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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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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...cis-regulatory elements. Here, CTCF binds in tandem with beta-catenin and TCF/LEF to increase cohesin stalling and induce the formation of chromatin loops that contribute to the upregulation of a subset of Wnt target genes (Fig. 7). This, to our knowledge, represents a previously unknown mechanism...
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Method: Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
- J. Omar Yáñez-Cuna,
- Huy Q. Dinh,
- Evgeny Z. Kvon,
- Daria Shlyueva,
- and Alexander Stark
Genome Res. October 2012 22: 2018-2030; Published in Advance April 25, 2012, doi:10.1101/gr.132811.111
...predict context-specific binding and that the predictions work across different Drosophila species suggests that characteristic motif combinations are shared between sites, revealing context-specific motif codes ( cis -regulatory signatures), which appear to be conserved during evolution. Taken together...
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LETTER: Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
- David C. King,
- James Taylor,
- Laura Elnitski,
- Francesca Chiaromonte,
- Webb Miller,
- and Ross C. Hardison
Genome Res. August 2005 15: 1051-1060; Published in Advance July 15, 2005, doi:10.1101/gr.3642605
...Evaluation of regulatory potential and conservation scores for detecting cis -regulatory modules in aligned mammalian genome sequences David C. King 1 , 2 , James Taylor 1 , 3 , Laura Elnitski 1 , 2 , 6 , Francesca Chiaromonte 1 , 4...
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LETTER: Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
- David C. King,
- James Taylor,
- Ying Zhang,
- Yong Cheng,
- Heather A. Lawson,
- Joel Martin,
- ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis,
- Francesca Chiaromonte,
- Webb Miller,
- and Ross C. Hardison
Genome Res. June 2007 17: 775-786; doi:10.1101/gr.5592107
...as a predictor of cis -regulatory modules (CRMs) ( Gumucio et al. 1996 ; Frazer et al. 2003 ). Notable success has been achieved with this approach (e.g., Elnitski et al. 1997 ; Loots et al. 2000 ; Nobrega et al. 2003 ). The underlying assumption is that orthologous DNA sequences serving a function common...
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Research: Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- Weisheng Wu,
- Yong Cheng,
- Cheryl A. Keller,
- Jason Ernst,
- Swathi Ashok Kumar,
- Tejaswini Mishra,
- Christapher Morrissey,
- Christine M. Dorman,
- Kuan-Bei Chen,
- Daniela Drautz,
- Belinda Giardine,
- Yoichiro Shibata,
- Lingyun Song,
- Max Pimkin,
- Gregory E. Crawford,
- Terrence S. Furey,
- Manolis Kellis,
- Webb Miller,
- James Taylor,
- Stephan C. Schuster,
- Yu Zhang,
- Francesca Chiaromonte,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. October 2011 21: 1659-1671; Published in Advance July 27, 2011, doi:10.1101/gr.125088.111
...by the actions of transcription factors that bind to specific DNA sequences in cis-regulatory modules (CRMs), such as promoters and enhancers. Chromatin containing active CRMs is in an open or accessible configuration, leading to DNase hypersensitivity (Gross and Garrard 1988). Active modules are associated...
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METHODS: Detection and Visualization of Compositionally Similar cis-Regulatory Element Clusters in Orthologous and Coordinately Controlled Genes
- Anil G. Jegga,
- Shawn P. Sherwood,
- James W. Carman,
- Andrew T. Pinski,
- Jerry L. Phillips,
- John P. Pestian,
- and Bruce J. Aronow
Genome Res. September 1, 2002 12: 1408-1417; doi:10.1101/gr.255002
...in the context of higher-order chromatin structure. Computationally, however, we have little ability to identify cis -regulatory regions from primary sequence and even less ability to predict cellular compartments into which expression is specified. Improved ability to do so will advance our understanding...
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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
...in KLF1 ChIP-seq peak regions (Fig. 1C) and the preferential orientations of CACC and GATAmotifs, we suggest that SCL is likely to be one factor at the center of the KLF1GATA1 erythroid complex in a small subset of erythroid cis-regulatory modules (Fig. 5C). Transcription factor partners for KLF1 Our...
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Research: Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
- Pouya Kheradpour,
- Jason Ernst,
- Alexandre Melnikov,
- Peter Rogov,
- Li Wang,
- Xiaolan Zhang,
- Jessica Alston,
- Tarjei S. Mikkelsen,
- and Manolis Kellis
Genome Res. May 2013 23: 800-811; Published in Advance March 19, 2013, doi:10.1101/gr.144899.112
...a general strategy for deciphering cis -regulatory elements by systematic large-scale manipulation and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to develop predictive models of gene expression. Footnotes ↵ 6 Corresponding author E...
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Article: Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- Yong Cheng,
- Weisheng Wu,
- Swathi Ashok Kumar,
- Duonan Yu,
- Wulan Deng,
- Tamara Tripic,
- David C. King,
- Kuan-Bei Chen,
- Ying Zhang,
- Daniela Drautz,
- Belinda Giardine,
- Stephan C. Schuster,
- Webb Miller,
- Francesca Chiaromonte,
- Yu Zhang,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2009 19: 2172-2184; Published in Advance November 3, 2009, doi:10.1101/gr.098921.109
..., Pennsylvania 16802, USA Abstract The transcription factor GATA1 regulates an extensive program of gene activation and repression during erythroid development. However, the associated mechanisms, including the contributions of distal versus proximal cis -regulatory modules, co-occupancy with other...
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