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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
...into how changes at the genomic level manifest in the organization of chromatin structure and the orchestration of transcriptional activity. Moreover, integrating our results with existing large-scale data sets encompassing transcriptomic, metabolomic, proteomic, and epigenomic information in the future...
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Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...integrative summary of such data sets. Here, we present the ENCODE4 Catalog of Segway Annotations, a set of sample-specific -wide chromatin state annotations of 234 human biosamples inferred from 1,794 genomics experiments. This catalog identifies genomic elements, accurately captures cell type...
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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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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
...function and links to practical research tools – Tools oriented specifically toward gene regulation, which allow reliable data mining, such as the excellent Gene Transcription Regulation Database (Kolmykov et al. 2021), the main advantage of which is seamless integration of ChIP-seq, ChIP-exo, DNase...
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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
...Haiyue Liu and Lea H. Gregersen Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark Corresponding author: leag@sund.ku.dkAbstractTranscription is regulated at multiple levels, including initiation, elongation, and termination...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...decreased variability (negative drift). Integration with single-cell RNA-seq data demonstrates that positive drift-CpGs are associated with increased transcriptional variability and upregulation in specific cell types, whereas negative drift-CpGs exhibit the opposite effect. We develop epigenetic drift...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...) that innervate skeletal muscles. However, certain MN groups including ocular MNs, are relatively resilient. To reveal key drivers of resilience versus vulnerability in ALS, we investigate the transcriptional dynamics of four distinct MN populations in SOD1G93A ALS mice using LCM-seq and single...
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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
...@pennmedicine.upenn.eduAbstractAutism spectrum disorder (ASD) is a highly heterogenous neurodevelopmental disorder with numerous genetic risk factors. Notably, a disproportionate number of risk genes encode transcription regulators including transcription factors and proteins that regulate chromatin. Here, we test the function of nine such ASD...
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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
...chromatin (Supplemental Fig. S4A).Promoter-bound RNAPII bears signs of canonical transcriptionAll epitopes of the RNAPII complex that we targeted using ChIP-qPCR follow the same trend of enrichment at promoters (Fig. 4B; Supplemental Fig. S4C), thereby indicating presence of the whole catalytic RNAPII...
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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
...that Dex on its own has only a limited transcriptional response at the single VCaP cell level. Integration of single cells from all four treatment groups resulted in 16 subpopulations of cells (SP0–SP15) (Fig. 4B). Single cells derived from EtOH- and Dex-treated samples were in SP2, SP3, SP5, SP6, SP7, SP9...
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