Searching journal content for articles similar to Chaudhari and Cohen 28 (2): 171.

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Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
.... Using the ATAC-seq data, we developed a machine learning approach to determine the transcription factors (TFs) regulating the subtypes of GC. We identified TFs driving the mesenchymal (RUNX2, ZEB1, SNAI2, AP-1 dimer) and the epithelial (GATA4, GATA6, KLF5, HNF4A, FOXA2, GRHL2) states in GC. We...
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Research: AP-1 subunits converge promiscuously at enhancers to potentiate transcription
- Jungkyun Seo,
- D. Dewran Koçak,
- Luke C. Bartelt,
- Courtney A. Williams,
- Alejandro Barrera,
- Charles A. Gersbach,
- and Timothy E. Reddy
Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
...in vitro have suggested differences in TRE or CRE affinity (Isakova et al. 2017). Massively parallel reporter assay (MPRA) analyses have also shown that AP-1-mediated cis-regulatory activity depends on sequences beyond the core TRE (Chaudhari and Cohen 2018). It remains unresolved whether AP-1 subunits...
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Method: Massively parallel cis-regulatory analysis in the mammalian central nervous system
- Susan Q. Shen,
- Connie A. Myers,
- Andrew E.O. Hughes,
- Leah C. Byrne,
- John G. Flannery,
- and Joseph C. Corbo
Genome Res. February 2016 26: 238-255; Published in Advance November 17, 2015, doi:10.1101/gr.193789.115
..., California 94720, USA Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies...
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Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
- Xiaoyu Zhuo,
- Silas Hsu,
- Deepak Purushotham,
- Prashant Kumar Kuntala,
- Jessica K. Harrison,
- Alan Y. Du,
- Samuel Chen,
- Daofeng Li,
- and Ting Wang
Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
...-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Cell 184: 5541–5558.e22. doi:10.1016/j.cell.2021.09.021 ↵Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. 2014. Comparative assembly hubs: web-accessible browsers for comparative...
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Methods: Footer: A quantitative comparative genomics method for efficient recognition of cis-regulatory elements
- David L. Corcoran,
- Eleanor Feingold,
- Jessica Dominick,
- Marietta Wright,
- Jo Harnaha,
- Massimo Trucco,
- Nick Giannoukakis,
- and Panayiotis V. Benos
Genome Res. June 2005 15: 840-847; doi:10.1101/gr.2952005
...Footer: A quantitative comparative genomics method for efficient recognition of cis -regulatory elements David L. Corcoran 1 , 2 , Eleanor Feingold 1 , 2 , Jessica Dominick 2 , Marietta Wright 4 , Jo Harnaha 4 , Massimo Trucco 4...
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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
...Detection and Visualization of Compositionally Similar cis -Regulatory Element Clusters in Orthologous and Coordinately Controlled Genes Anil G. Jegga 1 , Shawn P. Sherwood 1 , James W. Carman 1 , Andrew T. Pinski 1 , Jerry L. Phillips 1...
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Research: TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
- Morgan A. Sammons,
- Jiajun Zhu,
- Adam M. Drake,
- and Shelley L. Berger
Genome Res. February 2015 25: 179-188; Published in Advance November 12, 2014, doi:10.1101/gr.181883.114
...and dynamic local chromatin environments We explored distinguishing chromatin features between induced TP53 binding sites. Transcriptional regulatory elements can be distinguished by specific patterns of chromatinmodification, such Figure 1. Epigenomic analysis of TP53 activation in primary human fibroblasts...
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Research: Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
- J. Omar Yáñez-Cuna,
- Cosmas D. Arnold,
- Gerald Stampfel,
- Łukasz M. Boryń,
- Daniel Gerlach,
- Martina Rath,
- and Alexander Stark
Genome Res. July 2014 24: 1147-1156; Published in Advance April 8, 2014, doi:10.1101/gr.169243.113
...requirements (Fig. 5A) in which two different types of sequence elements are important: (1) motifs for cell type-specific TFs (GATA, E-box, or Fkh motifs) or broadly expressed activators (AP-1 or STAT), and (2) CA, GA, and CG DRMs. DRMs are novel enhancer features that are enriched and required in cell type...
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Research: Functional characterization of enhancer activity during a long terminal repeat's evolution
- Alan Y. Du,
- Xiaoyu Zhuo,
- Vasavi Sundaram,
- Nicholas O. Jensen,
- Hemangi G. Chaudhari,
- Nancy L. Saccone,
- Barak A. Cohen,
- and Ting Wang
Genome Res. October 2022 32: 1840-1851; Published in Advance October 3, 2022, doi:10.1101/gr.276863.122
...regulatory activity has evolved. We systematically tested the human LTR18A subfamily for regulatory activity using massively parallel reporter assay (MPRA) and found AP-1- and CEBP-related binding motifs as drivers of enhancer activity. Functional analysis of evolutionarily reconstructed ancestral sequences...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...compartments and having fewer sequence constraints, which enable the generation of quasi-primes. We also utilized regulatory elements as categorized by ENCODE (The ENCODE Project Consortium et al. 2020) to examine the distribution of human quasi-primes across cis-regulatory elements. The set of cis-regulatory...
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