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Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Updated: Jul 11, 2025

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential.

Youtao Lu¹, Jaehee Lee², Jifen Li²

¹Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.

Nature Communications

|November 14, 2023

Summary

This summary is machine-generated.

Researchers developed CHEX-seq to map single-stranded DNA (ssDNA) within cells. This technique reveals the genome-wide ssDNA landscape and unexpectedly discovered catalytic activity in genomic ssDNA.

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Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

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The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Molecular Biology
Genomics
Cellular Biology

Background:

Genomic DNA (gDNA) dynamically transitions between single- and double-stranded forms during essential cellular processes like transcription, repair, and replication.
Understanding the distribution and function of single-stranded DNA (ssDNA) is crucial for cellular homeostasis.

Purpose of the Study:

To introduce and validate a novel method, CHEX-seq, for identifying and mapping ssDNA within individual cells.
To investigate the genome-wide ssDNA landscape and its dynamic regulation.
To explore potential functional roles of genomic ssDNA.

Main Methods:

CHEX-seq utilizes 3'-terminal blocked, light-activatable probes to initiate the synthesis of complementary DNA from ssDNA.
The synthesized complementary DNA is then sequenced to generate a genome-wide map of ssDNA.
The method was benchmarked in human K562 cells and applied to mouse and human brain cells, including spatially localized neurons.

Main Results:

CHEX-seq successfully mapped the genome-wide single-stranded chromatin landscape in situ.
The abundance of ssDNA was observed to be dynamically regulated in response to cellular perturbations.
Single-stranded regions were identified in both nuclear and mitochondrial DNA.
Surprisingly, specific ssDNA loci in mouse and human gDNA demonstrated catalytic activity for porphyrin metalation in vitro.

Conclusions:

CHEX-seq is a powerful tool for visualizing the ssDNA landscape at a single-cell resolution.
Genomic ssDNA is dynamically regulated and present in both nuclear and mitochondrial DNA.
Genomic ssDNA may possess intrinsic catalytic functions, suggesting a novel enzymatic role for endogenous DNA.