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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
..., organization, signaling, and transport among the most variable expressed genes in nonneuronal cells. We therefore indicate that unique species-specific gene sets can deliver cell-specific information, highlighting a connection to a heritable disease mechanism. We also observe that human quasi...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...-existing Chromoviridae-related Gypsy clades independently expanded in different truffle lineages, leading to increased size and high gene-family turnover rates, but without resulting in highly rearranged s. Additionally, we uncover a significant enrichment of ECM-induced gene families stemming from ancestral duplication...
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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. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...low proportion of cCRE–gene 389 17 links conserved in the human brain dataset(Adams et al. 2024). This may reflect the previously 390 reported species specificity of both cCREs and their associated orthologous genes(Li et al. 391 2023). In addition, our analysis was restricted to cis-regulatory links...
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Research: Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation
- Michael S. Werner,
- Bogdan Sieriebriennikov,
- Neel Prabh,
- Tobias Loschko,
- Christa Lanz,
- and Ralf J. Sommer
Genome Res. November 2018 28: 1675-1687; Published in Advance September 19, 2018, doi:10.1101/gr.234872.118
..., or “orphan” genes account for 10%–30% of eukaryotic s. Although initially considered to have limited function, an increasing number of orphan genes have been shown to provide important phenotypic innovation. How new genes acquire regulatory sequences for proper temporal and spatial expression is unknown...
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Research: Human-specific features of spatial gene expression and regulation in eight brain regions
- Chuan Xu,
- Qian Li,
- Olga Efimova,
- Liu He,
- Shoji Tatsumoto,
- Vita Stepanova,
- Takao Oishi,
- Toshifumi Udono,
- Katsushi Yamaguchi,
- Shuji Shigenobu,
- Akiyoshi Kakita,
- Hiroyuki Nawa,
- Philipp Khaitovich,
- and Yasuhiro Go
Genome Res. August 2018 28: 1097-1110; Published in Advance June 13, 2018, doi:10.1101/gr.231357.117
...modification data allows us to assess the influence of various regulatory mechanisms on the species-specific alterations of spatial expression profiles represented by the 24 gene modules. Specifically, we assessed the influence of (1) H3K27ac modification levels at promoter regions, (2) H3K27ac modification...
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Research: Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
- Alexandre Laverré,
- Eric Tannier,
- and Anamaria Necsulea
Genome Res. February 2022 32: 280-296; Published in Advance December 20, 2021, doi:10.1101/gr.275901.121
...-regulatory landscapes, we processed and analyzed Promoter Capture Hi-C (PCHi-C) data derived from 16 human cell types and eight mouse cell types (Methods; Supplemental Table S1). The PCHi-C technique was designed to detect interactions between gene promoters and other genomic regions, with high sensitivity and spatial...
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Resource: A comparison of gene expression and DNA methylation patterns across tissues and species
- Lauren E. Blake,
- Julien Roux,
- Irene Hernando-Herraez,
- Nicholas E. Banovich,
- Raquel Garcia Perez,
- Chiaowen Joyce Hsiao,
- Ittai Eres,
- Claudia Cuevas,
- Tomas Marques-Bonet,
- and Yoav Gilad
Genome Res. February 2020 30: 250-262; Published in Advance January 17, 2020, doi:10.1101/gr.254904.119
...differences between species.In this study, we used a comparative catalog to identify species-specific and, in particular, tissue-specific regulatory patterns, because these genes are often drug targets (Dezső et al. 2008) and are likely important for the evolution of human traits (Blekhman et al. 2008). We...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
...for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis- and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several...
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Research: Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes
- Neel Prabh,
- Waltraud Roeseler,
- Hanh Witte,
- Gabi Eberhardt,
- Ralf J. Sommer,
- and Christian Rödelsperger
Genome Res. November 2018 28: 1664-1674; Published in Advance September 19, 2018, doi:10.1101/gr.234971.118
...as a plausible explanation. Further, since the spatial distribution of age classes coincided with the distribution of dS and previous analysis of evolutionary constraint suggested old genes to be under stronger selection (Fig. 4B), we hypothesized that differences in proportion of age classes may cause...
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Research: Coordinated histone modifications are associated with gene expression variation within and between species
- Misook Ha,
- Danny W-K. Ng,
- Wen-Hsiung Li,
- and Z. Jeffrey Chen
Genome Res. April 2011 21: 590-598; Published in Advance February 4, 2011, doi:10.1101/gr.116467.110
...modifications confer distinct gene expression patterns. H3K9ac and H3K4me3 are related to temporal and spatial regulation of gene expression, depending on the location of these modifications relative to the TSS. For example, among the highly expressed genes (G1 and G2), the H3K9ac and H3K4me3 levels peaked...

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