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Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
- Xiaoyu Zhuo,
- Silas Hsu,
- Deepak Purushotham,
- Prashant Kumar Kuntala,
- Jessica K. Harrison,
- Alan Y. Du,
- Samuel Chen,
- Daofeng Li,
- and Ting Wang
Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
...similar or different epigenomic features and genomic structural boundaries, providing a powerful tool for validating discoveries made from -wide analysis. The browser also allows the integration and comparison of data from different sources, which can be used to generate new hypotheses about the evolution...
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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...for structural variation to serve as raw material for adaptive evolution.Structural variants (SVs) in s are a ubiquitous component of within and between species genomic variation (Mérot et al. 2020; Zhang et al. 2021). The larger size of SVs, when compared with single nucleotide polymorphisms (SNPs), may...
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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: Impact of the X Chromosome and sex on regulatory variation
- Kimberly R. Kukurba,
- Princy Parsana,
- Brunilda Balliu,
- Kevin S. Smith,
- Zachary Zappala,
- David A. Knowles,
- Marie-Julie Favé,
- Joe R. Davis,
- Xin Li,
- Xiaowei Zhu,
- James B. Potash,
- Myrna M. Weissman,
- Jianxin Shi,
- Anshul Kundaje,
- Douglas F. Levinson,
- Philip Awadalla,
- Sara Mostafavi,
- Alexis Battle,
- and Stephen B. Montgomery
Genome Res. June 2016 26: 768-777; Published in Advance April 21, 2016, doi:10.1101/gr.197897.115
...nucleotide polymorphisms (SNPs) located on the autosomes and X Chromosome on the Illumina HumanOmni1-Quad BeadChip and then imputed using the 1000 Genomes Phase 1 reference panel (Methods).Sex-specific expression variation across the Sex-specific patterns of gene expression have been well studied...
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Research: DNA methylation contributes to natural human variation
- Holger Heyn,
- Sebastian Moran,
- Irene Hernando-Herraez,
- Sergi Sayols,
- Antonio Gomez,
- Juan Sandoval,
- Dave Monk,
- Kenichiro Hata,
- Tomas Marques-Bonet,
- Liewei Wang,
- and Manel Esteller
Genome Res. September 2013 23: 1363-1372; Published in Advance August 1, 2013, doi:10.1101/gr.154187.112
...about their contribution to natural human variation. To determine their contribution to variability, we have generated genome-scale DNA methylation profiles of three human populations (Caucasian-American, African-American, and Han Chinese-American) and examined the differentially methylated CpG sites...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...lines and strains, and a high rate of gene retroposition. Our study offers novel insights into mammalian evolution and highlights the importance of repetitive elements in shaping genomic diversity.All forms of genetic variation originate from new mutations, so it is important to know the rate at which...
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Resource: Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- Ashlyn G. Anderson,
- Belle A. Moyers,
- Jacob M. Loupe,
- Ivan Rodriguez-Nunez,
- Stephanie A. Felker,
- James M.J. Lawlor,
- William E. Bunney,
- Blynn G. Bunney,
- Preston M. Cartagena,
- Adolfo Sequeira,
- Stanley J. Watson,
- Huda Akil,
- Eric M. Mendenhall,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. August 2024 34: 1224-1234; Published in Advance August 16, 2024, doi:10.1101/gr.278601.123
...of allele-specific gene regulation. Finally, we highlight an interesting example of ASB identified in our data sets.ResultsGraph s improve read mapping and reduce reference allele biasTo study the impact of genetic variation on TF binding, we first performed linked-read sequencing (10x Genomics) to generate...
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Research: Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
- Vera B. Kaiser,
- Lana Talmane,
- Yatendra Kumar,
- Fiona Semple,
- Marie MacLennan,
- Deciphering Developmental Disorders Study,
- David R. FitzPatrick,
- Martin S. Taylor,
- and Colin A. Semple
Genome Res. November 2021 31: 1994-2007; Published in Advance August 20, 2021, doi:10.1101/gr.275407.121
...regions, whereas CNVs arising from nonhomologous mechanisms are enriched in late replicating regions (Koren et al. 2012). Local chromatin structure also influences the mutation rate. However, finer-scale variation (<1 Mb) in the germline mutation rate has so far only been related to genomic features...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...’ assemblies to define orthologous transcripts (Supplemental Fig. S10; Supplemental Methods), highlighting the high genomic conservation of transcript structures (Supplemental Data S5, S6). In addition to this high conservation, we found 61 species-specific exons without an orthologous counterpart in the most...
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Research: Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
- Stefan Washietl,
- Manolis Kellis,
- and Manuel Garber
Genome Res. April 2014 24: 616-628; Published in Advance January 15, 2014, doi:10.1101/gr.165035.113
...(indicated by a, b, c). Example D shows a lincRNA well-supported in human and chimpanzee but absent in all replicates in themore distantly relatedmammals. Example E shows a transcript conserved in all species also supported by all replicates. Evolutionary dynamics of human lincRNAs Genome Research 619 www...

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