title: Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain.
abstract: Plant meristems, like animal stem cell niches, maintain a pool of multipotent, undifferentiated cells that divide and differentiate to give rise to organs. In Arabidopsis (Arabidopsis thaliana), the carpel margin meristem is a vital meristematic structure that generates ovules from the medial domain of the gynoecium, the female floral reproductive structure. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present a novel approach to analyze the transcriptional signature of the medial domain of the Arabidopsis gynoecium, highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development. Using a floral synchronization system and a SHATTERPROOF2 (SHP2) domain-specific reporter, paired with FACS and RNA sequencing, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. This analysis reveals a set of genes that are differentially expressed within the SHP2 expression domain, including genes that have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Global analyses of the transcriptomic data set indicate a similarity of the pSHP2-expressing cell population to previously characterized meristematic domains, further supporting the meristematic nature of this gynoecial tissue. Our method identifies additional genes including novel isoforms, cis-natural antisense transcripts, and a previously unrecognized member of the REPRODUCTIVE MERISTEM family of transcriptional regulators that are potential novel regulators of medial domain development. This data set provides genome-wide transcriptional insight into the development of the carpel margin meristem in Arabidopsis.
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Gonzalo H
authors.initials: GH
authors.lastname: Villarino
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Qiwen
authors.initials: Q
authors.lastname: Hu
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Silvia
authors.identifier: 0000-0001-6241-4143
authors.initials: S
authors.lastname: Manrique
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Miguel
authors.initials: M
authors.lastname: Flores-Vergara
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Bhupinder
authors.initials: B
authors.lastname: Sehra
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Linda
authors.identifier: 0000-0002-7815-5905
authors.initials: L
authors.lastname: Robles
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Javier
authors.initials: J
authors.lastname: Brumos
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Anna N
authors.initials: AN
authors.lastname: Stepanova
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Lucia
authors.identifier: 0000-0001-8415-1399
authors.initials: L
authors.lastname: Colombo
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Eva
authors.initials: E
authors.lastname: Sundberg
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.).
authors.forename: Steffen
authors.initials: S
authors.lastname: Heber
authors.affiliation: Department of Plant and Microbial Biology (G.H.V., M.F.-V., B.S., L.R., J.B., A.N.S., R.G.F.) and Department of Computer Science and Bioinformatics Research Center (Q.H., S.H.), North Carolina State University, Raleigh, North Carolina 27606;Università degli Studi di Milano Dip. di BioScienze, Sezione di Botanica Generale, Milan, Italy 20133 (S.M., L.C.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 (E.S.) rgfranks@ncsu.edu.
authors.forename: Robert G
authors.identifier: 0000-0002-3978-1030
authors.initials: RG
authors.lastname: Franks
mesh_terms: D017360:Arabidopsis / Q000033:anatomy & histology / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000302:isolation & purification; D001483:Base Sequence; D002697:Chloral Hydrate; D016373:DNA, Antisense; D035264:Flowers / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D017403:In Situ Hybridization; D007210:Indoleacetic Acids / Q000494:pharmacology; D026161:MADS Domain Proteins / Q000235:genetics* / Q000302:isolation & purification; D018519:Meristem / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D018613:Microscopy, Confocal; D056771:Ovule / Q000166:cytology / Q000254:growth & development / Q000378:metabolism; D020033:Protein Isoforms; D011523:Protoplasts; D018749:RNA, Plant / Q000737:chemistry / Q000302:isolation & purification; D012639:Seeds / Q000254:growth & development; D016415:Sequence Alignment; D014157:Transcription Factors; D015533:Transcriptional Activation; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D016373:DNA, Antisense; D007210:Indoleacetic Acids; D026161:MADS Domain Proteins; D020033:Protein Isoforms; D018749:RNA, Plant; C419045:SHP2 protein, Arabidopsis; D014157:Transcription Factors; D002697:Chloral Hydrate