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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...wild isolate VSL2202 and ZF1220 compared with C. briggsae strains. (E) Heatmap showing cDNA sequence identity of Cni-shls-1 (top), Cni-otub-3 (middle), and Cni-neib-1 (bottom) across all C. nigoni strains. Note that Cni-neib-1 sequences are 100% identical across all strains. (F) Gene models flanking...
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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
.... This has made it difficult to distinguish genes that are expressed and potentially functional from pseudogenes. To address this limitation, we sequenced HiFi, full-length nonchimeric (FLNC) cDNA using a PacBio isoform sequencing (Iso-Seq) assay (Methods) (Dougherty et al. 2018). We generated or analyzed...
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ARTICLE: Regional Patterns of Gene Expression in Human and Chimpanzee Brains
- Philipp Khaitovich,
- Bjoern Muetzel,
- Xinwei She,
- Michael Lachmann,
- Ines Hellmann,
- Janko Dietzsch,
- Stephan Steigele,
- Hong-Hai Do,
- Gunter Weiss,
- Wolfgang Enard,
- Florian Heissig,
- Thomas Arendt,
- Kay Nieselt-Struwe,
- Evan E. Eichler,
- and Svante Pääbo
Genome Res. August 2004 14: 1462-1473; doi:10.1101/gr.2538704
...for which the chimpanzee DNA sequence is known, 207 are more highly expressed in humans and 199 in chimpanzees. Thus, although the up-regulation of genes on the human lineage may be real, further work is needed to verify it. This might be done using cDNA arrays that are less sensitive to DNA sequence...
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LETTER: A genome-wide survey of structural variation between human and chimpanzee
- Tera L. Newman,
- Eray Tuzun,
- V. Anne Morrison,
- Karen E. Hayden,
- Mario Ventura,
- Sean D. McGrath,
- Mariano Rocchi,
- and Evan E. Eichler
Genome Res. October 2005 15: 1344-1356; Published in Advance September 16, 2005, doi:10.1101/gr.4338005
...-specific evolution because of their potential for dramatic and irreversible mutation. The low-quality nature of the current chimpanzee genome assembly precludes the reliable identification of many of these differences. To circumvent this, we applied a method to optimally map chimpanzee fosmid paired-end sequences...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...of 366 sequences obtained by RELA ChIP in HeLa cells combined with the analysis of ENCODE RELA ChIP-seq (26-bp single-end data) from the lymphoblast cell line GM12878 and led to the conclusion that ∼11% of NF-kB-bound regions contain an Alu-derived NF-kB motif (Antonaki et al. 2011). Although our study...
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LETTER: Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA
- Ines Hellmann,
- Sebastian Zöllner,
- Wolfgang Enard,
- Ingo Ebersberger,
- Birgit Nickel,
- and Svante Pääbo
Genome Res. May 1, 2003 13: 831-837; doi:10.1101/gr.944903
...not contain a gene annotation and was not an EST entry, Genscan ( Burge and Karlin 1997 ) was applied to the human sequence starting 50 kb before and ending 50 kb after the alignment to the chimpanzee cDNA contig. Identified coding regions were extracted and collected in a local database, which was again...
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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...characterize these complex regions to gain insight into the impact of genomic diversity on health and disease. Here we resolve the organization of complete major histocompatibility complex (MHC) class II regions in rhesus macaques by using a long-read sequencing strategy (Oxford Nanopore Technologies...
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Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...(Chambers et al. 2009; Ohnuki et al. 2014).To generate RNA-seq data, we used three clones of three human individuals and four clones of two cynomolgus macaque individuals. After 5 days of differentiation, the cells showed characteristics of neural progenitors and were harvested at days 5, 7, and 9. cDNA...
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LETTER: Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla
- Gary M. Wilson,
- Stephane Flibotte,
- Perseus I. Missirlis,
- Marco A. Marra,
- Steven Jones,
- Kevin Thornton,
- Andrew G. Clark,
- and Robert A. Holt
Genome Res. February 2006 16: 173-181; Published in Advance December 19, 2005, doi:10.1101/gr.4456006
...), partial coverage genomic arrays ( Locke et al. 2003 ), cDNA arrays ( Fortna et al. 2004 ), end-sequence profiling ( Newman et al. 2005 ), draft sequence ( Chimpanzee Sequencing and Analysis Consortium 2005 ), and high-quality sequence from chimp Chromosome 21 (orthologous to human Chromosome 22...
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LETTER: Independent intrachromosomal recombination events underlie the pericentric inversions of chimpanzee and gorilla chromosomes homologous to human chromosome 16
- Violaine Goidts,
- Justyna M. Szamalek,
- Pieter J. de Jong,
- David N. Cooper,
- Nadia Chuzhanova,
- Horst Hameister,
- and Hildegard Kehrer-Sawatzki
Genome Res. September 2005 15: 1232-1242; doi:10.1101/gr.3732505
.... RNA isolation and cDNA preparation Cytoplasmic RNA was isolated from lymphoblastoid and fibroblast cell cultures derived from three chimpanzees and four humans, as well as lymphoblastoid cells from one bonobo, one gorilla, one orangutan, and one macaque, using the RNeasy kit (Qiagen). First strand cDNA...

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