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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
...regulatory effects of multiple enhancers for a given gene) for each promoter using a unified set of PEIs from all haplotypes of a given tissue (see Supplemental Methods; Li et al. 2022; Zhi et al. 2022). As expected, genes with a larger RPS had higher expression within haplotypes (Supplemental Fig. S14H...
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Method: Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
- Prashant S. Emani,
- Maya N. Geradi,
- Gamze Gürsoy,
- Monica R. Grasty,
- Andrew Miranker,
- and Mark B. Gerstein
Genome Res. December 2023 33: 2156-2173; Published in Advance December 14, 2023, doi:10.1101/gr.278322.123
...sequence-based variant discovery (Gürsoy et al. 2020), and inference using gene expression values and associated loci (Harmanci and Gerstein 2016). The ubiquity of large-scale omics projects make this source of variants especially concerning (Gürsoy et al. 2020). Several studies have showed identification...
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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
...previously introduced ANEVA, a method for assessing the gene expression distribution based on allelic expression (AE) of heterozygotic SNPs or eQTLs (Mohammadi et al. 2019). Recently, we have further extended this principle to use allelic expression over entire haplotypes (ANEVA-h), improving robustness...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...are more likely to overlap binding sites of multiple TFs, suggesting that they may be crucial regulatory focal points at coordinated caQTL signals.Identifying target genes for caPeaksWe used four approaches to link caPeaks to putative target genes (Fig. 3A; Supplemental Tables 9, 14–17): proximity...
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Research: Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes
- Alexandra J. Scott,
- Colby Chiang,
- and Ira M. Hall
Genome Res. December 2021 31: 2249-2257; Published in Advance September 20, 2021, doi:10.1101/gr.275488.121
...to predict from current annotations. Both common and rare SVs often affect the expression of multiple genes: SV-eQTLs affect an average of 1.82 nearby genes, whereas SNV- and indel-eQTLs affect an average of 1.09 genes, and 21.34% of rare expression-altering SVs show effects on two to nine different genes...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
.... S8). Considering that previous expression quantitative trait loci studies showed that gene expression is both cis- and trans-regulated (Lu et al. 2018, 2020a) whereas most known gene regulators from eQTL analyses are cis-regulators (Lu et al. 2018), the clustered dysregulation pattern suggests...
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Research: Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease
- Stephanie Y. Yang,
- Christina A. Castellani,
- Ryan J. Longchamps,
- Vamsee K. Pillalamarri,
- Brian O'Rourke,
- Eliseo Guallar,
- and Dan E. Arking
Genome Res. March 2021 31: 349-358; Published in Advance January 13, 2021, doi:10.1101/gr.269381.120
...sets obtained from the Molecular Signatures Database (MSigDB) (Ashburner et al. 2000; Xie et al. 2005; Liberzon et al. 2011; Meng et al. 2019; The Gene Ontology Consortium 2019). Previous studies have shown that cross-mappability can lead to false pseudogene positives in eQTL association studies (Saha...
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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
...and females, and in response to dietary fat. We also found 45 genes with inconsistent ASE biases that switched direction across tissues and/or environments. Finally, we integrated ASE and QTL data from published intercrosses of the LG/J and SM/J strains. Our ASE genes are often enriched in QTLs for metabolic...
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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 previously predicted functional elements. As an example, we investigated the gene Pkd2301 (Fig. 8). This gene had a strong local eQTL (LOD = 144.8) that had been previously identified302 (Gatti et al., 2017; Chick et al., 2016), and large amounts of variance explained (R2 = 0.6) by both303 chromatin state...
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Research: The motif composition of variable number tandem repeats impacts gene expression
- Tsung-Yu Lu,
- Paulina N. Smaruj,
- Geoffrey Fudenberg,
- Nicholas Mancuso,
- and Mark J.P. Chaisson
Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
...[https://www.ncbi.nlm.nih.gov/bioproject/] accession number PRJEB36890) (Byrska-Bishop et al. 2022).Maternal and paternal haplotypes were referred to as h0 and h1 in the text for brevity.WGS samples (n = 879), gene expression matrices of 49 tissues, and covariates for eQTL mapping of GTEx s were...
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