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Resource: A genome-wide interactome of DNA-associated proteins in the human liver
- Ryne C. Ramaker,
- Daniel Savic,
- Andrew A. Hardigan,
- Kimberly Newberry,
- Gregory M. Cooper,
- Richard M. Myers,
- and Sara J. Cooper
Genome Res. November 2017 27: 1950-1960; Published in Advance October 11, 2017, doi:10.1101/gr.222083.117
...of high DAP occupancy are factor dependent. Although some of our observations were similar to what has been observed in vitro, our analysis highlights the value in performing ChIP-seq analysis in primary tissue to characterize tissue-specific gene regulation. The DNA-binding proteins we analyzed show...
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Research: Estrogen-independent molecular actions of mutant estrogen receptor 1 in endometrial cancer
- Zannel Blanchard,
- Jeffery M. Vahrenkamp,
- Kristofer C. Berrett,
- Spencer Arnesen,
- and Jason Gertz
Genome Res. September 2019 29: 1429-1441; Published in Advance July 30, 2019, doi:10.1101/gr.244780.118
...and warrant investigation. We used a CRISPR/Cas9-mediated epitope tagging strategy called CETCH-seq (Savic et al. 2015) in Ishikawa cells, an endometrial adenocarcinoma cell line that exhibits ESR1 genomic binding similar to endometrial tumor samples (Rodriguez et al. 2019a), to model a common ESR1 LBD...
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Method: Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN
- Xiangxiu Wang,
- Wen Wang,
- Yiman Wang,
- Jia Chen,
- Guifen Liu,
- and Yong Zhang
Genome Res. February 2022 32: 378-388; Published in Advance December 29, 2021, doi:10.1101/gr.275837.121
...transfected eGFP-ELF1 K562 cell lines was constructed and then a standard ChIP-seq experiment was performed. The FLAG-ATF1 data set was generated by CETCh-seq (CRISPR Epitope Tagging ChIP-seq) which introduced the FLAG tag to endogenous locus of ATF1 by CRISPR and then performed a traditional ChIP-seq...
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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
...patterns of five AP-1 subunits by using CRISPR to introduce a common antibody tag on each subunit. We find limited evidence for strong dimerization preferences between subunits at steady state and find that, under a stimulus, dimerization patterns reflect changes in the transcriptome. Further, our analysis...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...for 1139 DAPs using both traditional antibody ChIP-seq and epitope-tagged ChIP-seq methods (The ENCODE Project Consortium 2012; The ENCODE Project Consortium et al. 2020; Partridge et al. 2020). The human liver cancer–derived cell line HepG2 currently has the largest number (n = 814) of ENCODE-released ChIP-seq...
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Method: Probabilistic association of differentially expressed genes with cis-regulatory elements
- Brian S. Roberts,
- Ashlyn G. Anderson,
- E. Christopher Partridge,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. April 2024 34: 620-632; Published in Advance April 17, 2024, doi:10.1101/gr.278598.123
...plots are presented with CRISPR data from Gasperini et al. as the standard with same conventions as A–C. Predictions are based on data from Reed et al. H3K27ac ChIP-seq at 2 h (E), Sanchez-Priego et al. H3K27ac Cut and Run from H1 GABA late (F), and Hiatt et al. ZMYM3 CETCh-seq with R1274W variant using...
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Method: Domain-adaptive neural networks improve cross-species prediction of transcription factor binding
- Kelly Cochran,
- Divyanshi Srivastava,
- Avanti Shrikumar,
- Akshay Balsubramani,
- Ross C. Hardison,
- Anshul Kundaje,
- and Shaun Mahony
Genome Res. March 2022 32: 512-523; Published in Advance January 18, 2022, doi:10.1101/gr.275394.121
...species should generalize to closely matched cell types in a related species. To assess the viability of cross-species TF binding prediction, we train neural networks to discriminate ChIP-seq peak locations from genomic background and evaluate their performance within and across species. Cross...
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Method: Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo
- Luca Tosti,
- James Ashmore,
- Boon Siang Nicholas Tan,
- Benedetta Carbone,
- Tapan K. Mistri,
- Valerie Wilson,
- Simon R. Tomlinson,
- and Keisuke Kaji
Genome Res. April 2018 28: 592-605; Published in Advance March 23, 2018, doi:10.1101/gr.227124.117
..., they still require 10,000–500,000 cells to identify targets of the TF SPI1 (also known as PU.1). The use of CETCh-seq (CRISPR epitope tagging followed by ChIP-seq) overcomes the need for TF-specific ChIP-grade antibodies, but it does not reduce the required numbers of cells (Savic et al. 2015). DNA adenine...
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