Transcriptional Regulation: a Genomic Overview

Abstract

The availability of the Arabidopsis thaliana genome sequence allows a comprehensive analysis of transcriptional regulation in plants using novel genomic approaches and methodologies. Such a genomic view of transcription first necessitates the compilation of lists of elements. Transcription factors are the most numerous of the different types of proteins involved in transcription in eukaryotes, and the Arabidopsis genome codes for more than 1,500 of them, or approximately 6% of its total number of genes. A genome-wide comparison of transcription factors across the three eukaryotic kingdoms reveals the evolutionary generation of diversity in the components of the regulatory machinery of transcription. However, as illustrated by Arabidopsis, transcription in plants follows similar basic principles and logic to those in animals and fungi. A global view and understanding of transcription at a cellular and organismal level requires the characterization of the Arabidopsis transcriptome and promoterome, as well as of the interactome, the localizome, and the phenome of the proteins involved in transcription. Introduction. The Arabidopsis Book ©2002 American Society of Plant BiologistsFirst published on April 4, 2002 doi: 10.1199/tab.0085 : e0085. The Arabidopsis Book 2 of 46In addition, gene expression profiling technologies, such as DNA microarrays, allow monitoring transcription factor activity at a genome-wide level. These studies should eventually lead to an understanding of the interplay of the transcription factors with the genome whose expression they control.This chapter intends to provide a genomic perspective on transcriptional regulation in Arabidopsis. The first section briefly reviews the different types of proteins directly involved in transcription in eukaryotes, and our current understanding on how they function. The following sections consist of a description of the Arabidopsis complement of genes and proteins involved in transcriptional control, in particular sequence-specific DNA-binding transcription factors and chromatin-related proteins. Transcriptional regulators often act in a combinatorial fashion, and this mode of action is reviewed in the context of Arabidopsis promoters and cis-regulatory sequences, and of protein-protein interactions. Finally, genome-wide functional analyses of transcription factors, the characterization of the Arabidopsis promoterome, and of the transcriptome by gene expression profiling experiments, are considered. The availability of the genome sequence of different prokaryotic and eukaryotic organisms has provided for new ways of searching for unity and diversity among biological systems, and given birth to the field of comparative genomics. Although the subject of this book is Arabidopsis, reference is made in this chapter to other eukaryotic organisms, in order to situate the Arabidopsis genome information in a broader biological context. Transcription machinery: concepts, components, and mechanismsIn eukaryotic organisms, regulation of gene expression proceeds ...

The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development

“…4). This confirms the preliminary finding of Windhö vel et al (2001) and definitively places this group of factors in a class of their own (Riechmann, 2002). Furthermore, the phylogenetic analyses suggest that certain ZF-HD family members are more closely related to each other than to other members (Fig.…”

“…The ZF (CX1NHAX 3 GX 4 DGCXEFX 8-15 CX 2 CXCHRXFH) is characterized by a CHCC3H2 motif with a variable length spacer between the first CHC residues and the more carboxy terminal C3H2 residues. It forms a distinct group compared with other ZF motifs characterized in Arabidopsis (Takatsuji, 1998;Riechmann, 2002). The length of the spacer may have a crucial role in dimerization, since members with shorter spacers do not appear to effectively dimerize with other members of the ZF-HD family (see below).…”

“…In Arabidopsis (Arabidopsis thaliana), about 100 HDencoding genes have been identified, and they belong to a few specific classes (Chan et al, 1998;Riechmann, 2002). The members of these classes share not only sequence similarity, but in general they play related roles in planta as well.…”

TheArabidopsis JAGGEDgene encodes a zinc finger protein that promotes leaf tissue development

“…5B). JAG belongs to a large family of C2H2-type zinc finger transcription factors that contains 112 members in Arabidopsis (Riechmann, 2002). JAG contains a single 31 amino acid single C2H2-type zinc finger motif (amino acid positions 51-81) that may have a function in DNA binding.…”

Gene network analysis in plant development by genomic technologies

“…These methods have been reviewed elsewhere (Riechmann, 2002) and therefore will not be described in detail here; rather, we illustrate with some examples how they are currently being used for the analysis of development.…”