Searching journal content for articles similar to Fiore and Cohen 26 (6): 778.

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Research: A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells
- Gurdeep Singh,
- Shanelle Mullany,
- Sakthi D. Moorthy,
- Richard Zhang,
- Tahmid Mehdi,
- Ruxiao Tian,
- Andrew G. Duncan,
- Alan M. Moses,
- and Jennifer A. Mitchell
Genome Res. April 2021 31: 564-575; Published in Advance March 12, 2021, doi:10.1101/gr.272468.120
...reveals that pluripotent stem cell enhancers contain a conserved regulatory codeTo decipher the regulatory code in pluripotent cells, we investigated regions bound by multiple transcription factors in mouse and human embryonic stem cells (ESCs) (* in Fig. 1A), as these regions are more likely to show...
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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 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...to identify and characterize HCNE CRMs acting in the endoderm throughout jawed vertebrate evolution through the integration of the resulting zebrafish data with functional genomic data from human embryonic stem cells (hESCs) that have undergone directed differentiation to represent distinct endoderm cell...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...localization, stability, and translational efficiency. To rigorously investigate mRNA isoform-specific ribosome association, we generated subcellular fractionation and sequencing (Frac-seq) libraries using both conventional short reads and long reads from human embryonic stem cells (ESCs) and neural progenitor...
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Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
- Jennifer Hammelman,
- Konstantin Krismer,
- Budhaditya Banerjee,
- David K. Gifford,
- and Richard I. Sherwood
Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
...motifs on cell type–specific accessibility between mouse embryonic stem cells and embryonic stem cell–derived definitive endoderm cells, screening 7905 distinct DNA sequences. MIAA recapitulates differential accessibility patterns of 100-nt sequences derived from natively differential genomic regions...
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Research: Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures
- Federico Comoglio,
- Hyun Jung Park,
- Stefan Schoenfelder,
- Iros Barozzi,
- Daniel Bode,
- Peter Fraser,
- and Anthony R. Green
Genome Res. March 2018 28: 295-309; Published in Advance February 2, 2018, doi:10.1101/gr.227272.117
..., Medical Research Council/Wellcome Trust Stem Cell Institute, and Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom; 2Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom; 3Lawrence Berkeley National Laboratory, Berkeley, California...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
....ICR: a multifaceted cis-regulatory regionAllelic DNA methylation at ICRs, although constitutive, orchestrates the complex spatiotemporal expression patterns of imprinted genes by modulating a combination of regulatory mechanisms. In embryonic stem (ES) cells, allelic expression is initially confined to genes in close...
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Method: Dynamic regulatory module networks for inference of cell type–specific transcriptional networks
- Alireza Fotuhi Siahpirani,
- Sara Knaack,
- Deborah Chasman,
- Morten Seirup,
- Rupa Sridharan,
- Ron Stewart,
- James Thomson,
- and Sushmita Roy
Genome Res. July 2022 32: 1367-1384; Published in Advance June 15, 2022, doi:10.1101/gr.276542.121
...and Histone + Motif features (Fig. 2B,C,E,F; blue for RMN and red for DRMN). On motifs, the difference between the models was dependent upon the cell line and the number of modules, k (Fig. 2D,G). In particular, both DRMN-Fused and DRMN-ST outperformed RMN on the induced pluripotent stem cell (iPSC)/embryonic...
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Research: Enhancers display constrained sequence flexibility and context-specific modulation of motif function
- Franziska Reiter,
- Bernardo P. de Almeida,
- and Alexander Stark
Genome Res. March 2023 33: 346-358; Published in Advance March 20, 2023, doi:10.1101/gr.277246.122
...associated with enhancer activity is consistent with repressive homotypic interactions between pluripotency TFs found by thermodynamic modeling (Fiore and Cohen 2016); the mechanisms, however, are still unclear. Intermotif distances can impact the synergy between TFs at the level of DNA binding or after...

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