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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...-seq information to improve the accuracy of genomic selection.Genomic selection has had a tremendous impact on livestock breeding in the past 10 yr (e.g., García-Ruiz et al. 2016). Nevertheless, the accuracy of selection remains inferior to what may be achievable given the heritability of the selected traits...
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Research: Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
- Charles Y. Feigin,
- Axel H. Newton,
- and Andrew J. Pask
Genome Res. October 2019 29: 1648-1658; Published in Advance September 18, 2019, doi:10.1101/gr.244251.118
...as a powerful approach to study patterns of selection on CREs. It has been used to identify positive selection on forelimb-specific enhancers in bats (Booker et al. 2016) and across numerous traits in recent radiations of anole lizards (Tollis et al. 2018). This approach has also proven valuable for studying...
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Research: RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts
- Yang I. Li,
- Luis Sanchez-Pulido,
- Wilfried Haerty,
- and Chris P. Ponting
Genome Res. January 2015 25: 1-13; Published in Advance December 18, 2014, doi:10.1101/gr.181990.114
...-exons require splicing-enhancing genomic features to be processed, the splicing of hundreds of micro-exons is enhanced by the adjacent binding of splice factors in the introns of pre-messenger RNAs. Notably, splicing of a significant number of micro-exons was found to be facilitated by the binding of RBFOX...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...established to provide a comprehensive atlas of regulatory variants across a range of farmed animals. It has completed the pilot phase for cattle, pigs, and chickens, providing novel insights into molecular regulatory mechanisms of complex traits of economic and ecological value (Liu et al. 2022b; Teng et al...
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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
...that these elements are under extreme negative selection (Drake et al. 2006; Chen et al. 2007; Katzman et al. 2007).UCEs have also been found to encompass various functions, including enhancer, promoter, splicing, and repressive activities (Pennacchio et al. 2006; Poitras et al. 2010; Snetkova et al. 2022). In vivo...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
...noncoding SNPs) associated with specific traits or diseases were enriched in enhancers in the pig (mean SNP enrichment scores in enhancers vs. nonenhancer regions: 1.34 vs. 0.97, P = 0.002, paired Student's t-test) (Supplemental Fig. S27A), confirming the functional importance of enhancers (Maurano et al...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...a single . Epigenetic modifications have also been shown to vary across47 individuals in humans (McVicker et al., 2013; Kang et al., 2021), rats (Rintisch et al., 2014), cattle48 (Prowse-Wilkins et al., 2022), and mice, including some of the DO/CC founders (Link et al., 2018;49 Schilling et al., 2009; Zhou...
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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
...in homozygosity. A more cautious hypothesis would be to consider that this event corresponds to a sequence rearrangement or omission in the dog to which wolf reads map poorly.CNV-GWASGiven the lack of global maps for -wide CNV analyses, absolute copy number has never been globally assessed for trait associations...
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Research: Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome
- Weibing Shi,
- Christina D. Moon,
- Sinead C. Leahy,
- Dongwan Kang,
- Jeff Froula,
- Sandra Kittelmann,
- Christina Fan,
- Samuel Deutsch,
- Dragana Gagic,
- Henning Seedorf,
- William J. Kelly,
- Renee Atua,
- Carrie Sang,
- Priya Soni,
- Dong Li,
- Cesar S. Pinares-Patiño,
- John C. McEwan,
- Peter H. Janssen,
- Feng Chen,
- Axel Visel,
- Zhong Wang,
- Graeme T. Attwood,
- and Edward M. Rubin
Genome Res. September 2014 24: 1517-1525; Published in Advance June 6, 2014, doi:10.1101/gr.168245.113
...revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially...

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