Original Research ARTICLE
Secondary wall regulating NACs differentially bind at the promoter at a CELLULOSE SYNTHASE A4 cis-eQTL
- 1Biology Department, University of Massachusetts Amherst, United States
Arabidopsis thaliana CELLULOSE SYNTHASE A4/7/8 (CESA4/7/8) are three non-redundant subunits of the secondary cell wall cellulose synthase complex. Transcript abundance of these genes can vary among genotypes and expression quantitative trait loci (eQTL) were identified in a recombinant population of the accessions Bay-0 and Shahdara. Genetic mapping and analysis of the transcript levels of CESAs between two distinct near isogenic lines confirmed a change in CESA4 expression that segregates within that interval. We sequenced the promoters and identified sixteen polymorphisms differentiating CESA4Sha and CESA4Bay. In order to determine which of these SNPs could be responsible for this eQTL, we screened for transcription factor protein affinity with promoter fragments of CESA4Bay, CESA4Sha, and the reference genome CESA4Col. The wall thickening activator proteins NAC SECONDARY WALL THICKENING PROMOTING FACTOR2 (NST2) and NST3 exhibited a decrease in binding with the CESA4Sha promoter with a tracheary element-regulating cis-element (TERE) polymorphism. While near isogenic lines harboring the TERE polymorphisms exhibited significantly different CESA4 expression, cellulose crystallinity and cell wall thickness were indistinguishable. These results suggest that the TERE polymorphism resulted in differential transcription factor binding and CESA4 expression; yet A. thaliana is able to tolerate this transcriptional variability without compromising the structural elements of the plant, providing insight into the elasticity of gene regulation as it pertains to cell wall biosynthesis and regulation. We also explored available DNA affinity purification sequencing data to resolve a core binding site, C(G/T)TNNNNNNNA(A/C)G, for secondary wall NACs referred to as the VNS element.
Keywords: CELLULOSE SYNTHASE A4, NAC transcription factor, Expression QTL, VNS element, tracheary element-regulating cis-element
Received: 11 Oct 2018;
Accepted: 06 Dec 2018.
Edited by:Charles T. Anderson, Pennsylvania State University, United States
Reviewed by:Kanwarpal S. Dhugga, Consultative Group on International Agricultural Research (CGIAR), United States
Nobutaka Mitsuda, National Institute of Advanced Industrial Science and Technology (AIST), Japan
Copyright: © 2018 Olins, Lin, Lee, Trabucco, MacKinnon and Hazen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Dr. Samuel P. Hazen, University of Massachusetts Amherst, Biology Department, Amherst, 01003, Massachusetts, United States, email@example.com