Plant Gene Regulatory Networks

This volume presents protocols that analyze and explore gene regulatory networks (GRNs) at different levels in plants. This book is divided into two parts: Part I introduces different experimental techniques used to study genes and their regulatory interactions in plants. Part II highlights different computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. This part of the book also provides information on essential database resources that grant access to gene-regulatory and molecular interactions in different plant genomes, with a specific focus on Arabidopsis thaliana. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Plant Gene Regulatory Networks: Methods and Protocols is a valuable resource for scientists and researchers interested in expanding their knowledge of GRNs.

During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.

Gene regulatory networks are composed of molecular regulators such as transcription factors which bind short, non-coding DNA sequences. These sequences are also called cis-regulatory elements and are located in the promoter region of a gene. Transcription regulators form an interconnected regulatory network which integrates endogenous and environmental signals into changes in gene expression. Gene regulatory networks provide an insight about organization of plant cells and their functions. They consist of thousands of connections between the target genes and transcription factors. Together, they regulate many cellular functions. They also help in understanding the regulation of genes under various conditions. The book studies, analyses and upholds the pillars of gene regulatory networks and its utmost significance in modern times. From theories to research to practical applications, case studies related to all contemporary topics of relevance to this field have been included herein. As this field is emerging at a rapid pace, the contents of this book will help the readers understand the modern concepts and applications of the subject.

During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.

This volume aims to provide a timely view of the state-of-the-art in systems biology. The editors take the opportunity to define systems biology as they and the contributing authors see it, and this will lay the groundwork for future studies. The volume is well-suited to both students and researchers interested in the methods of systems biology. Although the focus is on plant systems biology, the proposed material could be suitably applied to any organism.

Regulation of transcription represents a major, controlling step in plant gene expression, as it determines the tissue-specific and developmental stage-specific activity of many genes. Changes in gene expression have been shown to underlie the responses to environmental cues and stresses, the response against pathogens, the regulation of metabolic pathways, and the regulation of photosynthesis, for example. Regulation by transcription factors is an integral part of a highly complex network. In recent years, research on the regulation of transcription has made impressive progress. This volume provides a broad overview of the regulation of transcription in plants, introducing the key elements, the way in which it works in practice, and the potential within plant biotechnology. It is directed at researchers and professionals in plant molecular biology, biochemistry and biotechnology.

This book covers various state-of-the-art techniques regarding the associations between transcription factors (TFs) and genes, with a focus on providing methodological and practical references for researchers. The contents cover diverse protocols and summaries of TFs including screening of TF-DNA interactions, detection of open chromatin regions, identification of epigenetic regulations, engineering TFs with genome editing tools, detection of transcriptional activities, computational analysis of TF networks, functions and druggabilities of TFs in biomedical research, and much more. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice from the experts to ensure successful research results. Authoritative and cutting-edge, Transcription Factor Regulatory Networks aims to benefit readers who are interested in using state-of-the-art techniques to study TFs and their myriad effects in cellular life.