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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...manipulation of this modification in mRNAs. Here, we present Dem6A-Vec, an “all-in-one” plasmid vector designed for site-specific m6A demethylation in human mRNAs. Dem6A-Vec integrates the expression of a catalytically inactive RfxCas13d fused to the m6A demethylase ALKBH5 and a U6-driven customizable guide...
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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
...A STARR-seq assay reveals thousands of enhancers active in immune-stimulated cells 94 To identify the enhancers that regulate the Drosophila innate immune response, we performed a 95 STARR-seq experiment in S2* cells (Samakovlis et al. 1992; Cherbas et al. 2011). Briefly, a 96 -wide library of plasmids...
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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. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...and to associated organs including the liver and pancreas. We used functional genomic approaches to identify highly conserved endodermal cis-regulatory modules (CRMs) functioning across the 400 million years of evolution separating zebrafish and humans. Our analyses suggest that there are few endoderm-specific CRMs...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...CRE–gene links (Supplemental Table S6) were conserved in humans based on comparison with cCRE–gene correlations reported in a previous human brain study (Adams et al. 2024). We observed moderate overlap between cCRE-gene links, age-associated DEGs, and DACs. For instance, in oligodendrocytes, 116 age...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...02912, USA Corresponding author: emilia_huerta-sanchez@brown.eduAbstractThe exchange and subsequent incorporation of genetic material between distinct lineages, known as introgression, has emerged as a crucial concept in understanding human evolutionary history. With the advent of high...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
..., the Polycomb landscape of differentiated cell types remains unexplored. Differentiated cells comprise the majority of the gut epithelium and directly impact both tissue and whole organismal aging. Using single-cell chromatin profiling of the Drosophila intestine, we identify cell type–specific chromatin...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...that are not conserved in Drosophila (Fig. 2). For example, orthologous genes that correspond to SNCA (Parkinson's disease), PRNP (prion diseases), and MECP2 (Rett syndrome) are not found in the Drosophila . However, ectopic overexpression of these human proteins can cause scorable phenotypes in flies (Feany and Bender...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
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Research: Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
- Yang Li and
- Jianzhi Zhang
Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
...function, we compare the transcriptomic and proteomic effects of systematic gene deletions in budding yeast (Saccharomyces cerevisiae) with those effects in fission yeast (Schizosaccharomyces pombe). Despite evidence for functional conservation of orthologous genes, their deletions result in no more...
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