Recent developments in DNA and RNA sequencing technologies opened up the opportunity to improve understanding of the cis-regulatory code underlying plant development. An expanding collection of sequenced plant genomes allows biologists to study macro- and micro-evolution of cis-regulatory elements. Meanwhile, the growing number of bulk and single-cell transcriptome data allows studying the functionality of the cis-regulatory code in plant growth and response to the environment. Many cutting-edge methods are being developed or applied to various plant species to profile the genome-wide distributions of putative cis-regulatory features such as open chromatin regions, transcription factor-binding sites, conserved non-coding sequences, and enhancer elements. Highly efficient genome editing tools now make it possible to genetically interrogate the functional impacts of cis-regulatory elements.
The development of new bioinformatics methods and models, e.g. machine-learning (ML) approaches, is of great value for studying cis-regulatory code. However, we need plant biologists to apply new, as well as classical, approaches to study cis-regulatory code behind particular aspects of plant development and physiology. We encourage contributions on plant cis-regulatory elements in silico, in vitro, in vivo, or in planta.
The collection will include Original Research, Reviews, and Opinions about the following topics:
- study of a transcription factor binding profiles and targets in plants;
- analysis of cis-regulatory syntax and search for composite elements and modules;
- exploration of the repertoire of cis-elements behind a transcriptional response to environmental conditions or treatments;
- study of conservation in cis-regulatory sequences;
- experimental validation of cis-regulatory elements functionality;
- development and application of new methods to infer and annotate the cis-regulatory code.
Recent developments in DNA and RNA sequencing technologies opened up the opportunity to improve understanding of the cis-regulatory code underlying plant development. An expanding collection of sequenced plant genomes allows biologists to study macro- and micro-evolution of cis-regulatory elements. Meanwhile, the growing number of bulk and single-cell transcriptome data allows studying the functionality of the cis-regulatory code in plant growth and response to the environment. Many cutting-edge methods are being developed or applied to various plant species to profile the genome-wide distributions of putative cis-regulatory features such as open chromatin regions, transcription factor-binding sites, conserved non-coding sequences, and enhancer elements. Highly efficient genome editing tools now make it possible to genetically interrogate the functional impacts of cis-regulatory elements.
The development of new bioinformatics methods and models, e.g. machine-learning (ML) approaches, is of great value for studying cis-regulatory code. However, we need plant biologists to apply new, as well as classical, approaches to study cis-regulatory code behind particular aspects of plant development and physiology. We encourage contributions on plant cis-regulatory elements in silico, in vitro, in vivo, or in planta.
The collection will include Original Research, Reviews, and Opinions about the following topics:
- study of a transcription factor binding profiles and targets in plants;
- analysis of cis-regulatory syntax and search for composite elements and modules;
- exploration of the repertoire of cis-elements behind a transcriptional response to environmental conditions or treatments;
- study of conservation in cis-regulatory sequences;
- experimental validation of cis-regulatory elements functionality;
- development and application of new methods to infer and annotate the cis-regulatory code.
