Casilio: a versatile CRISPR-Cas9-Pumilio hybrid for gene regulation and genomic labeling

Cheng, Albert W.; Jillette, Nathaniel; Lee, Phoebe; Plaskon, Dylan; Fujiwara, Yasuhiro; Wang, Wenbo; Taghbalout, Aziz; Wang, Haoyi

doi:10.1038/cr.2016.3

Cited by 135 publications

(132 citation statements)

References 14 publications

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“…dCas9-CBPHAT was targeted using the Casilio (CRISPR/Cas9-Pumilio) system, which harbours an scRNA containing multiple PUF binding sites (PBS), to recruit additional CBPHAT domains via fusions with Pumilio/FBF (PUF) RNA-binding domains. Similar to dCas9-p300, targeting dCas9-CBPHAT to promoters or proximal and distal enhancer caused increased expression of the target genes (Cheng et al, 2016). dCas9 has also been used to introduce DNA methylation by targeting the catalytic domain of the de novo DNA methyltransferase 3A (DNMT3A) to specific loci.…”

Section: Applications Of the Dcas9 Toolmentioning

confidence: 99%

“…2.2B), secondary RNA structures specifically recognized by RNA-binding proteins, to form a scaffolding RNA (scRNA) (Mali et al, 2013a;Konermann et al, 2015;Zalatan et al, 2015). Using scRNAs with RNA aptamers such as MS2, PP7, com or the PUF binding site (PBS), effectors can be recruited to the dCas9-sgRNA complex indirectly via fusion to corresponding RNA-binding proteins (Mali et al, 2013a;Zalatan et al, 2015;Cheng et al, 2016). Recruiting effectors simultaneously via a dCas9 gene fusion and via aptamers present in the sgRNA has been shown to yield strong synergistic transactivation Xu et al, 2016).…”

Section: Class II -Indirect Effector Recruitmentmentioning

confidence: 99%

“…The two effectors behave somewhat differently in terms of their impact on histone acetylation state, as p300 directly catalyses H3K27ac (Ogryzko et al, 1996;Delvecchio et al, 2013), whereas VP64 recruits subsequent transactivation components, amongst which is p300 (Memedula and Belmont, 2003). Also the histone acetyltransferase domain of the CREB-binding protein has been fused to dCas9 (dCas9-CBPHAT) and has been used to catalyse locus-specific acetylation of histones (Cheng et al, 2016). dCas9-CBPHAT was targeted using the Casilio (CRISPR/Cas9-Pumilio) system, which harbours an scRNA containing multiple PUF binding sites (PBS), to recruit additional CBPHAT domains via fusions with Pumilio/FBF (PUF) RNA-binding domains.…”

Section: Applications Of the Dcas9 Toolmentioning

confidence: 99%

“…Both effectors exhibit complex mechanisms of transactivation via recruitment of secondary transcription factors (Mittler et al, 2003; (Groner et al, 2010). TEMs are designed based Gao et al, 2014;Gilbert et al, 2013;Hu et al, 2014;Kearns et al, 2014Kearns et al, , 2015Lawhorn et al, 2014;Thakore et al, 2015KRAB Cheng et al, 2016Zalatan et al, 2015SID4x Konermann et al, 2013Mxi1 Gilbert et al, 2013 Targeted epigenetic modifiers (TEMs) (McDonald et al, 2016;Vojta et al, 2016), TET1 5mC-hydroxylase (Maeder et al, 2013a;Xu et al, 2016), LSD1 histone demethylase (Mendenhall et al, 2013;Kearns et al, 2015) and the p300 and CBP histone acetyltransferases (Hilton et al, 2015;Cheng et al, 2016). Below, we discuss applications of epigenetic editing by TEMs or indirect modulation by TTFs using dCas9 as DNA-binding platform.…”

Section: Applications Of the Dcas9 Toolmentioning

confidence: 99%

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dCas9: A Versatile Tool for Epigenome Editing

Brocken¹,

Tark-Dame²,

Dame³

2018

Current Issues in Molecular Biology

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The epigenome is a heritable layer of information not encoded in the DNA sequence of the genome, but in chemical modifications of DNA or histones. These chemical modifications, together with transcription factors, operate as spatiotemporal regulators of genome activity. Dissecting epigenome function requires controlled site-specific alteration of epigenetic information. Such control can be obtained using designed DNA-binding platforms associated with effector domains to function as targeted transcription factors or epigenetic modifiers. Here, we review the use of dCas9 as a novel and versatile tool for fundamental studies on epigenetic landscapes, chromatin structure and transcription regulation, and the potential of this approach in basic research in these fields.

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Section: Applications Of the Dcas9 Toolmentioning

confidence: 99%

Section: Class II -Indirect Effector Recruitmentmentioning

confidence: 99%

Section: Applications Of the Dcas9 Toolmentioning

confidence: 99%

Section: Applications Of the Dcas9 Toolmentioning

confidence: 99%

See 2 more Smart Citations

dCas9: A Versatile Tool for Epigenome Editing

Brocken¹,

Tark-Dame²,

Dame³

2018

Current Issues in Molecular Biology

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“…53 This mRNA-binding domain can be reengineered to bind, in principle, any chosen octamers 54 and has been fused to other protein domains to either repress or activate translation. 55 Cheng et al 56 extended the gRNA with a variable number of Puf binding domains (PBS) and modified the bare Pum-HD with the addition of a transcriptional activation (VP64, p65, and HAT) or repression (KRAB) domain. The overall system, termed Casilio, was engineered in different variants by changing the Pum-HD and the number of the corresponding PBS along the gRNA.…”

Section: Crispr-dcas9 As a Scaffoldmentioning

confidence: 99%

CRISPR-Cas type II-based Synthetic Biology applications in eukaryotic cells

Marchisio

Huang

2017

RNA Biology

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The CRISPR-Cas system has rapidly reached a huge popularity as a new, powerful method for precise DNA editing and genome reengineering. In Synthetic Biology, the CRISPR-Cas type II system has inspired the construction of a novel class of RNA-based transcription factors. In their simplest form, they are made of a CRISPR RNA molecule, which targets a promoter sequence, and a deficient Cas9 (i.e. deprived of any nuclease activity) that has been fused to an activation or a repression domain. Up-and downregulation of single genes in mammalian and yeast cells have been achieved with satisfactory results. Moreover, the construction of CRISPR-based transcription factors is much simpler than the assembly of synthetic proteins such as the Transcription Activator-Like effectors. However, the feasibility of complex synthetic networks fully based on the CRISPR-dCas9 technology has still to be proved and new designs, which take into account different CRISPR types, shall be investigated.

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Innovative Precision Gene‐Editing Tools in Personalized Cancer Medicine

et al. 2020

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The development of clustered regularly interspaced short palindromic repeats (CRISPR) has spurred a successive wave of genome‐engineering following zinc finger nucleases and transcription activator‐like effector nucleases, and made gene‐editing a promising strategy in the prevention and treatment of genetic diseases. However, gene‐editing is not widely adopted in clinics due to some technical issues that challenge its safety and efficacy, and the lack of appropriate clinical regulations allowing them to advance toward improved human health without impinging on human ethics. By systematically examining the oncological applications of gene‐editing tools and critical factors challenging their medical translation, genome‐editing has substantial contributions to cancer driver gene discovery, tumor cell epigenome normalization, targeted delivery, cancer animal model establishment, and cancer immunotherapy and prevention in clinics. Gene‐editing tools, epitomized by CRISPR, are predicted to represent a promising strategy toward the precise control of cancer initiation and development. However, some technical problems and ethical concerns are serious issues that need to be appropriately addressed before CRISPR can be incorporated into the next generation of molecular precision medicine. In this light, new technical developments to limit off‐target effects are discussed herein, and the use of gene‐editing approaches for treating otherwise incurable cancers is brought into focus.

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Casilio: a versatile CRISPR-Cas9-Pumilio hybrid for gene regulation and genomic labeling

Cited by 135 publications

References 14 publications

dCas9: A Versatile Tool for Epigenome Editing

dCas9: A Versatile Tool for Epigenome Editing

CRISPR-Cas type II-based Synthetic Biology applications in eukaryotic cells

Innovative Precision Gene‐Editing Tools in Personalized Cancer Medicine

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