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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
Sanger Sequencing01:57

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...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Video

Updated: May 13, 2026

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter
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Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Published on: March 31, 2022

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.

Nicola Crosetto1, Abhishek Mitra, Maria Joao Silva

  • 1Institute of Biochemistry II, Goethe University Medical School, Frankfurt, Germany. crosetto@mit.edu

Nature Methods
|March 19, 2013
PubMed
Summary
This summary is machine-generated.

We developed BLESS, a novel method to map DNA double-strand breaks (DSBs) genome-wide at nucleotide resolution. This technique identifies regions sensitive to replication stress, many of which are implicated in human cancers.

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Published on: October 6, 2014

Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • DNA double-strand breaks (DSBs) are critical DNA lesions.
  • Understanding their genomic distribution is essential for cellular processes and disease.
  • Existing methods lack nucleotide resolution and genome-wide coverage.

Purpose of the Study:

  • To present a novel, high-resolution genome-wide method for mapping DSBs.
  • To characterize the genomic landscape of replication stress sensitivity.
  • To identify potential links between replication stress sensitivity and cancer.

Main Methods:

  • Developed BLESS (direct in situ breaks labeling, enrichment on streptavidin and next-generation sequencing).
  • Validated BLESS in human and mouse cells using various DSB-inducing agents and sequencing platforms.
  • Applied BLESS to map aphidicolin-sensitive regions (ASRs) in human cells.

Main Results:

  • BLESS accurately detected various DSB types, including telomere ends and endonuclease-induced breaks.
  • Identified over 2,000 nonuniformly distributed ASRs, enriched in genes and satellite repeats.
  • ASRs were found in cancer-rearranged regions, with cancer-associated genes showing high replication stress sensitivity.

Conclusions:

  • BLESS provides a powerful tool for high-resolution, genome-wide DSB mapping across diverse conditions.
  • Revealed a genomic landscape of replication stress sensitivity linked to cancer.
  • Highlights the role of replication stress in cancer development.