Transcriptome profiling of Arabidopsis tac1 and lazy1 mutant shoot tips under normal and gravistimulated conditions

This data is was generated in connection with a study on the 'Opposing influences of TAC1 and LAZY1 on Lateral Shoot Orientation in Arabidopsis'. RNA was extracted from individual shoot tips from wild type (Columbia; Col), tac1, and lazy1 plants that experienced either 0 or 45 minutes of gravistimulation by 90-degree reorientation. The summary of the entire project is as follows: TAC1 and LAZY1 are members of a gene family that regulates lateral shoot orientation in plants. TAC1 promotes outward orientations in response to light, while LAZY1 promotes upward shoot orientations in response to gravity via altered auxin transport. We performed genetic, molecular, and biochemical assays to investigate possible interactions between these genes. In Arabidopsis they were expressed in similar tissues and double mutants revealed the wide-angled lazy1 branch phenotype, indicating it is epistatic to the tac1 shoot phenotype. Surprisingly, the lack of TAC1 did not influence gravitropic shoot curvature responses. Combined, these results suggest TAC1 might negatively regulate LAZY1 to promote outward shoot orientations. However, additional results revealed that TAC1- and LAZY1 influence on shoot orientation is more complex than a simple direct negative regulatory pathway. Transcriptomes of Arabidopsis tac1 and lazy1 mutants compared to wild type under normal and gravistimulated conditions revealed few overlapping differentially expressed genes. Overexpression of each gene did not result in major branch angle differences. Shoot tip hormone levels were similar between tac1, lazy1, and Col, apart from exceptionally elevated levels of salicylic acid in lazy1. The data presented here provide a foundation for future study of TAC1 and LAZY1 regulation of shoot architecture. Overall design: Arabidopsis plants containing only a single inflorescence shoot, with a height of ~15-18 cm, and no more than 3 lateral shoots (each no larger than ~1 cm) were used for expression profiling. Prior to collection, plants were left for at least 12 hours in a dark chamber with wooden stakes to support primary shoots to ensure they would be vertical at the time of collection. Primary shoot tips from upright (t0) plants and plants after 45 minutes of gravistimulation in the dark by a 90° reorientation (t45 plants) were collected on the same day. The t0 collections were at ~10 AM and t45 collections were at ~10:45 AM (having been reoriented at ~10 AM). From all plants, the upper most ~1 cm of primary shoot apical tissue (minus any leaves, flowers, or opening buds) was harvested and immediately frozen in liquid nitrogen. Total RNA was extracted from apical tissues using the Qiagen Plant Mini RNeasy kit (Germantown, MD) including a DNAse treatment with Invitrogen Turbo DNA-free (Carlsbad, CA). Approximately 2 ug of total RNA for each sample was sent to the Cornell Weill Medical Genomics Resources Core Facility (New York, NY, USA) where RNA TruSeq 50 bp unpaired barcoded libraries were prepared for each and sequenced with nine libraries per lane on an Illumina HiSeq 2000.