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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
...Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epis Guanjue Xiang1,2,3, Xi He1, Belinda M. Giardine4, Kathryn J. Isaac5, Dylan J. Taylor5, Rajiv C. McCoy5, Camden Jansen4, Cheryl A. Keller4, Alexander Q. Wixom4, April...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...of fin regeneration through stage-specific gene regulatory network constructionTo elucidate how cis-regulatory elements orchestrate gene expression changes in major cell types, we integrated peak-to-gene links, TF motif footprint signals, gene expression correlation, and motif activity–TF expression...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...Yuning Zhang1,2, Tiffany D. Ho1,3, Nicolas E. Buchler4 and Raluca Gordân1,3,5 1Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; 2Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; 3Department...
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Research: Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
- Yaqiang Cao,
- Guoyu Chen,
- Gang Wu,
- Xiaoli Zhang,
- Joseph McDermott,
- Xingwei Chen,
- Chi Xu,
- Quanlong Jiang,
- Zhaoxiong Chen,
- Yingying Zeng,
- Daosheng Ai,
- Yi Huang,
- and Jing-Dong J. Han
Genome Res. January 2019 29: 40-52; Published in Advance November 19, 2018, doi:10.1101/gr.235747.118
...equally to this work. Corresponding author: jdhan@picb.ac.cnAbstractA few families of transposable elements (TEs) have been shown to evolve into cis-regulatory elements (CREs). Here, to extend these studies to all classes of TEs in the human , we identified widespread enhancer-like repeats (ELRs) and find...
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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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RESOURCE: CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting
- Eugene Berezikov,
- Victor Guryev,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. January 2004 14: 170-178; Published in Advance December 12, 2003, doi:10.1101/gr.1642804
.... 2002 . Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12 : 739 -748. ↵ Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K.D., Ovcharenko, I., Pachter, L., and Rubin, E.M. 2003 . Phylogenetic shadowing of primate sequences to find functional...
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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
...conservation, to identify regions most likely to be functional. To evaluate a strategy for phylogenetic footprinting using four other Caenorhabditis species, we dissected the cis -regulatory structure of a Hox cluster in the nematode Caenorhabditis elegans ( Fig. 1A ). View larger version: In this window...
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Method: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
- Alan P. Boyle,
- Lingyun Song,
- Bum-Kyu Lee,
- Darin London,
- Damian Keefe,
- Ewan Birney,
- Vishwanath R. Iyer,
- Gregory E. Crawford,
- and Terrence S. Furey
Genome Res. March 2011 21: 456-464; Published in Advance November 24, 2010, doi:10.1101/gr.112656.110
...delineate hundreds of thousands of base-pair resolution in vivo footprints in human cells that precisely mark individual transcription factor–DNA interactions. These annotations provide a unique resource for the investigation of cis -regulatory elements. We find that footprints for specific transcription...
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Research: Comprehensive identification and analysis of human accelerated regulatory DNA
- Rachel M. Gittelman,
- Enna Hun,
- Ferhat Ay,
- Jennifer Madeoy,
- Len Pennacchio,
- William S. Noble,
- R. David Hawkins,
- and Joshua M. Akey
Genome Res. September 2015 25: 1245-1255; Published in Advance June 23, 2015, doi:10.1101/gr.192591.115
...2008; McLean et al. 2010; Lindblad-Toh et al. 2011; Pertea et al. 2011), focuses on the discovery of sequences that are rapidly evolving or lost on the human lineage but that are otherwise phylogenetically conserved and thus likely functional. This approach has led to the discovery of several regions...
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LETTER: Novel transcription regulatory elements in Caenorhabditis elegans muscle genes
- Debraj GuhaThakurta,
- Lawrence A. Schriefer,
- Robert H. Waterston,
- and Gary D. Stormo
Genome Res. December 2004 14: 2457-2468; doi:10.1101/gr.2961104
...that the contributions of these sites to muscle expression were nonindependent, suggesting cooperative action of the elements. Results DNA regulatory elements identified by computational DNA pattern-recognition algorithms For a training set, we chose 19 well-characterized genes known to be expressed in muscle from...

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