Genome-wide Cleavage Sites
Genome-wide Cleavage Sites - Related Videos
10:43
Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
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Cited by 11 •
2017
We describe chromatin endogenous cleavage coupled with high-throughput sequencing (ChEC-seq), a chromatin immunoprecipitation (ChIP)-orthogonal method for mapping protein binding sites genome-wide with micrococcal nuclease (MNase) fusion proteins.
11:50
Genome-Wide Mapping of Histone Modifications and Transcription Factor Binding Sites in Neuroendocrine Small Cell Lung Cancer Cell Lines Using CUT&RUN
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2026
An optimized Cleavage Under Targets and Release Using Nuclease followed by next generation sequencing (CUT&RUN-seq) protocol is described for neuroendocrine small cell lung cancer cell lines. It enables genome-wide mapping of various histone modifications and transcription factor (e.g. E2F7) binding sites to investigate epigenetic and transcriptional deregulation in SCLC pathobiology.
11:19
Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
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Cited by 13 •
2010
Here we are presenting a chromatin immunoprecipitation (ChIP) procedure for genome-wide location analysis of protein isoforms that differ in a histone-binding domain. We are applying it to ChIP-Seq analysis to identify the targets of the KDM5A/JARID1A/RBP2 histone demethylase.
14:26
Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
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Cited by 59 •
2016
This paper presents a sensitive method called Circle-Seq for purifying extrachromosomal circular DNA (eccDNA). The method encompasses column purification, removal of remaining linear chromosomal DNA, rolling-circle amplification and high-throughput sequencing. Circle-Seq is applicable to genome-scale screening of eukaryotic eccDNA and studying genome instability and copy-number variation.
08:40
Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library
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Cited by 1 •
2012
The Target ID Library is a plasmid-based, genome-wide collection of cloned cDNA used to identify miRNA targets. Here we demonstrate its use and application.
FAQs
Cleavage patterns depend on both the nuclease’s sequence-recognition behavior and the surrounding chromosomal environment. A target sequence alone does not fully determine where activity occurs, because chromatin context can influence access to DNA. Mapping cleavage positions therefore helps distinguish sequence-driven specificity from effects associated with genome organization and reveals why nuclease activity varies across genomic regions.
Double- and single-strand breaks represent different forms of DNA damage and can produce different repair consequences. Recording which type of break is associated with a cleavage event makes the resulting map more informative than simply counting affected locations. This distinction supports interpretation of nuclease activity, DNA repair outcomes, and potential effects on genome stability.
The distribution shows whether activity is concentrated at intended targets or appears at additional genomic positions. Enrichment near the designed site can support evidence of editing efficiency, whereas cleavage elsewhere identifies possible off-target breaks. Comparing these patterns helps researchers evaluate how precisely a nuclease recognizes DNA and guides improvements in genome-engineering strategies.
Researchers identify these sites by capturing DNA ends produced by cleavage events and then sequencing or enriching fragments near those breaks. The resulting sequence information is aligned with genomic positions to generate a cleavage-site map. This workflow converts otherwise dispersed DNA-damage signals into location-based evidence that can be used to assess nuclease activity across the genome.
Maps of cleavage positions provide a way to measure editing efficiency while also checking for unintended breaks. They can reveal whether a CRISPR-based or other engineered nuclease acts predominantly at its intended location or produces additional cleavage elsewhere. These results inform assessments of editing precision and help guide efforts to improve the safety of genome engineering.
Cleavage-site data connect nuclease activity with the genomic locations where repair processes respond to DNA damage. Researchers can use these maps alongside repair-outcome measurements to study how breaks are resolved and whether damage is distributed broadly or selectively. This makes the approach useful for examining genome stability as well as the genetic consequences of engineered cleavage.