CRISPR-Mediated Reorganization of Chromatin Loop Structure
Open accessAbstract
Recent studies have clearly shown that long-range, three-dimensional chromatin looping interactions play a significant role in the regulation of gene expression, but whether looping is responsible for or a result of alterations in gene expression is still unknown. Until recently, how chromatin looping affects the regulation of gene activity and cellular function has been relatively ambiguous, and limitations in existing methods to manipulate these structures prevented in-depth exploration of these interactions. To resolve this uncertainty, we engineered a method for selective and reversible chromatin loop re-organization using CRISPR-dCas9 (CLOuD9). The dynamism of the CLOuD9 system has been demonstrated by successful localization of CLOuD9 constructs to target genomic loci to modulate local chromatin conformation. Importantly, the ability to reverse the induced contact and restore the endogenous chromatin conformation has also been confirmed. Modulation of gene expression with this method establishes the capacity to regulate cellular gene expression and underscores the great potential for applications of this technology in creating stable de novo chromatin loops that markedly affect gene expression in the contexts of cancer and development.
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Forced looping between these loci could also be achieved in HEK293 cells, in which they are heterochromatic, but in this case β-globin derepression was not achieved.
“Forced looping between these loci could also be achieved in HEK293 cells, in which they are heterochromatic, but in this case β-globin derepression was not achieved [313].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [313]
The Representative Results report induced β-globin–LCR contacts in heterochromatic HEK 293T cells, without an increase in β-globin expression. The cited experiments used HEK 293T cells specifically, whereas the claim identifies them as HEK293 cells. (LLM, conf=0.83)
Experimental — accuracy not yet measuredForced looping between β-globin and its LCR was shown to rescue β-globin expression in K562 erythroid cells (which instead aberrantly express γ-globin) in a reversible manner.
“Forced looping between β-globin and its LCR was shown to rescue β-globin expression in K562 erythroid cells (which instead aberrantly express γ-globin) in a reversible manner [313].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [313]
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- Authors
- Morgan, S. L., Chang, E. Y., Mariano, N. C., Bermudez, A., Arruda, N. L., Wu, F., Luo, Y., Shankar, G., Huynh, S. K., Huang, C.-C., Pitteri, S. J., & Wang, K. C.
- Affiliations
- Stanford Medicine (US)
- Bridgewater State University (US)
- System Biosciences (United States) (US)
- ORCID
- Venue
- Journal of Visualized Experiments
- Publisher
- MyJove Corporation
- Published
- 2018-09-14
- Issue
- 139
- ISSN
- 1940-087X (ISSN-L)
- PMC
- PMC6235177
- OpenAlex
- W2889929670
- Semantic Scholar
- 6ce510c6f83b18ecaa57cc809ea091332a63488f
- Cited by
- 7
- References
- 19
- Citations by year
- 2026: 1 · 2024: 1 · 2023: 1 · 2021: 2 · 2020: 1 · 2018: 1
- FWCI
- 0.36
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Visualized Experiments (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Burroughs Wellcome Fund
- Donald E. and Delia B. Baxter Foundation
- National Cancer Institute (F99CA222541)
- National Institute of Environmental Health Sciences (27302C0028)
- 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 › Chromatin Remodeling and Cancer
- Keywords
- chromatin looping, three-dimensional chromatin structure, CRISPR/dCas9, gene expression regulation, long-range chromatin interactions
- MeSH terms
- Chromatin, Humans, Molecular Conformation, Clustered Regularly Interspaced Short Palindromic Repeats
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