Functional annotation of native enhancers with a Cas9–histone demethylase fusion
Open accessAbstract
Understanding of mammalian enhancers is limited by the lack of a technology to rapidly and thoroughly test the cell type-specific function. Here, we use a nuclease-deficient Cas9 (dCas9)-histone demethylase fusion to functionally characterize previously described and new enhancer elements for their roles in the embryonic stem cell state. Further, we distinguish the mechanism of action of dCas9-LSD1 at enhancers from previous dCas9-effectors.
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Additional dCas9-tethered domains have been shown to disrupt enhancer activity.
“Additional dCas9-tethered domains have been shown to disrupt enhancer activity (e.g. histone demethylase LSD1210, histone deacetylase 3211, and DNA methylators MQ212 or DNMT3A213-215), and could potentially be adapted to large-scale screens.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [210]
dCas9-KRAB does not specifically inactivate enhancers; it inhibits transcription at both promoters and enhancers.
“dCas9-KRAB does not specifically inactivate enhancers, but rather inhibits transcriptional activity both at promoters and enhancers35.”
From Targeted Perturb-seq enables genome-scale genetic screens in single cells (2020) · cites this paper as [35]
dCas9 fusion proteins-mediated CRISPRi, such as dCas9-KRAB and dCas9-LSD1, has been introduced.
“Most recently, dCas9 fusion proteins-mediated CRISPRi, such as dCas9-KRAB (Krüppel-associated box) and dCas9-LSD1 (lysine-specific histone demethylase 1) system, has been introduced [125–127].”
From Non-viral delivery systems for CRISPR/Cas9-based genome editing: challenges and opportunities (2018) · cites this paper as [127]
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- Authors
- Kearns, N. A., Pham, H., Tabak, B., Genga, R. M., Silverstein, N. J., Garber, M., & Maehr, R.
- Affiliations
- University of Massachusetts Chan Medical School (US)
- Corresponding author
- Maehr, René
- Venue
- Nature Methods
- Published
- 2015-03-16
- Volume
- 12
- Issue
- 5
- Pages
- 401-403
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC4414811
- OpenAlex
- W2055790209
- Cited by
- 656
- References
- 32
- Citations by year
- 2026: 26 · 2025: 31 · 2024: 48 · 2023: 39 · 2022: 56 · 2021: 62 · 2020: 61 · 2019: 73 · 2018: 86 · 2017: 72 · 2016: 71 · 2015: 30 · 2014: 1
- FWCI
- 37.47
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship@UMassChan (submittedVersion)
- Funders
- National Institutes of Health (1uc4dk104218-01)
- National Human Genome Research Institute (U01HG007910)
- National Institute of Allergy and Infectious Diseases (R21AI119885, R56AI114525)
- National Institute of Diabetes and Digestive and Kidney Diseases (UC4-DK-104218)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD080224)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- enhancers, dCas9, histone demethylase, LSD1, epigenetic modifications, enhancer function, embryonic stem cells, CRISPR/Cas9 genome editing
- MeSH terms
- Animals, Bacterial Proteins, Cells, Cultured, Enhancer Elements, Genetic, Histones, Neisseria meningitidis, Recombinant Proteins, Gene Expression Regulation, Enzymologic, Genes, Reporter, Mice, Caspase 9, Embryonic Stem Cells, Histone Demethylases
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