Bakken...
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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
....gullerova@path.ox.ac.ukAbstractDNA damage triggers a complex transcriptional response that involves both activation and repression of gene expression. In this study, we investigated global changes in transcription in response to ionizing irradiation (IR), which induces double-strand breaks in DNA. We used mNET-seq to profile nascent...
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