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ARTICLE: Identification of mouse Duffy Antigen Receptor for Chemokines (Darc) as a BMD QTL gene
- Bouchra Edderkaoui,
- David J. Baylink,
- Wesley G. Beamer,
- Jon E. Wergedal,
- Ryan Porte,
- Asok Chaudhuri,
- and Subburaman Mohan
Genome Res. May 2007 17: 577-585; Published in Advance April 6, 2007, doi:10.1101/gr.6009507
...) QTL that was detected from a cross involving high BMD CAST/EiJ (CAST) and low BMD C57BL/6J (B6) mice. To this end, we have combined several approaches including: (1) fine mapping the BMD QTL in Chr 1 of the B6.CAST F 2 female mice using a large number of polymorphic markers; (2) the generation...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...-TRs in GTEx v8 data, consisting of WGS of 838 donors and RNA-seq of 15,253 samples from 49 tissues, by using FastQTL (Fig. 1; Supplemental Table S1; Ongen et al. 2016; The GTEx Consortium 2020). TRs were sized using GangSTR, which handles TRs with motifs of up to 20 bp (n = 40,598 after quality control...
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Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
- Benjamin P. Barré,
- Johan Hallin,
- Jia-Xing Yue,
- Karl Persson,
- Ekaterina Mikhalev,
- Agurtzane Irizar,
- Sylvester Holt,
- Dawn Thompson,
- Mikael Molin,
- Jonas Warringer,
- and Gianni Liti
Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
....liti@unice.frAbstractAging varies among individuals due to both genetics and environment, but the underlying molecular mechanisms remain largely unknown. Using a highly recombined Saccharomyces cerevisiae population, we found 30 distinct quantitative trait loci (QTLs) that control chronological life span (CLS) in calorie...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...(Mannion et al. 2014) rescues the embryonic lethality of Adar mutant mice (Hartner et al. 2004, 2009; Wang et al. 2004), the absence of ADAR editing activity (Liddicoat et al. 2015; Pestal et al. 2015) was shown to activate the upstream cytosolic dsRNA sensor IFIH1 (also known as MDA5), subsequently...
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Research: AP-1 subunits converge promiscuously at enhancers to potentiate transcription
- Jungkyun Seo,
- D. Dewran Koçak,
- Luke C. Bartelt,
- Courtney A. Williams,
- Alejandro Barrera,
- Charles A. Gersbach,
- and Timothy E. Reddy
Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
..., guides for each Cas nuclease were tested individually for their ability to mediate precise editing. We intentionally used polyclonal tagged lines to avoid clone-specific effects that could confound our analysis (Ben-David et al. 2018).View larger version: In this window In a new window Figure 1...
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Research: Shroom3 contributes to the maintenance of the glomerular filtration barrier integrity
- Nan Cher Yeo,
- Caitlin C. O’Meara,
- Jason A. Bonomo,
- Kerry N. Veth,
- Ritu Tomar,
- Michael J. Flister,
- Iain A. Drummond,
- Donald W. Bowden,
- Barry I. Freedman,
- Jozef Lazar,
- Brian A. Link,
- and Howard J. Jacob
Genome Res. January 2015 25: 57-65; Published in Advance October 1, 2014, doi:10.1101/gr.182881.114
...candidate gene. Transferring a 6.1-Mb region containing the wild-type Shroom3 gene significantly improved the kidney glomerular function in FHH (fawn-hooded hypertensive) rat. The wild-type Shroom3 allele, but not the FHH Shroom3 allele, rescued glomerular defects induced by knockdown of endogenous shroom3...
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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
...-372. ↵ Georges, M. 1997 . QTL mapping to QTL cloning: Mice to the rescue. Genome Res. 7 : 663 -665. ↵ Haldi, M., Perrot, V., Saumier, M., Desai, T., Cohen, D., Cherif, D., Ward, D., and Lander, E.S. 1994 . Large human YACs constructed in a rad52 strain show a reduced rate of chimerism. Genomics 24...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...recovered the 13.6-Mb D. melanogaster-specific 3R inversion (In(3R)84F1; 93F6–7; 3R:8,049,180–21,735,108) that was initially characterized cytologically (Sturtevant and Plunkett 1926) and confirmed by breakpoint cloning (Fig. 2; Ranz et al. 2007). Among nine inversions shared in all sim-complex species...
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Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- Santosh S. Atanur,
- İnanç Birol,
- Victor Guryev,
- Martin Hirst,
- Oliver Hummel,
- Catherine Morrissey,
- Jacques Behmoaras,
- Xose M. Fernandez-Suarez,
- Michelle D. Johnson,
- William M. McLaren,
- Giannino Patone,
- Enrico Petretto,
- Charles Plessy,
- Kathleen S. Rockland,
- Charles Rockland,
- Kathrin Saar,
- Yongjun Zhao,
- Piero Carninci,
- Paul Flicek,
- Ted Kurtz,
- Edwin Cuppen,
- Michal Pravenec,
- Norbert Hubner,
- Steven J.M. Jones,
- Ewan Birney,
- and Timothy J. Aitman
Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
.... Abstract The spontaneously hypertensive rat (SHR) is the most widely studied animal model of hypertension. Scores of SHR quantitative loci (QTLs) have been mapped for hypertension and other phenotypes. We have sequenced the SHR/OlaIpcv genome at 10.7-fold coverage by paired-end sequencing on the Illumina...
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PERSPECTIVE: Impact of genomics on research in the rat
- Jozef Lazar,
- Carol Moreno,
- Howard J. Jacob,
- and Anne E. Kwitek
Genome Res. December 2005 15: 1717-1728; doi:10.1101/gr.3744005
...disease gene discovery. Genetic mapping and positional cloning QTL mapping Quantitative trait locus (QTL) mapping is a proven useful resource to assign the biology of the rat onto the genomic sequence by identifying chromosomal regions that contain genes affecting complex phenotypes. While a QTL...

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