μChIP-seq for genome-wide mapping of in vivo TF-DNA interactions in Arabidopsis root protoplasts

Alessia Para*, Ying Li, Gloria M. Coruzzi

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

Abstract

Chromatin immunoprecipitation (ChIP) is a widely used method to map the position of DNA-binding proteins such as histones and transcription factors (TFs) upon their interaction with particular regions of the genome. To examine the genomic distribution of a TF in specific cell types in response to a change in nitrogen concentration, we developed a micro-ChIP (μChIP) protocol that requires only ~5000 Arabidopsis cells transiently expressing the Arabidopsis TF Basic Leucine Zipper 1 (bZIP1) fused to the glucocorticoid receptor (GR) domain that mediates nuclear import in the presence of dexamethasone. The DNA fragments obtained from the immunoprecipitation of bZIP1-DNA complexes were analyzed by next-generation sequencing (ChIP-seq), which helped uncover genome-wide associations between a bZIP1 and its targets in plant cells upon fluctuations in nitrogen availability.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages249-261
Number of pages13
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1761
ISSN (Print)1064-3745

Keywords

  • Chromatin immunoprecipitation
  • Cross-linking
  • Library preparation
  • Next-generation sequencing
  • Plant protoplasts
  • Transcription factor

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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    Para, A., Li, Y., & Coruzzi, G. M. (2018). μChIP-seq for genome-wide mapping of in vivo TF-DNA interactions in Arabidopsis root protoplasts. In Methods in Molecular Biology (pp. 249-261). (Methods in Molecular Biology; Vol. 1761). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7747-5_19