Transcriptomic Characterization of a Synergistic Genetic Interaction during Carpel Margin Meristem Development in Arabidopsis thaliana

Abstract

In flowering plants the gynoecium is the female reproductive structure. In Arabidopsis thaliana ovules initiate within the developing gynoecium from meristematic tissue located along the margins of the floral carpels. When fertilized the ovules will develop into seeds. SEUSS (SEU) and AINTEGUMENTA (ANT) encode transcriptional regulators that are critical for the proper formation of ovules from the carpel margin meristem (CMM). The synergistic loss of ovule initiation observed in the seu ant double mutant suggests that SEU and ANT share overlapping functions during CMM development. However the molecular mechanism underlying this synergistic interaction is unknown. Using the ATH1 transcriptomics platform we identified transcripts that were differentially expressed in seu ant double mutant relative to wild type and single mutant gynoecia. In particular we sought to identify transcripts whose expression was dependent on the coordinated activities of the SEU and ANT gene products. Our analysis identifies a diverse set of transcripts that display altered expression in the seu ant double mutant tissues. The analysis of overrepresented Gene Ontology classifications suggests a preponderance of transcriptional regulators including multiple members of the REPRODUCTIVE MERISTEMS (REM) and GROWTH-REGULATING FACTOR (GRF) families are mis-regulated in the seu ant gynoecia. Our in situ hybridization analyses indicate that many of these genes are preferentially expressed within the developing CMM. This study is the first step toward a detailed description of the transcriptional regulatory hierarchies that control the development of the CMM and ovule initiation. Understanding the regulatory hierarchy controlled by SEU and ANT will clarify the molecular mechanism of the functional redundancy of these two genes and illuminate the developmental and molecular events required for CMM development and ovule initiation.

Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain

“…Published in situ hybridization patterns indicate enriched medial domain expression patterns for REM34/ATREM1 and VDD/REM20 (FrancoZorrilla et al, 2002;Matias-Hernandez et al, 2010;Wynn et al, 2011). Additionally, the expression of AT5G60142, a previously unnamed member of the REM family, is enriched approximately 11-fold in the YFP-positive sample (Supplemental Table S3).…”

“…Members of the ABI3/VP1 transcription factor family that includes the REM and NGA family transcription factors were found to be statistically overrepresented (Supplemental Table S7; corrected P , 9.97E-06). The REMs belong to the plant-specific B3 superfamily of transcription factors, and the expression of many REM family members is observed in meristematic tissues, such as the inflorescence meristem, floral meristem, and CMM (Franco-Zorrilla et al, 2002;Swaminathan et al, 2008;Romanel et al, 2009;Wynn et al, 2011;Mantegazza et al, 2014aMantegazza et al, , 2014b. The numerical designations used to describe the REM family members in this article are taken from Romanel et al (2009).…”

“…This approach fits well with the data in this work, as samples do not cluster based on technology platforms but rather based on the apparent cell type similarities of gene reads per kilobase of transcript per million mapped reads (RPKM) expression levels. Wynn et al (2011) previously carried out a related transcriptomic study and identified many genes that were shown via in situ hybridization to be expressed preferentially in the developing medial domain of the wild-type gynoecium. When comparing the 95 enriched DEGs from our RNA-seq experiment (Supplemental Table S2; Supplemental Fig.…”

“…When comparing the 95 enriched DEGs from our RNA-seq experiment (Supplemental Table S2; Supplemental Fig. S3) with a set of 210 medial domain-enriched genes from Wynn et al (2011), 23 genes were found in common (Table III). The 24% overlap of these two gene sets is significantly higher than expected by chance (hypergeometric test, P = 3.15 3 10…”

“…However, due to the complexity of the developing gynoecium and the heterogeneity of the gynoecial tissues, the ability to analyze the transcriptomic signature of the developing CMM or even other specific developing gynoecial structural domains has been limited. Wynn et al (2011) previously evaluated the transcriptional properties of the gynoecial medial domain using hand-dissected gynoecial samples from the seuss aintegumenta (seu ant) double mutants that display a loss of many medial domainderived structures, including ovules. They identified 210 genes displaying reduced expression in seu ant gynoecia from floral stages 8 to 10 (stages according to Smyth et al [1990]).…”