Modular fluorescence complementation sensors for live cell detection of epigenetic signals at endogenous genomic sites

Lungu, Cristiana; Pinter, Sabine; Broche, Julian; Rathert, Philipp; Jeltsch, Albert

doi:10.1038/s41467-017-00457-z

Cited by 64 publications

(60 citation statements)

References 69 publications

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“…Live-cell reporters of histone H3 55 and H4 56 lysine acetylation have also been developed. More recently, a fluorescence complementation sensor has been used for real-time visualization of DNA methylation and H3K9me3 marks at major satellite repeats 57 . It will be exciting to apply these reporters to the tracking of the long-term inheritance of these epigenetic marks in live cells.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Mechanisms for the epigenetic inheritance of stress response in single cells

Xue

Açar

2018

Curr Genet

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Cells have evolved to dynamically respond to different types of environmental and physiological stress conditions. The information about a previous stress stimulus experience by a mother cell can be passed to its descendants, allowing them to better adapt to and survive in new environments. In recent years, live-cell imaging combined with cell-lineage tracking approaches has elucidated many important principles that guide stress inheritance at the single-cell and population level. In this review, we summarize different strategies cells can employ to pass the ‘memory’ of previous stress responses to their descendants. Among these strategies, we focus on a recent discovery of how specific features of Msn2 nucleo-cytoplasmic shuttling dynamics could be inherited across cell lineages. We also discuss how stress response can be transmitted to progenies through changes in chromatin and through partitioning of anti-stress factors and/or damaged macromolecules between mother and daughter cells during cell division. Finally, we highlight how emergent technologies will help address open questions in the field.

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Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Mechanisms for the epigenetic inheritance of stress response in single cells

Xue

Açar

2018

Curr Genet

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“…In the case of ZFP57, selectivites for hmC and caC have been engineered . ZFP and other customizable DNA binding domains have also been combined with MBD for the detection of mC in DNA via signalling with split fluorescent proteins…”

Section: Design Of Protein Scaffolds With Selectivity For Oxidized MCmentioning

confidence: 99%

“…In the case of ZFP57, selectivites for hmC and caC have been engineered. [73] ZFP and other customizable DNA binding domains have also been combined with MBD for the detection of mC in DNA via signalling with split fluorescent proteins [111][112][113] Later, transcription-activator-like effectors (TALEs) have been discovered as alternatives to ZFP that feature a more simple and programmable binding mode. [114,115] TALEs bear a central domain consisting of concatenated repeats that each however recognize only one instead of three nucleobases, which reduces the number of required repeats to target any DNA sequence from 64 to only four ( Figure 5A and B show structural overviews).…”

Section: Scaffolds With Programmable Sequence Selectivitymentioning

confidence: 99%

“…[130,131] Natural and mutant TALE repeats were also analyzed for binding to the pro-and eukaryotic epigenetic nucleobase N6-methyladenine (6 mA) [132][133][134] and found to be highly promiscuous. [135] Similar to antibodies, TALE proteins can be employed for staining DNA in live and fixed cells, but allow to do so in a sequence specific manner [113,[136][137][138][139] Combination of TALEs bearing RVDs with epigenetic nucleobase selectivity and fluorescent protein domains or effector domains thus has potential to develop applications not offered by approaches based on nucleobase conversions or proteins without programmable selectivity. This includes live cell monitoring of epigenetic nucleobase dynamics in repetitive and potentially single loci, or for coupling the presence of epigenetic nucleobases to the control of specific chromatin properties.…”

Section: Scaffolds With Programmable Sequence Selectivitymentioning

confidence: 99%

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Recognition of Oxidized 5‐Methylcytosine Derivatives in DNA by Natural and Engineered Protein Scaffolds

Muñoz‐López

Summerer

2017

The Chemical Record

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Methylation of genomic cytosine to 5-methylcytosine is a central regulatory element of mammalian gene expression with important roles in development and disease. 5-methylcytosine can be actively reversed to cytosine via oxidation to 5-hydroxymethyl-, 5-formyl-, and 5-carboxylcytosine by ten-eleven-translocation dioxygenases and subsequent base excision repair or replication-dependent dilution. Moreover, the oxidized 5-methylcytosine derivatives are potential epigenetic marks with unique biological roles. Key to a better understanding of these roles are insights into the interactions of the nucleobases with DNA-binding protein scaffolds: Natural scaffolds involved in transcription, 5-methylcytosine-reading and -editing as well as general chromatin organization can be selectively recruited or repulsed by oxidized 5-methylcytosines, forming the basis of their biological functions. Moreover, designer protein scaffolds engineered for the selective recognition of oxidized 5-methylcytosines are valuable tools to analyze their genomic levels and distribution. Here, we review recent structural and functional insights into the molecular recognition of oxidized 5-methylcytosine derivatives in DNA by selected protein scaffolds.

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“…1,2 In particular, uorescence sensors with modied uorophores, which are based on deoxyribonucleic acid (DNA), appear to be promising for application due to their stability, high specicity, and sensitivity. 3,4 Fluorescence sensors to detect the presence of a target molecule are typically based on the uorescence resonance energy transfer (FRET) process, 5 thus the choice of the receptor pair usually determines the analytical performance of the uorescence sensor. 6 To reduce the limitations that characterize the receptor pairs, studies have shown that novel nanomaterials, which exhibit an effective quenching ability in a broad range of emission wavelengths, can be used as broad-spectrum quenching molecules.…”

Section: Introductionmentioning

confidence: 99%

A strategy for preparing non-fluorescent graphene oxide quantum dots as fluorescence quenchers in quantitative real-time PCR

Yang

Song

et al. 2020

RSC Adv.

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In recent years, graphene oxide quantum dots (GOQDs) have emerged as novel nanomaterials for optical sensing, bioimaging, clinical testing, and environmental testing. However, GOQDs demonstrate unique photoluminescence properties, with GOQDs having quantum limitations and edge effects that often affect the accuracy of the test results in the sensory field. Herein, GOQDs with a large content of hydroxyl groups and low fluorescence intensity were first prepared via an improved Fenton reaction in this study, which introduces a large amount of epoxy groups to break the C-C bonds. The synthesized GOQDs show no significant variation in the fluorescence intensity upon ultraviolet and visible light excitations. We further utilized the GOQDs as fluorescence quenchers for different fluorescent dyes in real-time fluorescence quantitative polymerase chain reaction (qRT-PCR), and verified that the addition of GOQDs (5.3 mg ml À1 ) into a qRT-PCR system could reduce the background fluorescence intensity of the reaction by fluorescence resonance energy transfer (FRET) during its initial stage and its non-specific amplification, and improve its specificity. In addition, the qRT-PCR method could detect two different lengths of DNA sequences with a high specificity in the 10 4 to 10 10 copies per ml range. It is of paramount importance to carry out further investigations to establish an efficient, sensitive, and specific RT-PCR method based on the use of GOQD nanomaterials as fluorescence quenchers.

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Modular fluorescence complementation sensors for live cell detection of epigenetic signals at endogenous genomic sites

Cited by 64 publications

References 69 publications

Mechanisms for the epigenetic inheritance of stress response in single cells

Mechanisms for the epigenetic inheritance of stress response in single cells

Recognition of Oxidized 5‐Methylcytosine Derivatives in DNA by Natural and Engineered Protein Scaffolds

A strategy for preparing non-fluorescent graphene oxide quantum dots as fluorescence quenchers in quantitative real-time PCR

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