April 15, 2014

Review: The Most Deeply Conserved Noncoding Sequences in Plants Serve Similar Functions to Those in Vertebrates Despite Large Differences in Evolutionary Rates

Published online before print March 2014, The Plant Cell tpc.113.121905

Diane Burgess* and Michael Freeling

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
* Corresponsing author

Several types of non-coding DNA serve regulatory functions in the genomes of plants. Burgess and Freeling1 report recently on conserved non-coding sequences (CNSs) in plants that apparently arose early in the evolution of life as they are also represented in vertebrates as long (>100 bp), highly conserved regulatory sequences that may lie megabases away from their targets, particularly in the case of mammals. Identifying such regulatory sequences in the non-coding regions of plants has been complicated by the fact that the corresponding sequences of plants are much shorter (approx. 25 bp) and have greater sequence variability. Burgess and Freeling apply robust bioinformatics methods to identify a group of 37 CNSs that are conserved among all flowering plants. Plants CNSs are also different from their vertebrate counterparts in that they are frequently no more than 11 kb away from their targets. They may occur either upstream or downstream of their targets, or in intronic regions within the target gene itself.
How CNSs function to regulate gene expression is not well understood, but these sequences are often highly enriched in transcription factor binding sites. G-boxes, which are frequent motifs in light responsive genes, are common in CNSs, as are WRKY-box motifs (related to biotic and abiotic stress responses) and MYC2 bind sites, which are closely linked to jasmonic acid responses.
Many of the intragenic CNSs identified by Burgess and Freeling form RNA secondary structures which convey their regulatory function. One example is the 3’UTR of THIC, which acts as a riboswitch, changing conformation by finding thiamine pyrophosphate which ultimately promotes alternative splicing and affects transcript stability2. CNSs may also play a role in alternative splicing, especially those located in alternative exons with premature stop codons.
Despite the highly conserved nature of these regulatory sequences across diverse plant lines, very few have been studied on a functional level. Until more functional data becomes available for these regulators, the function of most is largely the subject of speculation. However, comparisons can be drawn to vertebrate systems to gain some insight into their function, and Burgess and Freeling reference the different life strategies employed by animals and plants which may also reflect on how their respective CNSs have evolved. For instance, they note that polyploidy is a frequent occurrence in plant genomes and that this may be responsible for plant CNSs being shorter and less conserved than similar sequences in vertebrates since polyploidy may lead to a relaxation of the constraints which lead to conservation of sequence. It is also interesting to note that plants have evolved more efficient mechanisms to remove junk DNA from their genomes than animals. Animals typically rely on a slow pathway involving pseudogenization of redundant or non-functional genes whereas plant genomes remove redundant and functionless DNA through a deletion mechanism. Finally, the higher offspring number of plants means they can afford to lose larger numbers to purifying selection, which ultimately leads to shorter CNSs which evolve more quickly. The present work should provide a useful framework for contextualizing future discoveries of functional regulatory sequences, and facilitate the distinction of truly functional non-coding sequences from the significant portion of all eukaryotic genomes with no apparent function whatsoever.

1.         Burgess, D. & Freeling, M. The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates. Plant Cell (2014).
2.         Wachter, A. et al. Riboswitch control of gene expression in plants by splicing and alternative 3'end processing of mRNAs. Plant Cell 19, 3437-3450 (2007).

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