Specific expression of LATERAL SUPPRESSOR is controlled by an evolutionarily conserved 3′ enhancer

Abstract

SUMMARYAerial plant architecture is largely based on the activity of axillary meristems (AMs), initiated in the axils of leaves. The Arabidopsis gene LATERAL SUPPRESSOR (LAS), which is expressed in well-defined domains at the adaxial boundary of leaf primordia, is a key regulator of AM formation. The precise definition of organ boundaries is an essential step for the formation of new organs in general and for meristem initiation; however, mechanisms leading to these specific patterns are not well understood. To increase understanding of how the highly specific transcript accumulation in organ boundary regions is established, we investigated the LAS promoter. Analysis of deletion constructs revealed that an essential enhancer necessary for complementation is situated about 3.2 kb downstream of the LAS open reading frame. This enhancer is sufficient to confer promoter specificity as upstream sequences in LAS could be replaced by non-specific promoters, such as the 35S minimal promoter. Further promoter swapping experiments using the PISTILLATA or the full 35S promoter demonstrated that the LAS 3¢ enhancer also has suppressor functions, largely overwriting the activity of different 5¢ promoters. Phylogenetic analyses suggest that LAS function and regulation are evolutionarily highly conserved. Homologous elements in downstream regulatory sequences were found in all LAS orthologs, including grasses. Transcomplementation experiments demonstrated the functional conservation of non-coding sequences between Solanum lycopersicum (tomato) and Arabidopsis. In summary, our results show that a highly conserved enhancer/suppressor element is the main regulatory module conferring the boundary-specific expression of LAS.

Separate elements of the TERMINAL FLOWER 1 cis-regulatory region integrate pathways to control flowering time and shoot meristem identity

“…Although examples exist of essential cis-regulatory elements located at the 3′ end of plant genes, they are relatively scarce (Larkin et al, 1993;Brand et al, 2002;Konishi and Yanagisawa, 2011;Raatz et al, 2011). As discussed by Raatz et al (2011), this could reflect the fact that not enough attention has been paid to possible 3′ cis-regulatory elements in studies on plant promoters.…”

“…Although examples exist of essential cis-regulatory elements located at the 3′ end of plant genes, they are relatively scarce (Larkin et al, 1993;Brand et al, 2002;Konishi and Yanagisawa, 2011;Raatz et al, 2011). As discussed by Raatz et al (2011), this could reflect the fact that not enough attention has been paid to possible 3′ cis-regulatory elements in studies on plant promoters. Other studies (Castaings et al, 2014), however, indicate that sequence conservation in the 3′ end of orthologous plant genes is not so common, which might suggest that relevant cis-regulatory elements are not frequently located in their 3′ intergenic regions.…”

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

“…While many CNS are expected to function as cis-regulatory regions involved in regulating transcription and chromatin structure, the specific function of most plant CNSs remains unknown (Freeling and Subramaniam, 2009). As with mammals (Loots et al, 2000), there are several cases in plants of CNSs being proved to contain functioning cis-regulatory regions, as reviewed (Freeling and Subramaniam, 2009) and (Raatz et al, 2011). An early genome-wide analysis of CNSs in plants focused on duplicate genes in arabidopsis ( Arabidopsis thaliana, At ) resulting from an ancient whole genome duplication (Thomas et al, 2007).…”

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

“…Thus, enhancers can be located in the front or at the ends of genes, within or far away from genes, which makes enhancers significantly more difficult to identify than promoters. Remarkably, only a handful of enhancers, especially those that are located in intergenic regions, have been identified in plants (Yang et al, 2005;Clark et al, 2006;McGarry and Ayre, 2008;Schauer et al, 2009;Raatz et al, 2011).…”