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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
...regulating a gene), with transcription factors being most robust to cis-acting, but most influenced by trans-acting, variation.The development of a multicellular organism requires tight regulation of gene expression in both space and time to ensure that reproducible phenotypes are obtained across individuals...
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Letter: Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences
- Elmar Schilling,
- Carol El Chartouni,
- and Michael Rehli
Genome Res. November 2009 19: 2028-2035; Published in Advance August 17, 2009, doi:10.1101/gr.095562.109
...disease- and age-related) processes in mammals. In essence, our results imply that the majority of DNA sequences (at nonimprinted loci) carry intrinsic information that recruits cis-acting factors and determines its DNA methylation status during mammalian development. Methods A full description of all...
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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
...K4me3 and gene expression is more408 complex that simple activation.409 The merging of DO expression quantitative trait loci with inbred chromatin state maps offers a410 potential method to identify cis-regulatory regions. The Pkd2 example illustrates how this could be411 done. Given...
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Research: Gene regulation underlies environmental adaptation in house mice
- Katya L. Mack,
- Mallory A. Ballinger,
- Megan Phifer-Rixey,
- and Michael W. Nachman
Genome Res. November 2018 28: 1636-1645; Published in Advance September 7, 2018, doi:10.1101/gr.238998.118
...performed expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses to study the genetic architecture of regulatory variation in wild house mice (Mus musculus domesticus) using individuals from five populations collected along a latitudinal cline in eastern North America...
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Research: Gene regulation and speciation in house mice
- Katya L. Mack,
- Polly Campbell,
- and Michael W. Nachman
Genome Res. April 2016 26: 451-461; Published in Advance February 1, 2016, doi:10.1101/gr.195743.115
...in gene regulation might be important in reproductive isolation. More recently, Turner et al. (2014) mapped sterility quantitative trait loci (QTL) and expression QTL (eQTL) in an F2 cross using different strains of M. m. musculus and M. m. domesticus. They identified a Corresponding author: katyamack...
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PERSPECTIVE: Genomics of the future: Identification of quantitative trait loci in the mouse
- Lorraine Flaherty,
- Bruce Herron,
- and Derek Symula
Genome Res. December 2005 15: 1741-1745; doi:10.1101/gr.3841405
....C., and Lander, E.S. 1992 . A genetic map of the mouse suitable for typing intraspecific crosses. Genetics 131 : 423 -447. ↵ Doss, S., Schadt, E.E., Drake, T.A., and Lusis, A.J. 2005 . Cis -acting expression quantitative trait loci in mice. Genome Res. 15 : 681 -691. ↵ Ewart, S.L., Kuperman, D., Schadt, E...
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Resource: Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
- Elizabeth G. King,
- Chris M. Merkes,
- Casey L. McNeil,
- Steven R. Hoofer,
- Saunak Sen,
- Karl W. Broman,
- Anthony D. Long,
- and Stuart J. Macdonald
Genome Res. August 2012 22: 1558-1566; Published in Advance April 10, 2012, doi:10.1101/gr.134031.111
...to allelic variation at the Adh locus, and additionally identify several previously unknown modest-effect trans-acting QTL (quantitative trait loci). Using a unique property of multiparental linkage mapping designs, for each QTL we highlight a relatively small set of candidate causative variants for follow...
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LETTER: Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice
- Guangming He,
- Xiaojin Luo,
- Feng Tian,
- Kegui Li,
- Zuofeng Zhu,
- Wei Su,
- Xiaoyin Qian,
- Yongcai Fu,
- Xiangkun Wang,
- Chuanqing Sun,
- and Jinshui Yang
Genome Res. May 2006 16: 618-626; Published in Advance April 10, 2006, doi:10.1101/gr.4814006
...techniques, it is important to identify the genetic component of important agronomic traits, which often take the form of quantitative phenotypes. The genetic variation underlying quantitative phenotypes results from the segregation of numerous quantitative trait loci (QTLs), each responsible for a portion...
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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...-coding SHROOM3 variants and CFM-associated expression quantitative trait loci (eQTLs) of SHROOM3 expression. Further investigations implicate specific eQTL combinations, such as rs1001322 or rs344131, in combination with other significant CFM-associated eQTLs, which we term combined eQTL phenotype modifiers (Ce...
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Resource: A high-resolution association mapping panel for the dissection of complex traits in mice
- Brian J. Bennett,
- Charles R. Farber,
- Luz Orozco,
- Hyun Min Kang,
- Anatole Ghazalpour,
- Nathan Siemers,
- Michael Neubauer,
- Isaac Neuhaus,
- Roumyana Yordanova,
- Bo Guan,
- Amy Truong,
- Wen-pin Yang,
- Aiqing He,
- Paul Kayne,
- Peter Gargalovic,
- Todd Kirchgessner,
- Calvin Pan,
- Lawrence W. Castellani,
- Emrah Kostem,
- Nicholas Furlotte,
- Thomas A. Drake,
- Eleazar Eskin,
- and Aldons J. Lusis
Genome Res. February 2010 20: 281-290; Published in Advance January 6, 2010, doi:10.1101/gr.099234.109
..., Schadt EE, Drake TA, Lusis AJ. 2005. Cis-acting expression quantitative trait loci in mice. Genome Res 15: 681–691. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A,Walters GB, Gunnarsdottir S, et al. 2008. Genetics of gene expression and its effect on disease...

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