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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
...of the phyla Firmicutes, Actinobacteria, and Bacteroidetes, which are among the most abundant bacteria found in Pristionchus nematodes and their beetle hosts (Meyer et al. 2017). Eighty-four bacterial strains were selected for whole- sequencing based on criteria such as fast growth, ease of DNA extractions...
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Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
- Guanjue Xiang,
- Xi He,
- Belinda M. Giardine,
- Kathryn J. Isaac,
- Dylan J. Taylor,
- Rajiv C. McCoy,
- Camden Jansen,
- Cheryl A. Keller,
- Alexander Q. Wixom,
- April Cockburn,
- Amber Miller,
- Qian Qi,
- Yanghua He,
- Yichao Li,
- Jens Lichtenberg,
- Elisabeth F. Heuston,
- Stacie M. Anderson,
- Jing Luan,
- Marit W. Vermunt,
- Feng Yue,
- Michael E.G. Sauria,
- Michael C. Schatz,
- James Taylor,
- Berthold Göttgens,
- Jim R. Hughes,
- Douglas R. Higgs,
- Mitchell J. Weiss,
- Yong Cheng,
- Gerd A. Blobel,
- David M. Bodine,
- Yu Zhang,
- Qunhua Li,
- Shaun Mahony,
- and Ross C. Hardison
Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
...of the GLOD5/Glod5 genes (Fig. 6A). Thus, the interspecies sequence alignments provide limited information about this distal regulatory element.View larger version: In this window In a new window Figure 6. Epigenetic comparisons of regulatory landscapes and cCREs. (A,B) DNA sequence alignments...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...for the kidney. We combined publicly available data (cDNA from published s and kidney RNA-seq data) with newly generated RNA-seq data to obtain coding sequence and expression data in a variety of rodents, ensuring a reasonable overlap between the two types of data (12 families, 48 species out of which 33 species...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...allele-specific gene expression across large imprinted domains. In this review, we highlight the features that define ICRs as a distinct class of cis-regulatory regions, from their ability to maintain germline-inherited DNA methylation to their multifunctional roles in transcriptional control. For each...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...prior to the WGD. Analysis of individual TE insertions, however, revealed enrichment of TE-CREs originating from WGD-associated TE activity, particularly for the DTT (Tc1-Mariner) DNA elements. Furthermore, coexpression analyses supported the presence of TE-driven gene regulatory network evolution...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...such as histone acetylation and methylation contribute to 48 this regulation by altering DNA accessibility at enhancers and promoters (Mostafavi et al., 49 2016; Kan et al., 2022). Transposase-accessible chromatin with sequencing (ATAC-seq) 50 and chromatin immunoprecipitation and sequencing (ChIP-seq) are widely...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...reveal a highly significant association between endoderm HCNEs and genes encoding DNA-binding and gene regulatory proteins, including HMG domain-containing and chromatin binding factors. Notably, however, the endodermHCNEs appear to show a greater enrichment of such genes compared with all HCNEs...
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Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
- Emily Lowry,
- Yiqing Wang,
- Tal Dagan,
- and Amir Mitchell
Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
....mitchell@umassmed.eduAbstractColibactin produced primarily by Escherichia coli strains of the B2 phylogroup cross-links DNA and can promote colon cancer in human hosts. Here, we investigate the toxin's impact on colibactin producers and on bacteria cocultured with producing cells. Using -wide genetic screens and mutation accumulation experiments...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...and ultimately enable functional classification of regulatory variants identified by population studies.Most genetic associations with human diseases and traits lie within noncoding regulatory DNA (Maurano et al. 2012). Genome-scale methods to analyze the function of noncoding regulatory elements within...
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Method: Designing realistic regulatory DNA with autoregressive language models
- Avantika Lal,
- David Garfield,
- Tommaso Biancalani,
- and Gokcen Eraslan
Genome Res. September 2024 34: 1411-1420; Published in Advance September 25, 2024, doi:10.1101/gr.279142.124
...94080, USA Corresponding authors: lal.avantika@gene.com, eraslan.gokcen@gene.comAbstractCis-regulatory elements (CREs), such as promoters and enhancers, are DNA sequences that regulate the expression of genes. The activity of a CRE is influenced by the order, composition, and spacing of sequence motifs...
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