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ChIP and related techniques

Chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP) and cross-linking immunoprecipitation (CLIP) are related techniques to investigate the interaction between proteins and nucleic acids.


Chromatin Immunoprecipitation

Chromatin Immunoprecipitation (ChIP) is a method that uncovers the localization of interaction between proteins or protein modifications with certain genomic regions. For example, specific DNA sequence motifs interacting with transcription factors, remodeling complexes, epigenetic markers or histone variants can be revealed by ChIP. Importantly, ChIP interactions show a snapshot at a certain timepoint and therefore greatly depend on multiple factors such as physiological conditions, starvation, cell stimulation etc.

Basically, ChIP includes the following steps:

  • Chromatin crosslinking with formaldehyde
  • DNA fragmentation
  • Co-immunoprecipitation (Co-IP) of the cross-linked protein-DNA complexes using an antibody or Nanobody
  • Reverse cross-linking to release the DNA fragments
  • DNA sequencing

RNA immunoprecipitation

In contrast to ChIP, RNA immunoprecipitation (RIP) targets RNA-binding proteins or protein complexes and corresponding RNA sequences. The protein-RNA complex is pulled down with an antibody or Nanobody. Subsequently, the RNA sequences can be identified.



CLIP (cross-linking immunoprecipitation) is closely related to RNA immunoprecipitation (RIP). Unlike RIP, CLIP includes a UV cross-linking step for tethering protein to RNA.


Looking for references? Please check our literature database.

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