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Resource: Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
- Ekaterina Khrameeva,
- Ilia Kurochkin,
- Dingding Han,
- Patricia Guijarro,
- Sabina Kanton,
- Malgorzata Santel,
- Zhengzong Qian,
- Shen Rong,
- Pavel Mazin,
- Marat Sabirov,
- Matvei Bulat,
- Olga Efimova,
- Anna Tkachev,
- Song Guo,
- Chet C. Sherwood,
- J. Gray Camp,
- Svante Pääbo,
- Barbara Treutlein,
- and Philipp Khaitovich
Genome Res. May 2020 30: 776-789; Published in Advance May 18, 2020, doi:10.1101/gr.256958.119
..., chimpanzee, bonobo, and macaque brain constructed using conventional RNA sequencing (bulk RNA-seq) and single-nuclei sequencing (snRNA-seq).ResultsGlobal gene expression variation analysisWe used bulk RNA-seq to examine RNA expression in 33 brain regions from four humans, three chimpanzees, three bonobos...
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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
...2000). To ensure similar evolutionary backgrounds, we retrieved the “one-to-one” human–chimpanzee orthologous genes and the corresponding pairwise Ka/Ks ratios (12,830 genes) from the Ensembl database (Supplemental Table S6). We also evaluated whether the pattern is consistent with Ka/Ks ratios...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...to vary structurally in our lineage (Bitar et al. 2019). Since the initial publication of the human and chimpanzee s, investigations of human-specific SD genes have found that they most often are implicated in xenobiotic recognition, metabolism, immunity, and neuronal development, playing an important...
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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
...classified far fewer DE genes between humans and chimpanzees than between either of these species and rhesus macaques (Supplemental Table S4B).It is a common notion that genes with tissue-specific expression patterns may underlie tissue-specific functions. Previous catalogs of such patterns in primates were...
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Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids
- Carina F. Mugal,
- Mi Wang,
- Niclas Backström,
- David Wheatcroft,
- Murielle Ålund,
- Marie Sémon,
- S. Eryn McFarlane,
- Ludovic Dutoit,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
...are suggestive of different modes of gene expression inheritance across tissues, that is, pied-dominant inheritance in brain, collared-dominant inheritance in heart, kidney, and liver, and additive inheritance in testis. Direct inclusion of F1 hybrids into the PCA revealed consistent inheritance patterns (Fig. 2...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between g...
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Research: Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system
- Dan Sun,
- Donna L. Maney,
- Thomas S. Layman,
- Paramita Chatterjee,
- and Soojin V. Yi
Genome Res. October 2019 29: 1673-1684; Published in Advance September 23, 2019, doi:10.1101/gr.248641.119
...hypermethylated region 2 [MHM2]; CGNC: 80602). The MHM1 and MHM2, despite little sequence similarity between them, bear similar molecular features that are likely associated with their functions. We present evidence consistent with female hypomethylation of MHMs and up-regulation of nearby genes. Therefore...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...regions. We recently characterized the abundance of snoRNAs and their host gene across several healthy human tissues and found that the level of most snoRNAs does not correlate with that of their host gene, with the observation that snoRNAs embedded within the same host gene often differ drastically...
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Research: Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures
- Giuliana Giannuzzi,
- Eugenia Migliavacca,
- and Alexandre Reymond
Genome Res. September 2014 24: 1455-1468; Published in Advance June 10, 2014, doi:10.1101/gr.167742.113
...regions are both gene-richer and the cradle of an abundance of recombination hotspots, it is possible that these two characteristics together with the higher divergence of these portion vis-a-vis the chimpanzee explain the observed enrichments. Additionally, we computed the content in repetitive elements...
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Research: Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders
- Ligia A. Papale,
- Andy Madrid,
- Qi Zhang,
- Kailei Chen,
- Lara Sak,
- Sündüz Keleş,
- and Reid S. Alisch
Genome Res. February 2022 32: 266-279; Published in Advance December 23, 2021, doi:10.1101/gr.276137.121
..., a brain region involved in the pathology of social behavior with high expression of the Cntnap2 gene since E14 and previously shown to be correlated with altered sociability in the Cntnap2−/− mice (Penagarikano et al. 2015). High-throughput sequencing resulted in a range of approximately 25 million to 43...

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