Academic journal article Genetics

Phylogenetic Analysis of 5'-Noncoding Regions from the ABA-Responsive Rab16/17 Gene Family of Sorghum, Maize and Rice Provides Insight into the Composition, Organization and Function of Cis-Regulatory Modules

Academic journal article Genetics

Phylogenetic Analysis of 5'-Noncoding Regions from the ABA-Responsive Rab16/17 Gene Family of Sorghum, Maize and Rice Provides Insight into the Composition, Organization and Function of Cis-Regulatory Modules

Article excerpt

ABSTRACT

Phylogenetic analysis of sequences from gene families and homologous genes from species of varying divergence can be used to identify conserved noncoding regulatory elements. In this study, phylogenetic analysis of 5'-noncoding sequences was optimized using rab17, a well-characterized ABA-responsive gene from maize, and five additional rab16/17 homologs from sorghum and rice. Conserved 5'-noncoding sequences among the maize, sorghum, and rice rab16/17 homologs were identified with the aid of the software program FootPrinter and by screening for known transcription-factor-binding sites. Searches for 7 of 8 (7/8)bp sequence matches within aligned 5'-noncoding segments of the rab genes identified many of the cis-elements previously characterized by biochemical analysis in maize rab17 plus several additional putative regulatory elements. Differences in the composition of conserved noncoding sequences among rab16/17 genes were related to variation in rab gene mRNA levels in different tissues and to response to ABA treatment using qRT-PCR. Absence of a GRA-like element in the promoter of sorghum dhn2 relative to maize rab17 was correlated with an ~85-fold reduction of dhn2 RNA in sorghum shoots. Overall, we conclude that phylogenetic analysis of gene families among rice, sorghum, and maize will help identify regulatory sequences in the noncoding regions of genes and contribute to our understanding of grass gene regulatory networks.

THE annotation of genome coding regions, intron/exon boundaries, and noncoding regulatory sequences is a central challenge in genome research. Annotation is significantly improved when genome sequences from related species are available for comparison (BOFFELLI et al. 2003; THOMAS et al. 2003; WEITZMAN 2003). Comparative analysis of the human and mouse genome sequences revealed that ~5% of these genomes are under functional constraint (WATERSTON et al. 2002). Surprisingly, only ~1.5% of the sequences under selection correspond to protein-coding sequences, underscoring the importance of noncoding regulatory sequences in genome function. Partly in response to this finding, the human genome project ENCODE was initiated to identify and elucidate the functions of the noncoding regulatory portions of the human genome sequence (COLLINS et al. 2003). Recent progress on sequencing plant genomes is creating a similar opportunity to identify and understand the function of noncoding regulatory sequences that regulate plant genes (HAO et al. 1998; ARABIDOPSIS GENOME INITIATIVE 2000; CHANDLER and BRENDEL 2002; RICE CHROMOSOME 10 SEQUENCING CONSORTIUM 2003).

The noncoding regulatory portion of eukaryotic genomes controls gene function through modulation of transcription initiation, RNA processing, RNA stability, translation, and chromatin structure. Promoter cis-regulatory elements that provide binding sites for transcription-factors (TFs) are of particular interest because they regulate gene transcription, guide development, and form the basis of gene regulatory networks (DAVIDSON et al. 2003). Like animal promoters, plant promoters contain regulatory modules composed of combinations of cis-elements that mediate changes in transcription in response to internal and external input. For example, an ~350-bp region of the promoter of maize rab17 contains a minimum of nine TF-binding sites that mediate responses to ABA and dehydration and regulate gene expression during seed and vegetative development (BUSK et al. 1997). Cis-elements are also important to define because phenotypic variation can be caused by mutations in these sequences. For example, sequence differences in the teosinte branched-1 promoter are correlated with changes in gene expression, morphology, and development associated with the evolution of cultivated maize from teosinte (WANG et al. 1999; CLARK et al. 2004). Similarly, sequence differences in a putative cis-element of the AP1 promoter have been proposed to be responsible for variation in vernalization requirements in wheat (YAN et al. …

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