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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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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...Methods) (Supplemental Table 1; Supplemental Fig. 10).FIEs associated with gene duplication can be timed using their estimated mutation copy number as likely to have occurred either before or after the gene duplication event. Preduplication mutations were defined as those with at least two mutant copies...
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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...RNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, USA. ♱Corresponding authors: izg5139@psu.edu, nadav.ahituv@ucsf.edu Abstract Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene...
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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
...that collate and integrate many different sources of data and databases because ease of use and reliability are key.Three types of tools should be applied in parallel: – Genome browsers with multiple annotation tracks, especially the unrivalled University of California at Santa Cruz (UCSC) browser (Perez et al...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...on CNVs.View larger version: In this window In a new window Figure 4. Amplified genes result in increased mRNA expression. (A) Replicate averaged log2 fold-change of all genes on Chr XI in each CNV strain compared with the euploid ancestor. Numbers indicate the copy number of genes within the CNV. (B) Log...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...-score-normalized expression of the top 60 coexpression modules across the different diets was visualized as a heat map. The expression of the biological replicates was averaged in order to produce a single expression profile for each of the 38 diets. Modules with more than 50 genes were randomly downsampled to aid...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...directed GRNs by manually distinguishing TFs from target genes. More recently, deep learning has been introduced into GRN inference, with methods such as CNNGRN, which leverages convolutional neural networks to analyze bulk time-series gene expression data and infer regulatory interactions between TFs...
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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
...'s intolerance to heterozygous deletion or loss-of-function variants. A related concept of triplosensitivity refers to intolerance to duplication. Beyond these large changes that affect one entire copy of a gene, especially noncoding genetic variants affect the expression of nearby genes. For many genes...
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Research: The asymmetric distribution of RNA polymerase II and nucleosomes on replicated daughter genomes is caused by differences in replication timing between the lagging and the leading strand
- Rahima Ziane,
- Alain Camasses,
- and Marta Radman-Livaja
Genome Res. February 2022 32: 337-356; Published in Advance January 18, 2022, doi:10.1101/gr.275387.121
...in parallel, with which we identified clusters of secondary origins surrounding known origins. We found a difference in the timing of lagging and leading strand replication on the order of minutes at most yeast genes. We propose a model in which the majority of old histones and RNA polymerase II (RNAPII) bind...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
..., respectively, and four residual convolutional blocks for learning and integrating the three inputs. In the computational blocks, Conv2D and MaxPool2D are applied to deal with genes and discrete cCREs in parallel by setting kernel size to 1 along the height axis. At last, the feature-learning module uses...
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