Optical control of mammalian endogenous transcription and epigenetic states

Konermann, Silvana; Brigham, Mark D.; Trevino, Alexandro; Hsu, Patrick; Heidenreich, Matthias; Cong, Le; Platt, Randall J.; Scott, David A.; Church, George M.; Zhang, Feng

doi:10.1038/nature20003

Cited by 88 publications

(135 citation statements)

References 10 publications

(11 reference statements)

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“…Current photoactivatable proteins can be combined with these new genome engineering tools to control the endogenous gene transcription. One such integration has been demonstrated by the engineering of light-inducible transcriptional effectors (LITEs), in which a TALE DNA-binding domain was fused to CRY2 and an effector (VP16) was fused to CIB1 [61], where . Light-induced binding between CRY2 and CIB1 activated endogenous gene ( Neurog2 ) transcription in mammalian cells.…”

Section: Concluding Remarks and Future Perspectivesmentioning

confidence: 99%

Optogenetic control of intracellular signaling pathways

Zhang

Cui

2015

Trends in Biotechnology

212

186

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Cells employ a plethora of signaling pathways to make their life-and-death decisions. Extensive genetic, biochemical, and physiological studies have led to the accumulation of knowledge about signaling components and their interactions within signaling networks. These conventional approaches, though useful, lack the ability to control the spatial and temporal aspects of signaling processes. The recently emerged optogenetic tools open up exciting opportunities by enabling signaling regulation with superior temporal and spatial resolution, easy delivery, rapid reversibility, fewer off-target side effects, and the ability to dissect complex signaling networks. Here we review recent achievements in using light to control intracellular signaling pathways, and discuss future prospects for the field, including integration of new genetic approaches into optogenetics.

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Section: Concluding Remarks and Future Perspectivesmentioning

confidence: 99%

Optogenetic control of intracellular signaling pathways

Zhang

Cui

2015

Trends in Biotechnology

212

186

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“…For example, several common hits that mediate resistance to the BRAF inhibitor, PLX-4720, were identified in CRISPR and shRNA loss-of-function screens. 9,107 Furthermore, there are overlapping hits between a CRISPR transcriptional activation screen conducted by Zhang and colleagues 11 and a cDNA overexpression screen carried out by the Garraway lab. 108 Specifically, each group identified genes that, when overexpressed, conferred resistance to inhibitors of the RAS/RAF/MAPK pathway.…”

Section: Discussionmentioning

confidence: 99%

“…24 Similar to the scRNA/CRISPRa approach, the SAM genome editing suite 11 employs a modified sgRNA that can recruit multiple transcriptional activators. Using this technology at the genome-wide scale has uncovered novel candidate genes involved in the resistance to a small molecular inhibitor of the BRAF V600E variant.…”

Section: System Choicesmentioning

confidence: 99%

“…98 Several lncRNAs were suppressed using CRISPRi, 13 whereas others were transcriptionally up-regulated using SAM. 11 Going beyond this, CRISPR/Cas9 could also be used to probe the functional significance of even nontranscribed regions. Circular RNAs (circRNAs) are also emerging as critical ncRNA biological regulators in many instances.…”

Section: Additional Applications and Improvementsmentioning

confidence: 99%

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High-Throughput Silencing Using the CRISPR-Cas9 System: A Review of the Benefits and Challenges

Wade

2015

SLAS Discovery

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The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system has been seized upon with a fervor enjoyed previously by small interfering RNA (siRNA) and short hairpin RNA (shRNA) technologies and has enormous potential for high-throughput functional genomics studies. The decision to use this approach must be balanced with respect to adoption of existing platforms versus awaiting the development of more "mature" next-generation systems. Here, experience from siRNA and shRNA screening plays an important role, as issues such as targeting efficiency, pooling strategies, and off-target effects with those technologies are already framing debates in the CRISPR field. CRISPR/Cas can be exploited not only to knockout genes but also to up-or down-regulate gene transcription-in some cases in a multiplex fashion. This provides a powerful tool for studying the interaction among multiple signaling cascades in the same genetic background. Furthermore, the documented success of CRISPR/Cas-mediated gene correction (or the corollary, introduction of disease-specific mutations) provides proof of concept for the rapid generation of isogenic cell lines for highthroughput screening. In this review, the advantages and limitations of CRISPR/Cas are discussed and current and future applications are highlighted. It is envisaged that complementarities between CRISPR, siRNA, and shRNA will ensure that all three technologies remain critical to the success of future functional genomics projects.

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“…[66][67][68] Targeting of such dCas9-based transcriptional activators or repressors to a large set of gene promoters with sgRNA libraries permits genome-wide screens. 69,70 Therapeutic considerations…”

Section: 46-51mentioning

confidence: 99%

A genome editing primer for the hematologist

Hoban

Bauer

2016

Blood

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Gene editing enables the site-specific modification of the genome. These technologies have rapidly advanced such that they have entered common use in experimental hematology to investigate genetic function. In addition, genome editing is becoming increasingly plausible as a treatment modality to rectify genetic blood disorders and improve cellular therapies. Genome modification typically ensues from site-specific double-strand breaks and may result in a myriad of outcomes. Even single-strand nicks and targeted biochemical modifications that do not permanently alter the DNA sequence (epigenome editing) may be powerful instruments. In this review, we examine the various technologies, describe their advantages and shortcomings for engendering useful genetic alterations, and consider future prospects for genome editing to impact hematology.

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Optical control of mammalian endogenous transcription and epigenetic states

Cited by 88 publications

References 10 publications

Optogenetic control of intracellular signaling pathways

Optogenetic control of intracellular signaling pathways

High-Throughput Silencing Using the CRISPR-Cas9 System: A Review of the Benefits and Challenges

A genome editing primer for the hematologist

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