Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping

Morgan, Stefanie L.; Mariano, Natasha C.; Bermudez, Abel; Arruda, Nicole L.; Wu, Fangting; Luo, Yunhai; Shankar, Gautam; Jia, Lin; Chen, Huiling; Hu, Ji-Fan; Hoffman, Andrew R.; Huang, Chiao-Chain; Pitteri, Sharon J.; Wang, Kevin C.

doi:10.1038/ncomms15993

Cited by 242 publications

(165 citation statements)

References 18 publications

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“…Similarly, we show here that transcription can be disrupted with minimal changes in enhancer-promoter interaction frequency, as has been observed at the b-globin locus 59 . In contrast, artificially stabilizing enhancer-promoter loops can activate transcription 24,[60][61][62][63][64] , indicating that the conversion of unproductive enhancer-promoter contacts to a functional complex may be dependent on the presence of additional factors.…”

Section: Discussionmentioning

confidence: 99%

BET inhibition disrupts transcription but retains enhancer-promoter contact

Crump

Ballabio

Godfrey

et al. 2019

Preprint

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In higher eukaryotes, enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. The formation of phase condensates is thought to be an essential component of enhancer function. Here, we show that pharmacological targeting of cells with inhibitors of BET (Bromodomain and Extra-Terminal domain) proteins can have a strong impact on transcription but very little impact on enhancer-promoter interactions. Treatment with 1,6-hexanediol, which dissolves phase condensate structures and reduces BET and Mediator protein binding at enhancers, can also have a strong effect on gene transcription, without disrupting enhancer-promoter interactions. These results suggest that activation of transcription and maintenance of enhancerpromoter interactions are separable events. Our findings further suggest that enhancer-promoter interactions are not dependent on high levels of BRD4 (Bromodomain-containing protein 4) and Mediator, and are likely maintained by a complex set of factors including additional activator complexes and loop extrusion by CTCF/cohesin.

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Section: Discussionmentioning

confidence: 99%

BET inhibition disrupts transcription but retains enhancer-promoter contact

Crump

Ballabio

Godfrey

et al. 2019

Preprint

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“…The non-coding RNAs might be able to regulate by utilizing the RNA-guided RNA endonucleases such as Cas13a [70]. Chromatin higher-order structures include biologically complex mechanisms, but recent study showed that chromosomal looping can be triggered with the CRISPR tool [71]. These new tools and methods will also open new doors for cancer epigenetics and potential therapy.…”

Section: Discussionmentioning

confidence: 99%

Cancer induction and suppression with transcriptional control and epigenome editing technologies

2017

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Cancer epigenetics is one of the most important research subjects in dissecting cancer mechanisms and therapeutic targets because the emergence and malignant transformation of various cancers are caused by unnatural expression of cancer-related genes attributed to their epigenetic errors. The original concept of cancer epigenetics basically stands on the analysis of the epigenetic status in naturally occurring cancer cells; however, the rapidly emerging technology called epigenome editing would change this situation drastically. Epigenome editing, the most promising derivative technology of genome editing, can modify the epigenetic states at the pre-defined genomic locus using the programmable effectors, consisting of various epigenetic factors combined with site-specific DNA-binding domains. This technology can be utilized in a reversible manner; i.e., cancer modeling can be achieved by introducing aberrant epigenetic marks in normal cells, and cancer suppression can be achieved by correcting the epigenetic errors in cancer cells. In this review, we summarize the basics of epigenome editing and cancer epigenetics, followed by the current examples of cancer induction and suppression with the transcriptional control and epigenome editing technologies.

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“…In contrast, HDAC3 functions as a corepressor by deacetylating the H3K27ac on enhancer elements (Hatzi et al 2013). Recently, CRISPR technology has also been successfully used to recruit endogenous chromatin regulators to targeted genomic loci (Braun et al 2017; Liszczak et al 2017) or manipulation of nuclear architecture and chromatin looping (Hao et al 2017; Morgan et al 2017). However, most of these studies have not yet been tested in vivo.…”

Section: Crispr-based Epigenome Editing and Transcriptional Modulatiomentioning

confidence: 99%

“…The fusion of the dCas9 to the catalytic domains of various epigenetic effectors has greatly expanded the scope of CRISPR applications to epigenome editing. These include: to modulate epigenetic marks and gene expression (Hilton et al 2015; Kearns et al 2015; Kwon et al 2017; Thakore et al 2015), manipulate nuclear architecture and chromatin loops (Hao et al 2017; Morgan et al 2017), and visualize chromosome organization and dynamics via chromosome imaging (Chen et al 2013; Ma et al 2015). In addition, stable and heritable alteration of epigenetic marks and gene expression can be achieved in post-mitotic tissues in adult animals in vivo without the need to genetically modify the DNA sequence.…”

Section: Introductionmentioning

confidence: 99%

In vivo epigenome editing and transcriptional modulation using CRISPR technology

Lau

Suh

2018

Transgenic Res

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The rapid advancement of CRISPR technology has enabled targeted epigenome editing and transcriptional modulation in the native chromatin context. However, only a few studies have reported the successful editing of the epigenome in adult animals in contrast to the rapidly growing number of in vivo genome editing over the past few years. In this review, we discuss the challenges facing in vivo epigenome editing and new strategies to overcome the huddles. The biggest challenge has been the difficulty in packaging dCas9 fusion proteins required for manipulation of epigenome into the adeno-associated virus (AAV) delivery vehicle. We review the strategies to address the AAV packaging issue, including small dCas9 orthologues, truncated dCas9 mutants, a split-dCas9 system, and potent truncated effector domains. We discuss the dCas9 conjugation strategies to recruit endogenous chromatin modifiers and remodelers to specific genomic loci, and recently developed methods to recruit multiple copies of the dCas9 fusion protein, or to simultaneous express multiple gRNAs for robust epigenome editing or synergistic transcriptional modulation. The use of Cre-inducible dCas9-expressing mice or a genetic cross between dCas9- and sgRNA-expressing flies has also helped overcome the transgene delivery issue. We provide perspective on how a combination use of these strategies can facilitate in vivo epigenome editing and transcriptional modulation.

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Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping

Cited by 242 publications

References 18 publications

BET inhibition disrupts transcription but retains enhancer-promoter contact

BET inhibition disrupts transcription but retains enhancer-promoter contact

Cancer induction and suppression with transcriptional control and epigenome editing technologies

In vivo epigenome editing and transcriptional modulation using CRISPR technology

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