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GrainGenes Reference Report: PNA-99-6147

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Reference	PNA-99-6147
Title	Utility and distribution of conserved noncoding sequences in the grasses
Journal	Proceedings of the National Academy of Sciences, USA
Year	2002
Volume	99
Pages	6147-6151
Author	Kaplinsky NJ Braun DM Penterman J Goff SA Freeling M
Abstract	Summary: Control of gene expression requires cis-acting regulatory DNA sequences. Historically these sequences have been difficult to identify. Conserved noncoding sequences (CNSs) have recently been identified in mammalian genes through cross-species genomic DNA comparisons, and some have been shown to be regulatory sequences. Using sequence alignment algorithms, we compared genomic noncoding DNA sequences of the liguleless1 (lg1) genes in two grasses, maize and rice, and found several CNSs in lg1. These CNSs are present in multiple grass species that represent phylogenetically disparate lineages. Six other maize/rice genes were compared and five contained CNSs. Based on nucleotide substitution rates, these CNSs exist because they have biological functions. Our analysis suggests that grass CNSs are smaller and far less frequent than those identified in mammalian genes and that mammalian gene regulation may be more complex than that of grasses. CNSs make excellent pan-grass PCR-based genetic mapping tools. They should be useful as characters in phylogenetic studies and as monitors of gene regulatory complexity
External Databases	Pubmed: 11972021
Keyword	[ Hide all but 1 of 34 ] 30 algorithms alignment biological function cluster complexes complexity dna gene gene expression gene regulation genetic mapping genome genomic dna lineage maize maize leaf development mapping multiple nucleotide nucleotide substitution nucleotide substitution rates protein regulation regulatory elements regulatory sequence rice sensitivity sequence sequence alignment substitution tool utility washington

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