ArticleProceedings of the National Academy of Sciences of the United States of America2019
Deciphering essential cistromes using genome-wide CRISPR screens.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 56 citations in OpenAlex.
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- ePerturbDB: enhancer's experimental perturbation database.Database : the journal of biological databases and curation · 2026Article
- Evaluating transportability of in vitro cellular models to in vivo human phenotypes using gene perturbation data.Nature communications · 2025Article
- A Functional Survey of the Regulatory Landscape of Estrogen Receptor-Positive Breast Cancer Evolution.Cancer discovery · 2024Article
- The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer.Genome biology · 2024Article
- Landscape of enhancer disruption and functional screen in melanoma cells.Genome biology · 2023Article
- CRISPR base editing of cis-regulatory elements enables the perturbation of neurodegeneration-linked genes.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- Multiplexed functional genomic assays to decipher the noncoding genome.Human molecular genetics · 2022Article
- A Distinct Chromatin State Drives Therapeutic Resistance in Invasive Lobular Breast Cancer.Cancer research · 2022Article
- Chromatin Variants Reveal the Genetic Determinants of Oncogenesis in Breast Cancer.Cold Spring Harbor perspectives in medicine · 2022Review
- FOXA1 regulates alternative splicing in prostate cancer.Cell reports · 2022Article
- MOZ and Menin-MLL Complexes Are Complementary Regulators of Chromatin Association and Transcriptional Output in Gastrointestinal Stromal Tumor.Cancer discovery · 2022Article
- Rapid Intraspecies Evolution of Fitness Effects of Yeast Genes.Genome biology and evolution · 2022Article
- IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia.Nature cancer · 2022Article
- To bind or not to bind: Cistromic reprogramming in prostate cancer.Frontiers in oncology · 2022Review
- CRISPR Screen Contributes to Novel Target Discovery in Prostate Cancer.International journal of molecular sciences · 2021Review
- Topological isolation of developmental regulators in mammalian genomes.Nature communications · 2021Article
- Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases.Molecular oncology · 2021Article
- Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens.Science advances · 2021Article
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
Although millions of transcription factor binding sites, or cistromes, have been identified across the human genome, defining which of these sites is functional in a given condition remains challenging. Using CRISPR/Cas9 knockout screens and gene essentiality or fitness as the readout, we systematically investigated the essentiality of over 10,000 FOXA1 and CTCF binding sites in breast and prostate cancer cells. We found that essential FOXA1 binding sites act as enhancers to orchestrate the expression of nearby essential genes through the binding of lineage-specific transcription factors. In contrast, CRISPR screens of the CTCF cistrome revealed 2 classes of essential binding sites. The first class of essential CTCF binding sites act like FOXA1 sites as enhancers to regulate the expression of nearby essential genes, while a second class of essential CTCF binding sites was identified at topologically associated domain (TAD) boundaries and display distinct characteristics. Using regression methods trained on our screening data and public epigenetic profiles, we developed a model to predict essential
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.