Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1629)

Abstract

Key transcription factors (TFs) controlling the morphogenesis of flowers and leaves have been identified in the model plant Arabidopsis thaliana. Recent genome-wide approaches based on chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) enable systematic identification of genome-wide TF binding sites (TFBSs) of these regulators. Here, we describe a computational pipeline for analyzing ChIP-seq data to identify TFBSs and to characterize gene regulatory networks (GRNs) with applications to the regulatory studies of flower development. In particular, we provide step-by-step instructions on how to download, analyze, visualize, and integrate genome-wide data in order to construct GRNs for beginners of bioinformatics. The practical guide presented here is ready to apply to other similar ChIP-seq datasets to characterize GRNs of interest.

Key words

Flower development Gene regulatory networks (GRNs) Transcription factors (TFs) DNA binding sites ChIP-seq Bioinformatics 
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Notes

Acknowledgments

K.K. wishes to thank the Alexander-von-Humboldt foundation and the BMBF for ongoing support.

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
  2. 2.Department for Plant Cell and Molecular Biology, Institute for BiologyHumboldt-Universität zu BerlinBerlinGermany

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