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Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
- Guanjue Xiang,
- Xi He,
- Belinda M. Giardine,
- Kathryn J. Isaac,
- Dylan J. Taylor,
- Rajiv C. McCoy,
- Camden Jansen,
- Cheryl A. Keller,
- Alexander Q. Wixom,
- April Cockburn,
- Amber Miller,
- Qian Qi,
- Yanghua He,
- Yichao Li,
- Jens Lichtenberg,
- Elisabeth F. Heuston,
- Stacie M. Anderson,
- Jing Luan,
- Marit W. Vermunt,
- Feng Yue,
- Michael E.G. Sauria,
- Michael C. Schatz,
- James Taylor,
- Berthold Göttgens,
- Jim R. Hughes,
- Douglas R. Higgs,
- Mitchell J. Weiss,
- Yong Cheng,
- Gerd A. Blobel,
- David M. Bodine,
- Yu Zhang,
- Qunhua Li,
- Shaun Mahony,
- and Ross C. Hardison
Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
...in the more mature erythroblasts (Fig. 2C,D, region boxed and labeled E). A similar pattern was obtained in both human and mouse. Those genomic intervals assigned to the enhancer- or promoter-like states contain candidates for regulatory elements, an inference that was supported by chromatin binding data...
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Research: Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma
- Gonzalo Lopez,
- Karina L. Conkrite,
- Miriam Doepner,
- Komal S. Rathi,
- Apexa Modi,
- Zalman Vaksman,
- Lance M. Farra,
- Eric Hyson,
- Moataz Noureddine,
- Jun S. Wei,
- Malcolm A. Smith,
- Shahab Asgharzadeh,
- Robert C. Seeger,
- Javed Khan,
- Jaime Guidry Auvil,
- Daniela S. Gerhard,
- John M. Maris,
- and Sharon J. Diskin
Genome Res. September 2020 30: 1228-1242; Published in Advance August 13, 2020, doi:10.1101/gr.252106.119
...of the functional relevance of SVs, we performed an expression quantitative trait loci (eQTL) analysis for each of the recurrent SV-associated genes (Supplemental Fig. S19A). The analysis, which was replicated in the two available transcriptional data sets (RNA-seq and HuEx array), reported consistent up...
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Resource: Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis
- Leslie O. Goodwin,
- Erik Splinter,
- Tiffany L. Davis,
- Rachel Urban,
- Hao He,
- Robert E. Braun,
- Elissa J. Chesler,
- Vivek Kumar,
- Max van Min,
- Juliet Ndukum,
- Vivek M. Philip,
- Laura G. Reinholdt,
- Karen Svenson,
- Jacqueline K. White,
- Michael Sasner,
- Cathleen Lutz,
- and Stephen A. Murray
Genome Res. March 2019 29: 494-505; Published in Advance January 18, 2019, doi:10.1101/gr.233866.117
....3%) lines, highlighting the challenge of identification of integration sites despite widespread acknowledgment that such information is useful and important. Low resolution mapping of transgenes can be achieved through FISH or linkage mapping, but these approaches offer little information about potential...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...out detailed surveys on individual dogs, thereby facilitating investigation of complex traits and gene-by-environment interactions.A role for rare variation in canine genomicsTo date, canine genomic research has prioritized analysis of common over rare variations in studies of trait mapping, as breed...
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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
...nos. FJ751937–FJ752004]. Epigenetic processes are fundamental to the differentiation and development of multicellular organisms by controlling chromatin accessibility and transcription (Bird 2002). Although phenotypic variation is mainly driven by genetic traits, there is also evidence that epigenetic...
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Research: Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells
- Luciano Pirola,
- Aneta Balcerczyk,
- Richard W. Tothill,
- Izhak Haviv,
- Antony Kaspi,
- Sebastian Lunke,
- Mark Ziemann,
- Tom Karagiannis,
- Stephen Tonna,
- Adam Kowalczyk,
- Bryan Beresford-Smith,
- Geoff Macintyre,
- Ma Kelong,
- Zhang Hongyu,
- Jingde Zhu,
- and Assam El-Osta
Genome Res. October 2011 21: 1601-1615; Published in Advance September 2, 2011, doi:10.1101/gr.116095.110
...loci, yet elevated glucose levels are thought to regulate -wide changes, and this still remains poorly understood. In this article we describe -wide histone H3K9/K14 hyperacetylation and DNA methylation maps conferred by hyperglycemia in primary human vascular cells. Chromatin immunoprecipitation (Ch...
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Resource: PRISM offers a comprehensive genomic approach to transcription factor function prediction
- Aaron M. Wenger,
- Shoa L. Clarke,
- Harendra Guturu,
- Jenny Chen,
- Bruce T. Schaar,
- Cory Y. McLean,
- and Gill Bejerano
Genome Res. May 2013 23: 889-904; Published in Advance February 4, 2013, doi:10.1101/gr.139071.112
...factors, their target genes in different biological contexts, and the regulatory elements such as promoters and enhancers through which they exert their effect (Michelson 2002). The recent coupling of chromatin immunoprecipitation with deep sequencing (ChIP-seq) is allowing unprecedented andmostly...
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