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Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...the experimental structures in the database still cover no more than half of the protein-coding genes in the human .It is widely accepted that tertiary structures of proteins are more conserved than their amino acid sequences (Chothia and Lesk 1986; Rost 1999; Wood and Pearson 1999; Illergård et al. 2009...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
...: a long relative tail length, supination of the ankle joints for head-first descents, and marbled/clouded pelage patterns. Yuan and colleagues identified two parallel amino acid substitutions in two candidate genes (MYSM1 and GOLGB1) with known roles in mammalian pigmentation formation that are otherwise...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...–human chimeric reads and exhibited frequent interchromosomal translocations with “fold-back” inversion patterns mediated by inserted HBV sequences. Such fold-back patterns implicate BFB cycles (Tanaka and Yao 2009), which can drive oncogene overexpression and contribute to both cancer initiation and therapeutic...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...′ UTR of the CD47 gene, significantly impacts gene splicing and is strongly associated with reproductive phenotypes. Additionally, we observe that neuronal cells generally possess longer 3′ UTRs—a pattern conserved across humans, mice, fruit flies, and pigs. Together, these findings enrich the 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
.... This signature encodes critical neuronal proteins including synaptic proteins, suggesting similar functional outcomes of these transcriptional disruptions. To test the functional implications of these transcriptomic changes, we measured neuronal firing patterns. Every transcriptional regulator tested affected...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...impacts and evolutionary patterns over time remain elusive in humans owing to the technical and ethical complexities of functional studies. Integrating gene age dating with Mendelian disease phenotyping, we reveal a gradual rise in disease gene proportion as gene age increases. Logistic regression...
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Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
...-exon consensus sequence alignments within a gene family (TPM on top, MAPK in the middle) or a gene (MYO1B, at the bottom). Each letter reported is the amino acid conserved in all sequences of the corresponding MSA (allowing one substitution). The color scheme is that of Clustal X (Thompson et al. 1997...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
...correlation between the probability of overall GC content with the use of GC in the degenerative positions of codons for amino acids with four and six degenerative codons suggests that compositional bias drives codon usage (Supplemental Figs. S2, S3).The difference between EENC and OENC indicates that factors...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...conservation of the X Chromosome gene content across broad swathes of the insect phylogeny, as well as temporal dynamics to the rate of X Chromosome evolution (Meisel et al. 2019; Chauhan et al. 2021).ResultsGenome featuresWe used PacBio HiFi sequencing to generate sequences for a female (XX) migratory locust...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...and Belmont 2017; Falk et al. 2019).Lamina-associated domains (LADs) are large, heterochromatic regions of the that interact with the transcriptionally repressive environment of the nuclear lamina. Some LADs are conserved across development, whereas others interact with the lamina only in particular cell...
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