title: RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation.
abstract: Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the genetic networks that regulate endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the maize (Zea mays) kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene coexpression network analysis identified coexpression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a coexpression module highly correlated with the basal endosperm transfer layer (BETL) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types.
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721.
authors.forename: Junpeng
authors.identifier: http://orcid.org/0000-0001-7353-7608
authors.initials: J
authors.lastname: Zhan
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721.
authors.forename: Dhiraj
authors.identifier: http://orcid.org/0000-0002-4870-5064
authors.initials: D
authors.lastname: Thakare
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721.
authors.forename: Chuang
authors.initials: C
authors.lastname: Ma
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, Utah 84112.
authors.forename: Alan
authors.initials: A
authors.lastname: Lloyd
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, Utah 84112.
authors.forename: Neesha M
authors.initials: NM
authors.lastname: Nixon
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, Utah 84112.
authors.forename: Angela M
authors.initials: AM
authors.lastname: Arakaki
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, Utah 84112.
authors.forename: William J
authors.initials: WJ
authors.lastname: Burnett
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, Utah 84112.
authors.forename: Kyle O
authors.initials: KO
authors.lastname: Logan
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721.
authors.forename: Dongfang
authors.initials: D
authors.lastname: Wang
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721.
authors.forename: Xiangfeng
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, Utah 84112.
authors.forename: Gary N
authors.initials: GN
authors.lastname: Drews
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721 yadegari@email.arizona.edu.
authors.forename: Ramin
authors.identifier: http://orcid.org/0000-0002-0975-2984
authors.initials: R
authors.lastname: Yadegari
mesh_terms: D001483:Base Sequence; D002451:Cell Compartmentation; D002454:Cell Differentiation / Q000235:genetics*; D056625:Endosperm / Q000166:cytology* / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D018392:Genomic Imprinting; D061346:Laser Capture Microdissection / Q000379:methods*; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics; D054817:Pollination; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D013997:Time Factors; D020798:Two-Hybrid System Techniques; D003313:Zea mays / Q000196:embryology* / Q000235:genetics
chemical_list: D012333:RNA, Messenger