Applications | Chromatin shearing

Chromatin Shearing

Chromatin immunoprecipitation (ChIP) is a common method to accurately study the regulation of gene expression at the protein level. ChIP is an ideal method to uncover how a specific protein interacts with the genome.

 

The steps for a successful ChIP experiment are:

  • Cell fixation (cross-linking) of chromatin-bound proteins such as histones or transcription factors to DNA followed by cell lysis
  • Shearing of chromatin (cross-linked DNA-protein complex) by sonication to optimal fragment sizes (up to 1000 bp; depending on the desired downstream application)
  • Capturing the protein-DNA complexes using specific ChIP grade or ChIP-seq grade antibodies against the histone or transcription factor of interest
  • Reversal of cross-links followed by proteinase K treatment and DNA purification
  • Analysis of purified DNA to identify the genomic regions where the specific protein was located by either qPCR, hybridization to microarrays (ChIP-chip) or by high-throughput ChIP-sequencing (ChIP-seq)

 

The most important steps for a succesful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, Diagenode's Bioruptor® uses state-of-the-art ultrasound ACT (Adaptive Cavitation Technology) to efficiently shear chromatin. ACT enables the highest chromatin quality for high IP efficiency and sensitivity for ChIP experiments with gentle yet highly effective shearing forces. Additionally, the Bioruptor® provides a precisely controlled temperature environment that preserves chromatin from heat degradation such that protein-DNA complexes are well-preserved for sensitive, unbiased, and accurate ChIP.

Diagenode's Bioruptor® is the instrument of choice for chromatin shearing used for a number of downstream applications such as qPCR and ChIP-seq that require optimally sheared, unbiased chromatin.

  Bioruptor® Sonicator Competitor C Sonicator Tip/Probe Sonicators
Desirable fragment sizes for sequencing NO
Consistent fragment sizes from 100 bp - 1000+ bp NO
Multiplexing capability NO NO
High-troughput NO NO
Simple operation
Consistency between samples within runs NO
100% recovery of sample NO NO
Cost of operation Low High Low
Value High Low Low

* Comparison made between the Bioruptor®, Competitor C and Tip/Probe sonicators

The Ultimate Guide for Chromatin Shearing Optimization with Bioruptor® | Download

>> See all the protocols

  Compatible models
Bioruptor® Pico
Bioruptor® Standard
Bioruptor® Plus
>> Learn more about specifications of the different Bioruptor® models.

>> See all applications possible with Bioruptor® technology.
Over 650 publications cited the Bioruptor
Over 650 publications cited the Bioruptor

Bioruptor® Plus

Time course sonication experiment with the Bioruptor Plus

Time course sonication experiment with the Bioruptor® PLUS using the buffers and protocol from Diagenode's Chromatin Shearing Optimization kit - Medium SDS

Chromatin Shearing Guide cover

Chromatin Shearing Guide