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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
...the possibility that parent-of-origin-specific TAD organization provides a structural context conducive to activation of imprinted genes (Monk et al. 2019).Although no altered boundary positions were detected between haplotypes of the two parental breeds, ∼190.97 Mb (∼8.43%) of genomic regions had allelic...
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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
...examination of the genomic organization of one of these Amerindian haplotypes, HG01109 H2, reveals that the entire 1.35 Mbp region bracketed by clusters 1 and 2 has been inverted, suggesting that inversion, as well as gene conversion, may be playing a role in relocating TBC1D3 paralogs between clusters 1...
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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
...of the global enrichment170 patterns shown in Figure 2. Although state 14 is generally depleted in gene bodies relative to171 intergenic regions, it is especially depleted at the TSS. In contrast, States 1 and 3 were both relatively172 abundant at the TSS. State 3 was very narrowly concentrated right at the TSS...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
...-fed mice (Gai et al. 2016).Sequence-dependent ASE arises from haplotype-specific genetic variationNext, we similarly characterized the expression profiles of the 2673 sequence-biased genes across our 27 tissue-by-context analyses to evaluate whether sequence-dependent ASE is also influenced by tissue...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...Assembly of a pan for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history Yang Zhou1,6, Lv Yang1,6, Xiaotao Han1, Jiazheng Han1, Yan Hu1, Fan Li1, Han Xia1, Lingwei Peng1, Clarissa Boschiero2, Benjamin D...
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Research: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
- Amanda J. Lea,
- Julie Peng,
- and Julien F. Ayroles
Genome Res. October 2022 32: 1826-1839; Published in Advance October 13, 2022, doi:10.1101/gr.276430.121
...environments in 544 immortalized B cell lines from the 1000 Genomes Project. We mapped the genetic basis of gene expression levels across environments and revealed a context-dependent genetic architecture: The average heritability of gene expression levels increased in treatment relative to control conditions...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
.... Corresponding authors: deepak.srivastava@gladstone.ucsf.edu, kpollard@gladstone.ucsf.eduAbstractExome sequencing of thousands of families has revealed many risk genes for congenital heart defects (CHDs), yet most cases cannot be explained by a single causal mutation. Even within the same family, individuals...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...enhancer activity in the phNPCs, and we link these regions to over 2200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including neuronal system, nervous system development, and developmental delay. We functionally validate a subset...
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Method: The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism
- Maximilian P.A. Salm,
- Stuart D. Horswell,
- Claire E. Hutchison,
- Helen E. Speedy,
- Xia Yang,
- Liming Liang,
- Eric E. Schadt,
- William O. Cookson,
- Anthony S. Wierzbicki,
- Rossi P. Naoumova,
- and Carol C. Shoulders
Genome Res. June 2012 22: 1144-1153; Published in Advance March 7, 2012, doi:10.1101/gr.126037.111
...intermediary substrates that sponsored inversion formation. In five data sets, mRNA levels of disease-associated genes were robustly associated with inversion genotype. Moreover, a haplotype associated with systemic lupus erythematosus was restricted to the derived inversion state. We conclude that the 8p23...
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Research: Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes
- Jeremy R.B. Newman,
- Ana Conesa,
- Matthew Mika,
- Felicia N. New,
- Suna Onengut-Gumuscu,
- Mark A. Atkinson,
- Stephen S. Rich,
- Lauren M. McIntyre,
- and Patrick Concannon
Genome Res. November 2017 27: 1807-1815; Published in Advance October 12, 2017, doi:10.1101/gr.217984.116
...-specific recognition of the 3′ splice site of INS intron 1. Hum Genet 128: 383–400. Kralovicova J, Gaunt TR, Rodriguez S, Wood PJ, Day INM, Vorechovsky I. 2006. Variants in the human insulin gene that affect pre-mRNA splicing: Is −23HphI a functional single nucleotide polymorphism at IDDM2? Diabetes 55: 260...

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