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Research: Impact of the X Chromosome and sex on regulatory variation
- Kimberly R. Kukurba,
- Princy Parsana,
- Brunilda Balliu,
- Kevin S. Smith,
- Zachary Zappala,
- David A. Knowles,
- Marie-Julie Favé,
- Joe R. Davis,
- Xin Li,
- Xiaowei Zhu,
- James B. Potash,
- Myrna M. Weissman,
- Jianxin Shi,
- Anshul Kundaje,
- Douglas F. Levinson,
- Philip Awadalla,
- Sara Mostafavi,
- Alexis Battle,
- and Stephen B. Montgomery
Genome Res. June 2016 26: 768-777; Published in Advance April 21, 2016, doi:10.1101/gr.197897.115
.... As sex-specific regulatory variants discovered in our study can inform sex differences in heritable disease prevalence, we integrated our data with -wide association study data for multiple immune traits identifying several traits with significant sex biases in genetic susceptibilities. Together, our...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...; Finucane et al. 2015; Gaulton et al. 2015; Quang et al. 2015; Varshney et al. 2017, 2021; Mahajan et al. 2018; Thurner et al. 2018; Rai et al. 2020), and variants associated with autoimmune disorders are enriched in immune cell–specific regulatory elements (Finucane et al. 2015). Variant enrichment in cell...
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Research: Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
- Olivia Corradin,
- Alina Saiakhova,
- Batool Akhtar-Zaidi,
- Lois Myeroff,
- Joseph Willis,
- Richard Cowper-Sal·lari,
- Mathieu Lupien,
- Sanford Markowitz,
- and Peter C. Scacheri
Genome Res. January 2014 24: 1-13; Published in Advance November 6, 2013, doi:10.1101/gr.164079.113
...regulation. As an example, we highlight rs2301436, a Crohn’s disease-associated locus on chromosome 6. This locus has three enhancer elements that share the motif for ELF1, a member of the ETS transcription factor family associated with autoimmune function (Gallant and Gilkeson 2006). Variants contained...
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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
...architecture of complex disease (Tyler et al., 2017), to37 identify genetic modifiers of Mendelian disease (Takemon et al., 2021), and to study the effects of38 genetic variation on susceptibility to infectious disease (Kurtz et al., 2020). These models have39 the potential to uncover mechanistic insights...
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Research: Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
- Timothy E. Reddy,
- Jason Gertz,
- Florencia Pauli,
- Katerina S. Kucera,
- Katherine E. Varley,
- Kimberly M. Newberry,
- Georgi K. Marinov,
- Ali Mortazavi,
- Brian A. Williams,
- Lingyun Song,
- Gregory E. Crawford,
- Barbara Wold,
- Huntington F. Willard,
- and Richard M. Myers
Genome Res. May 2012 22: 860-869; Published in Advance February 2, 2012, doi:10.1101/gr.131201.111
...into autoimmune disease The majority of genomic variants associated with disease using -wide association studies (GWAS) are intergenic and have unclear regulatory consequences. TF binding sites may give functional insights into the variants identified. Using our observations of TF binding and differential allelic...
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Perspective: Genetic architecture of quantitative traits in mice, flies, and humans
- Jonathan Flint and
- Trudy F.C. Mackay
Genome Res. May 2009 19: 723-733; doi:10.1101/gr.086660.108
...to susceptibility to three autoimmune disorders: psoriasis, Crohn’s disease, and ankylosing spondylitis (Duerr et al. 2006; Burton et al. 2007; Cargill et al. 2007), and a SNP within the intron of CDKAL1 has been associated with type 2 diabetes (T2D) and insulin secretion defects (Gudmundsson et al. 2007; Scott et...
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PERSPECTIVE: The mouse genome
- Jean Louis Guénet
Genome Res. December 2005 15: 1729-1740; doi:10.1101/gr.3728305
...will then have another way to understand the forces that shape the s. Comparing specific CNSs in a wider panel of species (rat, dog, pig, cattle, Maccaca monkeys, chimpanzee), and matching the results with tissue-specific transcriptomes, will be especially helpful for understanding gene regulation. The design...

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