ChIP in series: Sequential ChIP

Chapter

Abstract

  • In eukaryotes, essential processes in the nucleus such as transcription, replication, or DNA repair are carried out in the context of chromatin, a highly complex and variable structure consisting of DNA and proteins. Given its importance in regulating these crucial cellular activities, chromatin has been the focus of study for over 100 years. The advent of chromatin immunoprecipitation (ChIP) techniques has revolutionized the study of chromatin, as it allowed the precise mapping of chromatin components across the genome for the first time. However, while chromatin is highly complex, and multiple proteins are found regularly at the same genomic location, ChIP is able to only assay one chromatin component at a time. Sequential ChIP, also called re-ChIP, circumvents this limitation by utilizing back-to-back ChIP reactions to assay the co-occurrence of multiple chromatin components. Sequential ChIP has been used to address a variety of questions in the chromatin field, revealing for example the existence of so-called bivalent domains. In this review, we provide an overview of the techniques available to study the co-occurrence of chromatin proteins up to and including the invention of sequential ChIP. We highlight the advantages of sequential ChIP compared to other methods and discuss challenges remaining with this technique, in particular regarding experimental design and analysis.
  • Digital Object Identifier (doi)

    International Standard Book Number (isbn) 13

  • 9780128194140
  • Start Page

  • 297
  • End Page

  • 321