8 Result(s)
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Rahul M. Kohli
Life Sciences
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Article
Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects
Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulf...
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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...
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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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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
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
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...
