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Research: Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
- Swann Floc'hlay,
- Emily S. Wong,
- Bingqing Zhao,
- Rebecca R. Viales,
- Morgane Thomas-Chollier,
- Denis Thieffry,
- David A. Garfield,
- and Eileen E.M. Furlong
Genome Res. February 2021 31: 211-224; Published in Advance December 11, 2020, doi:10.1101/gr.266338.120
...).Taken together, these features show both the quality and richness of the data and their usefulness to further annotate the regulatory landscape of the Drosophila at these important stages of embryogenesis.Allele-specific variation is common across genotypes and regulatory layersTo quantify the impact of cis-acting...
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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
...the complementary nature of multilayer regulatory features in capturing phenotypic variation in complex traits. Among all features contributing to the integrated model, GRIN3A expression, as well as the 3′ end usage of COL17A1 in the shell gland, exhibited the highest importance scores (Fig. 2D). These two genes...
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Method: Highly accurate quantification of allelic gene expression for population and disease genetics
- Anna Saukkonen,
- Helena Kilpinen,
- and Alan Hodgkinson
Genome Res. August 2022 32: 1565-1572; Published in Advance July 6, 2022, doi:10.1101/gr.276296.121
...of cis-acting genetic variation using allelic fold change. Genome Res 27: 1872–1884. doi:10.1101/gr.216747.116 ↵Mohammadi P, Castel SE, Cummings BB, Einson J, Sousa C, Hoffman P, Donkervoort S, Jiang Z, Mohassel P, Foley AR, et al. 2019. Genetic regulatory variation in populations informs transcriptome...
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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
...expression regulation. We illustrate how DO gene expression can be27 aligned with inbred epigenetic states to identify putative cis-regulatory regions. Finally, we provide28 a data resource that documents strain-specific variation in chromatin state and DNA methylation29 in hepatocytes across nine widely...
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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
...and Innovation Centre, Scotland's Rural College, Barony Campus, Dumfries DG1 3NE, UK Corresponding author: michel.georges@uliege.beAbstractWe report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using...
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Research: Independent evolution of transcript abundance and gene regulatory dynamics
- Gat Krieger,
- Offir Lupo,
- Avraham A. Levy,
- and Naama Barkai
Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
..., the two alleles would show higher similarity than between the parents, as only cis-acting effects can lead to variation in this uniform trans environment. This was indeed the case: regulatory similarity scores between the hybrid alleles are typically higher than the regulatory similarities between species...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
..., structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis-regulatory...
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Research: Pathogenicity and selective constraint on variation near splice sites
- Jenny Lord,
- Giuseppe Gallone,
- Patrick J. Short,
- Jeremy F. McRae,
- Holly Ironfield,
- Elizabeth H. Wynn,
- Sebastian S. Gerety,
- Liu He,
- Bronwyn Kerr,
- Diana S. Johnson,
- Emma McCann,
- Esther Kinning,
- Frances Flinter,
- I. Karen Temple,
- Jill Clayton-Smith,
- Meriel McEntagart,
- Sally Ann Lynch,
- Shelagh Joss,
- Sofia Douzgou,
- Tabib Dabir,
- Virginia Clowes,
- Vivienne P.M. McConnell,
- Wayne Lam,
- Caroline F. Wright,
- David R. FitzPatrick,
- Helen V. Firth,
- Jeffrey C. Barrett,
- Matthew E. Hurles,
- and on behalf of the Deciphering Developmental Disorders study
Genome Res. February 2019 29: 159-170; Published in Advance December 26, 2018, doi:10.1101/gr.238444.118
...small nuclear RNAs (snRNA), along with more than 100 protein components and accessory molecules (Brody and Abelson 1985; Hang et al. 2015; Scotti and Swanson 2016). Accurate recruitment and function of the spliceosome is reliant on a plethora of cis-acting regulatory elements encoded within the pre...
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Research: Genetic architecture of regulatory variation in Arabidopsis thaliana
- Xu Zhang,
- Andrew J. Cal,
- and Justin O. Borevitz
Genome Res. May 2011 21: 725-733; Published in Advance April 5, 2011, doi:10.1101/gr.115337.110
...expression variation and suggest that polygenic control is common. Cis-acting polymorphisms are located in gene regulatory elements that affect the transcript abundance of the linked allele of the target gene. Transacting polymorphisms are located elsewhere in the and affect the transcript abundance of both...
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Research: Genetic variation in radiation-induced cell death
- Denis A. Smirnov,
- Lauren Brady,
- Krzysztof Halasa,
- Michael Morley,
- Sonia Solomon,
- and Vivian G. Cheung
Genome Res. February 2012 22: 332-339; Published in Advance August 15, 2011, doi:10.1101/gr.122044.111
.... 2010; Noon et al. 2010). In this study, we focused on radiation-induced cell death. We measured changes in gene expression and quantified cell death in irradiated B cells from 99 normal individuals and found extensive individual variation in these measurements. We took advantage of this variation...

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