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PlantRegMap: charting functional regulatory maps in plants.

Feng Tian^1,2,3, De-Chang Yang^1,2, Yu-Qi Meng^1,2

¹State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China.

Nucleic Acids Research

|November 9, 2019

Summary

This summary is machine-generated.

PlantRegMap charts plant transcriptional regulatory maps by identifying millions of functional transcription factor binding sites and interactions. This resource aids researchers in decoding complex plant gene regulation systems.

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Area of Science:

Plant biology
Genomics
Bioinformatics

Background:

Understanding plant transcriptional regulation is crucial for crop improvement and ecological studies.
Existing databases like PlantTFDB provide valuable information on transcription factors (TFs).
There is a need for comprehensive maps of TF-DNA interactions and regulatory elements.

Purpose of the Study:

To upgrade PlantTFDB into a comprehensive plant regulatory data and analysis platform named PlantRegMap.
To identify and map functional transcription factor binding sites (TFBSs) and their interactions across diverse plant species.
To provide a valuable resource for decoding plant transcriptional regulatory systems.

Main Methods:

Updated TF annotations and introduced 'extended TF repertoires' (TFext) for newly sequenced species.
Developed the FunTFBS algorithm integrating TF binding affinities and evolutionary conservation.
Established genome-wide conservation landscapes for 63 representative plants.

Main Results:

Identified over 20 million functional TFBSs and two million functional TF-cis-element interactions for 21,346 TFs.
Generated functional regulatory maps for 63 plant species.
Launched PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) and a mirror site (http://plantregmap.gao-lab.org/) for public access.

Conclusions:

PlantRegMap offers a powerful, integrated platform for plant regulatory genomics research.
The identified functional TFBSs and interactions provide critical insights into plant gene regulation.
This resource will accelerate research in plant biology, breeding, and synthetic biology.