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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...1 Functional genomics analysis of developing zebrafish and human endoderm reveals 1 highly conserved cis-regulatory modules acting during vertebrate organogenesis 2 3 Daniela M. Riley1,†, Randa Elsayed1,†, Mark D. Walsh2,†, Simaran Johal2, Ying Lin3,4, Harry 4 Walton1, Till Bretschneider5, Sascha...
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Resource: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
- Michal Pawlak,
- Katarzyna Z. Kedzierska,
- Maciej Migdal,
- Karim Abu Nahia,
- Jordan A. Ramilowski,
- Lukasz Bugajski,
- Kosuke Hashimoto,
- Aleksandra Marconi,
- Katarzyna Piwocka,
- Piero Carninci,
- and Cecilia L. Winata
Genome Res. March 2019 29: 506-519; Published in Advance February 13, 2019, doi:10.1101/gr.244491.118
.... Transcription is modulated by cis-regulatory elements in noncoding regions of the , which serve as binding sites for TFs (Shlyueva et al. 2014). Although these regulatory elements equally contribute to the molecular mechanism controlling development, there is still a lack of systematic resources...
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Method: MEDEA: analysis of transcription factor binding motifs in accessible chromatin
- Luca Mariani,
- Kathryn Weinand,
- Stephen S. Gisselbrecht,
- and Martha L. Bulyk
Genome Res. May 2020 30: 736-748; Published in Advance May 18, 2020, doi:10.1101/gr.260877.120
...indicate that the most accessible chromatin regions in a particular cell type may not accurately represent the cell-type-specific cis-regulatory information.MEDEA enhances the enrichment of TF binding motifs associated with lineage specifiersWe hypothesized that constitutively accessible regions can hinder...
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Research: Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells
- Daniel W. Hagey,
- Cécile Zaouter,
- Gaëlle Combeau,
- Monika Andersson Lendahl,
- Olov Andersson,
- Mikael Huss,
- and Jonas Muhr
Genome Res. July 2016 26: 908-917; Published in Advance May 2, 2016, doi:10.1101/gr.203513.115
...of specific gene expression in NSCs of the mouse cortex and the spinal cord.ResultsSimilar chromatin patterns in cortical and spinal cord NSCsTo address how the chromatin landscape reflects gene expression differences between subpopulations of neural precursor cells, we began by characterizing...
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Research: Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by SPI1 (PU.1)
- Jonas Ungerbäck,
- Hiroyuki Hosokawa,
- Xun Wang,
- Tobias Strid,
- Brian A. Williams,
- Mikael Sigvardsson,
- and Ellen V. Rothenberg
Genome Res. October 2018 28: 1508-1519; Published in Advance August 31, 2018, doi:10.1101/gr.231423.117
...Figure 3. Induction of PU.1 activity leads to chromatin opening, altered histone modifications, and cis-regulatory element-dependent gene activation. (A) Schematic showing approximate relationship of Scid.adh.2C2 cells to normal program of T-cell development, with experimental plan for panels D–G. (B...
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Research: A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells
- Michael R. Tallack,
- Tom Whitington,
- Wai Shan Yuen,
- Elanor N. Wainwright,
- Janelle R. Keys,
- Brooke B. Gardiner,
- Ehsan Nourbakhsh,
- Nicole Cloonan,
- Sean M. Grimmond,
- Timothy L. Bailey,
- and Andrew C. Perkins
Genome Res. August 2010 20: 1052-1063; Published in Advance May 27, 2010, doi:10.1101/gr.106575.110
...equally to this work. Abstract KLF1 regulates a diverse suite of genes to direct erythroid cell differentiation from bipotent progenitors. To determine the local cis -regulatory contexts and transcription factor networks in which KLF1 operates, we performed KLF1 ChIP-seq in the mouse. We found...
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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
...Park, Pennsylvania 16802, USA ↵† Deceased April 2, 2020. Corresponding author: rch8@psu.eduAbstractKnowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
...in the nucleus is in a multiprotein complex with the TFs GATA1 (or GATA2), LMO2, and LDB1; this complex binds to specific cis-regulatory elements in erythroid cells (Wadman et al. 1997; Anguita et al. 2004; Schuh et al. 2005; Cheng et al. 2009). In the hematopoietic precursor cell line HPC-7, which exhibits...
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LETTER: Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
- Yong Cheng,
- David C. King,
- Louis C. Dore,
- Xinmin Zhang,
- Yuepin Zhou,
- Ying Zhang,
- Christine Dorman,
- Demesew Abebe,
- Swathi A. Kumar,
- Francesca Chiaromonte,
- Webb Miller,
- Roland D. Green,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2008 18: 1896-1905; Published in Advance September 25, 2008, doi:10.1101/gr.083089.108
...chromatin immunoprecipitation as an approach unbiased by either evolutionary constraint or prior knowledge of regulatory activity to identify DNA segments within a 66-Mb region of mouse chromosome 7 that are occupied by the erythroid transcription factor GATA1. DNA segments bound by GATA1 were identified...
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Research: Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites
- Amber Hogart,
- Jens Lichtenberg,
- Subramanian S. Ajay,
- Stacie Anderson,
- NIH Intramural Sequencing Center,
- Elliott H. Margulies,
- and David M. Bodine
Genome Res. August 2012 22: 1407-1418; Published in Advance June 8, 2012, doi:10.1101/gr.132878.111
...regions upstream of and downstream from gene boundaries because we expected these flanking sequences to also contain cis regulatory elements. The remainder of the constitutes the intergenic partition. The distribution of methylation peaks in each cell-type category was compared with the relative...

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