title: Characterization of the tomato ARF gene family uncovers a multi-levels post-transcriptional regulation including alternative splicing.
abstract: BACKGROUND
  The phytohormone auxin is involved in a wide range of developmental processes and auxin signaling is known to modulate the expression of target genes via two types of transcriptional regulators, namely, Aux/IAA and Auxin Response Factors (ARF). ARFs play a major role in transcriptional activation or repression through direct binding to the promoter of auxin-responsive genes. The present study aims at gaining better insight on distinctive structural and functional features among ARF proteins.
  
  
  RESULTS
  Building on the most updated tomato (Solanum lycopersicon) reference genome sequence, a comprehensive set of ARF genes was identified, extending the total number of family members to 22. Upon correction of structural annotation inconsistencies, renaming the tomato ARF family members provided a consensus nomenclature for all ARF genes across plant species. In silico search predicted the presence of putative target site for small interfering RNAs within twelve Sl-ARFs while sequence analysis of the 5'-leader sequences revealed the presence of potential small uORF regulatory elements. Functional characterization carried out by transactivation assay partitioned tomato ARFs into repressors and activators of auxin-dependent gene transcription. Expression studies identified tomato ARFs potentially involved in the fruit set process. Genome-wide expression profiling using RNA-seq revealed that at least one third of the gene family members display alternative splicing mode of regulation during the flower to fruit transition. Moreover, the regulation of several tomato ARF genes by both ethylene and auxin, suggests their potential contribution to the convergence mechanism between the signaling pathways of these two hormones.
  
  
  CONCLUSIONS
  All together, the data bring new insight on the complexity of the expression control of Sl-ARF genes at the transcriptional and post-transcriptional levels supporting the hypothesis that these transcriptional mediators might represent one of the main components that enable auxin to regulate a wide range of physiological processes in a highly specific and coordinated manner.
authors.affiliation: Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France ; INRA, Génomique et Biotechnologie des Fruits, Auzeville, France.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Zouine
authors.affiliation: Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France ; INRA, Génomique et Biotechnologie des Fruits, Auzeville, France.
authors.forename: Yongyao
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France ; INRA, Génomique et Biotechnologie des Fruits, Auzeville, France.
authors.forename: Anne-Laure
authors.initials: AL
authors.lastname: Chateigner-Boutin
authors.affiliation: Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France ; INRA, Génomique et Biotechnologie des Fruits, Auzeville, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Mila
authors.affiliation: Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France ; INRA, Génomique et Biotechnologie des Fruits, Auzeville, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Frasse
authors.affiliation: Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France ; INRA, Génomique et Biotechnologie des Fruits, Auzeville, France.
authors.forename: Hua
authors.initials: H
authors.lastname: Wang
authors.affiliation: Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France ; INRA, Génomique et Biotechnologie des Fruits, Auzeville, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Audran
authors.affiliation: Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France ; INRA, Génomique et Biotechnologie des Fruits, Auzeville, France.
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Roustan
authors.affiliation: Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France ; INRA, Génomique et Biotechnologie des Fruits, Auzeville, France.
authors.forename: Mondher
authors.initials: M
authors.lastname: Bouzayen
mesh_terms: D020121:5' Untranslated Regions; D017398:Alternative Splicing; D016000:Cluster Analysis; D005638:Fruit / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000235:genetics*; D005810:Multigene Family; D016366:Open Reading Frames; D009928:Organ Specificity / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D034622:RNA Interference; D012323:RNA Processing, Post-Transcriptional; D020871:RNA Stability; D015533:Transcriptional Activation
chemical_list: D020121:5' Untranslated Regions; D010940:Plant Proteins