Mapping Recombination Initiation Sites Using Chromatin Immunoprecipitation

  • Yan He
  • Minghui Wang
  • Qi Sun
  • Wojciech P. PawlowskiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1429)


Genome-wide maps of recombination sites provide valuable information not only on the recombination pathway itself but also facilitate the understanding of genome dynamics and evolution. Here, we describe a chromatin immunoprecipitation (ChIP) protocol to map the sites of recombination initiation in plants with maize used as an example. ChIP is a method that allows identification of chromosomal sites occupied by specific proteins. Our protocol utilizes RAD51, a protein involved in repair of double-strand breaks (DSBs) that initiate meiotic recombination, to identify DSB formation hotspots. Chromatin is extracted from meiotic flowers, sheared and enriched in fragments bound to RAD51. Genomic location of the protein is then identified by next-generation sequencing. This protocol can also be used in other species of plants, animals, and fungi.

Key words

Chromosomes Chromatin Immunoprecipitation Antibody Maize Recombination Double-strand breaks (DSBs) 



Research to develop this protocol was supported by a grant from National Science Foundation (IOS-1025881) to WPP.


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Yan He
    • 1
  • Minghui Wang
    • 2
  • Qi Sun
    • 3
  • Wojciech P. Pawlowski
    • 4
    Email author
  1. 1.National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
  2. 2.Institute of Biotechnology, Biotechnology Resource Center and Section of Plant Biology in School of IntegrativePlant ScienceCornell UniversityIthacaUSA
  3. 3.Institute of Biotechnology, Biotechnology Resource CenterCornell UniversityIthacaUSA
  4. 4.Section of Plant Biology, School of Integrative Plant ScienceCornell UniversityIthacaUSA

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