Programmable Sensors of 5-Hydroxymethylcytosine

Kubik, Grzegorz; Batke, Sabrina; Summerer, Daniel

doi:10.1021/ja506022t

Cited by 36 publications

(52 citation statements)

References 38 publications

(56 reference statements)

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“…Although this traditional method provided early insights into the methylation status of CpG islands and was later coupled with deep sequencing, this approach is limited by the availability of selective restriction enzymes for diverse sequence contexts [42][43][44]. Immunoprecipitation with modification-specific antibodies allowed for enrichment prior to sequencing for analyzing the spatial distribution of epigenetic bases in the genome [36,37,[47][48][49], and transcription-activator-like effector (TALE)-based protein scaffolds were engineered to analyze 5mC and its oxidized derivatives with programmable sequence selectivity [50][51][52]. Immunoprecipitation with modification-specific antibodies allowed for enrichment prior to sequencing for analyzing the spatial distribution of epigenetic bases in the genome [36,37,[47][48][49], and transcription-activator-like effector (TALE)-based protein scaffolds were engineered to analyze 5mC and its oxidized derivatives with programmable sequence selectivity [50][51][52].…”

Section: Epigenetic Modifications Of Cytosinementioning

confidence: 99%

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

2018

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DNA methylation has a profound impact on the regulation of gene expression in normal cell development, and aberrant methylation has been recognized as a key factor in the pathogenesis of human diseases such as cancer. The discovery of modified nucleobases arising from 5-methylcytosine (5mC) through consecutive oxidation to give 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) has stimulated intense research efforts regarding the biological functions of these epigenetic marks. This Review focuses on the sensitive detection and quantitation of 5fC in DNA and RNA by chemoselective labeling, which aims at discriminating between 5fC and its thymine counterpart 5-formyluracil (5fU), and summarizes single-base resolution sequencing methods for locus-specific mapping of 5mC and its oxidized derivatives.

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Section: Epigenetic Modifications Of Cytosinementioning

confidence: 99%

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

2018

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“…The discovery of transcription activator-like effector (TALE) proteins from plant pathogens later offered a means for targeting single bases, and, like with ZFPs, concatenation of TALEs results in selective recognition of longer DNA motifs [14]. Structure-function insights into the TALE residues that contact nucleobases have permitted the development of constructs that differentiate unmodified cytosine from 5mC and ox-mCs [15–18]. Such modified TMs (TM*) have not yet been employed with different MMs, but the combination would make for a logical and anticipated advance.…”

Section: Targeting Modules (Tm)mentioning

confidence: 99%

Harnessing natural DNA modifying activities for editing of the genome and epigenome

DeNizio

Schutsky

Berríos

et al. 2018

Current Opinion in Chemical Biology

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The introduction of site-specific DNA modifications to the genome or epigenome presents great opportunities for manipulating biological systems. Such changes are now possible through the combination of DNA-modifying enzymes with targeting modules, including dCas9, that can localize the enzymes to specific sites. In this review, we take a DNA modifying enzyme-centric view of recent advances. We highlight the variety of natural DNA-modifying enzymes-including DNA methyltransferases, oxygenases, deaminases, and glycosylases-that can be used for targeted editing and discuss how insights into the structure and function of these enzymes has further expanded editing potential by introducing enzyme variants with altered activities or by improving spatiotemporal control of modifications.

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“…This sensitivity is also observed for all oxidized mC derivatives (unpublished results). In a follow‐up mutagenesis study, it was demonstrated that RVD NG binds mC, but not C and hmC, whereas RVD N* (*=deletion) binds C and mC, but not hmC . In principle, the unique interaction abilities of the five cytosine nucleobases in human DNA (see chapter 1.2) should allow for a fully selective recognition by appropriately designed proteins.…”

Section: Design Of Protein Scaffolds With Selectivity For Oxidized MCmentioning

confidence: 99%

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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Programmable Sensors of 5-Hydroxymethylcytosine

Cited by 36 publications

References 38 publications

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

Harnessing natural DNA modifying activities for editing of the genome and epigenome

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

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