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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...component of mole-rat adaptations. Last, we investigated the contribution of repetitive elements to lineage-specific gene regulation in the mole-rat clade.ResultsComparative epigenomics of liver and heart regulatory activities in mole-ratsTo investigate the contribution of enhancer evolution to tissue-specific...
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Research: The human genome contains over a million autonomous exons
- Nicholas Stepankiw,
- Ally W.H. Yang,
- and Timothy R. Hughes
Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
.... Presumably as a consequence, human exons are often associated with additional sequences that promote inclusion (known as splicing enhancers) (Liu et al. 1998; Reed 2000; Côté et al. 2001; Wang et al. 2004b; Zhang et al. 2005; Ke et al. 2011; Wang et al. 2012). Exon splicing therefore depends on a variety...
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Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham,
- Riza M. Daza,
- Louis Gevirtzman,
- Darren A. Cusanovich,
- Olubusayo Bolonduro,
- William Stafford Noble,
- Jay Shendure,
- and Robert H. Waterston
Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
...of the C. elegans embryo (Packer et al. 2019) and second larval stage (L2) (Cao et al. 2017) provide a survey of the full complement of genes expressed in each major cell type, and even some cells present only once in the worm (e.g., the ASEL and ASER gustatory neurons). Now, to understand how these tissue-specific...
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Research: Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes
- Alexandra J. Scott,
- Colby Chiang,
- and Ira M. Hall
Genome Res. December 2021 31: 2249-2257; Published in Advance September 20, 2021, doi:10.1101/gr.275488.121
...the total number of eVariants, with the indicated number of associated coding or noncoding eGenes above the y- and x-axes, respectively. (E) Distribution of tissue specificity of eQTLs across tissues as evaluated by METASOFT, separated into the lowest quartile, middle two quartiles, and top quartile, for e...
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Research: KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
...category are shown in blue and orange, respectively. Upon the loss of KDM1A in mESCs, both groups of induced and repressed genes show a significant increase (P < 2.2−16, Wilcoxon signed-rank test) in mRNA levels and nascent transcription. (D) Elevated transcription of Hmga2 and its nearby enhancers in Kdm1...
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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...Discovery of high-confidence human protein-coding genes and exons by whole- PhyloCSF helps elucidate 118 GWAS loci Jonathan M. Mudge1,9, Irwin Jungreis2,3,9, Toby Hunt1, Jose Manuel Gonzalez1, James C. Wright4, Mike Kay1, Claire Davidson1, Stephen Fitzgerald5, Ruth Seal1,6, Susan Tweedie1, Liang He...
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Research: Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- Andre J. Faure,
- Dominic Schmidt,
- Stephen Watt,
- Petra C. Schwalie,
- Michael D. Wilson,
- Huiling Xu,
- Robert G. Ramsay,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. November 2012 22: 2163-2175; Published in Advance July 10, 2012, doi:10.1101/gr.136507.111
...Cohesin regulates tissue-specific expression by stabilizing highly occupied cis -regulatory modules Andre J. Faure 1 , 7 , Dominic Schmidt 2 , 3 , 7 , Stephen Watt 2 , 3 , Petra C. Schwalie 1 , Michael D. Wilson 2 , 3 , 8...
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Research: RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts
- Yang I. Li,
- Luis Sanchez-Pulido,
- Wilfried Haerty,
- and Chris P. Ponting
Genome Res. January 2015 25: 1-13; Published in Advance December 18, 2014, doi:10.1101/gr.181990.114
...proteins, which promote their inclusion in the brain, muscle, and heart. Our analyses suggest that accurate regulation of micro-exon inclusion by RBFOX proteins and PTBP1 plays an important role in the maintenance of tissue-specific protein–protein interactions.Most vertebrate pre-mRNA are divided...
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Research: Transcription factor redundancy and tissue-specific regulation: Evidence from functional and physical network connectivity
- Steven G. Kuntz,
- Brian A. Williams,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. October 2012 22: 1907-1919; Published in Advance June 22, 2012, doi:10.1101/gr.133306.111
...by binding selectively near muscle-specific targets to activate them. We tested this model by measuring the number, identity, and tissue-specificity of functional regulatory targets for each factor. Some joint regulatory targets (218) are BWM-specific and enriched for nearby HLH-1 binding. However, contrary...
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Research: Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb
- Justin Cotney,
- Jing Leng,
- Sunghee Oh,
- Laura E. DeMare,
- Steven K. Reilly,
- Mark B. Gerstein,
- and James P. Noonan
Genome Res. June 2012 22: 1069-1080; Published in Advance March 15, 2012, doi:10.1101/gr.129817.111
...Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb Justin Cotney 1 , Jing Leng 2 , Sunghee Oh 1 , 6 , Laura E. DeMare 1 , Steven K. Reilly 1 , Mark B. Gerstein 2...

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