Articles
Genome-wide exploration of transcription factor targets through DAPBrowse: a DAP-seq data genome-browser hosted in the Vitis Visualization platform
Article number
1390_25
Pages
205 – 210
Language
English
Abstract
Transcription factors (TFs) act on cis-regulatory DNA sequences that determine when, where, and how genes are expressed.
Several studies in plant model species have shown that development-related TFs are able to bind thousands of genes and directly regulate the expression of a considerable fraction of them.
However, the extent of this massive regulation (a term also referred to as orchestration) has not been explored for specialized metabolism-related regulators.
In grapevine, many TFs controlling specialized metabolism have been characterized to date but just a few targets are known for most of them, representing an ideal case for addressing the extent of their binding landscapes (cistromes). Accordingly, we have examined the cistromes of previously characterized R2R3-MYB regulators using the in vitro genome-wide approach, DNA affinity purification sequencing (DAP-seq). We demonstrate how this approach can also be used to identify novel pathway genes which can later be characterized.
To visualize the cistromes of different TFs we have created a Jbrowse-based application called DAPBrowse, which is currently hosted for the grapevine community.
This application provides a way to explore DAP-seq data for specialized metabolism TFs in the context of all recent PN40024 genome assemblies.
The application is provided as part of the Vitis Visualization (VitViz) platform, a publicly available resource with a range of analytical and visualization tools for grapevine.
Several studies in plant model species have shown that development-related TFs are able to bind thousands of genes and directly regulate the expression of a considerable fraction of them.
However, the extent of this massive regulation (a term also referred to as orchestration) has not been explored for specialized metabolism-related regulators.
In grapevine, many TFs controlling specialized metabolism have been characterized to date but just a few targets are known for most of them, representing an ideal case for addressing the extent of their binding landscapes (cistromes). Accordingly, we have examined the cistromes of previously characterized R2R3-MYB regulators using the in vitro genome-wide approach, DNA affinity purification sequencing (DAP-seq). We demonstrate how this approach can also be used to identify novel pathway genes which can later be characterized.
To visualize the cistromes of different TFs we have created a Jbrowse-based application called DAPBrowse, which is currently hosted for the grapevine community.
This application provides a way to explore DAP-seq data for specialized metabolism TFs in the context of all recent PN40024 genome assemblies.
The application is provided as part of the Vitis Visualization (VitViz) platform, a publicly available resource with a range of analytical and visualization tools for grapevine.
Authors
D. Navarro-Payá, L. Orduña, C. Zhang, A. Santiago, N. Francillonne, M. Li, A.-F. Adam-Blondon, C. Huang, J.T. Matus
Keywords
Vitis, visualisation tools, transcription factors, cistromes, DNA affinity purification sequencing
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