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Article
Peptide cyclization catalysed by the thioesterase domain of tyrocidine synthetase
In the biosynthesis of many macrocyclic natural products by multidomain megasynthases, a carboxy-terminal thioesterase (TE) domain is involved in cyclization and product release1,2; however, it has not been deter...
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Article
Biomimetic synthesis and optimization of cyclic peptide antibiotics
Molecules in nature are often brought to a bioactive conformation by ring formation (macrocyclization)1. A recurrent theme in the enzymatic synthesis of macrocyclic compounds by non-ribosomal and polyketide synth...
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Article
Grand Challenge Commentary: The chemistry of a dynamic genome
In the postsequencing era, chemical biology is uniquely situated to investigate genomic DNA alterations arising through epigenetic modifications, genetic rearrangements or active mutation. These transformation...
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Article
AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation
AID/APOBEC deaminases, which convert cytosine bases to uracils in DNA and RNA, have recently been assigned a role in epigenetic regulation as components of DNA demethylation pathways. A systematic study shows ...
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Article
TET enzymes, TDG and the dynamics of DNA demethylation
DNA methylation has a profound impact on genome stability, transcription and development. Although enzymes that catalyse DNA methylation have been well characterized, those that are involved in methyl group re...
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Article
Mechanisms for targeted, purposeful mutation revealed in an APOBEC–DNA complex
Targeted deamination of cytosine bases in DNA by AID/APOBEC-family enzymes is critical for proper immune function, but it also poses risks to genomic integrity. New structures reported by Harris, Aihara and co...
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Article
Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine
Saturation mutagenesis, molecular modeling and biochemical analysis revealed that active site interactions involving Thr1372 of TET2 are responsible for controlling its proficiency for stepwise oxidation of 5-...
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Article
Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells
Cancer immunotherapy based on genetically redirecting T cells has been used successfully to treat B cell malignancies1–3. In this strategy, the T cell genome is modified by integration of viral vectors or transpo...
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Article
Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase
A bisulfite-free sequencing method yields high-confidence 5hmC profiles in low-input samples.
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Article
A vitamin-C-derived DNA modification catalysed by an algal TET homologue
Methylation of cytosine to 5-methylcytosine (5mC) is a prevalent DNA modification found in many organisms. Sequential oxidation of 5mC by ten-eleven translocation (TET) dioxygenases results in a cascade of add...
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Article
Open AccessHigh-performance CRISPR-Cas12a genome editing for combinatorial genetic screening
CRISPR-based genetic screening has revolutionized cancer drug target discovery, yet reliable, multiplex gene editing to reveal synergies between gene targets remains a major challenge. Here, we present a simpl...
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Article
Open AccessModular affinity-labeling of the cytosine demethylation base elements in DNA
5-methylcytosine is the most studied DNA epigenetic modification, having been linked to diverse biological processes and disease states. The elucidation of cytosine demethylation has drawn added attention the ...
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Protocol
High-Resolution Analysis of 5-Hydroxymethylcytosine by TET-Assisted Bisulfite Sequencing
DNA cytosine modification is an important epigenetic mechanism that serves critical functions in a variety of biological processes in development and disease. 5-Methylcytosine (5mC) and 5-hydroxymethylcytosine...
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Protocol
Harnessing Alternative Substrates to Probe TET Family Enzymes
TET family enzymes normally oxidize 5-methylcytosine (5mC) in DNA, and play critical roles in sha** the epigenome. Despite their importance, assessing TET activity can be difficult, particularly given the ch...
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Protocol
Bisulfite-Free Sequencing of 5-Hydroxymethylcytosine with APOBEC-Coupled Epigenetic Sequencing (ACE-Seq)
Here, we provide a detailed protocol for our previously published technique, , which localizes 5-hydroxymethylcytosine at single nucleotide resolution using nanogram quantities of input genomic DNA. In addit...
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Article
Controllable genome editing with split-engineered base editors
DNA deaminase enzymes play key roles in immunity and have recently been harnessed for their biotechnological applications. In base editors (BEs), the combination of DNA deaminase mutator activity with CRISPR–C...
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Article
Direct enzymatic sequencing of 5-methylcytosine at single-base resolution
5-methylcytosine (5mC) is the most important DNA modification in mammalian genomes. The ideal method for 5mC localization would be both nondestructive of DNA and direct, without requiring inference based on de...
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Article
Open AccessExpanded palette of RNA base editors for comprehensive RBP-RNA interactome studies
RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and ST...
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Article
Efficient engineering of human and mouse primary cells using peptide-assisted genome editing
Simple, efficient and well-tolerated delivery of CRISPR genome editing systems into primary cells remains a major challenge. Here we describe an engineered Peptide-Assisted Genome Editing (PAGE) CRISPR–Cas sys...
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Article
The LexA–RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation
The bacterial SOS response plays a key role in adaptation to DNA damage, including genomic stress caused by antibiotics. SOS induction begins when activated RecA*, an oligomeric nucleoprotein filament that for...
