title: High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.
abstract: The extent to which alternative splicing and long intergenic noncoding RNAs (lincRNAs) contribute to the specialized functions of cells within an organ is poorly understood. We generated a comprehensive dataset of gene expression from individual cell types of the Arabidopsis root. Comparisons across cell types revealed that alternative splicing tends to remove parts of coding regions from a longer, major isoform, providing evidence for a progressive mechanism of splicing. Cell-type-specific intron retention suggested a possible origin for this common form of alternative splicing. Coordinated alternative splicing across developmental stages pointed to a role in regulating differentiation. Consistent with this hypothesis, distinct isoforms of a transcription factor were shown to control developmental transitions. lincRNAs were generally lowly expressed at the level of individual cell types, but co-expression clusters provided clues as to their function. Our results highlight insights gained from analysis of expression at the level of individual cell types.
authors.affiliation: Department of Biology and HHMI, Duke University, Durham, NC 27708, USA.
authors.forename: Song
authors.initials: S
authors.lastname: Li
authors.affiliation: Department of Biology and HHMI, Duke University, Durham, NC 27708, USA.
authors.forename: Masashi
authors.initials: M
authors.lastname: Yamada
authors.affiliation: Department of Biology and HHMI, Duke University, Durham, NC 27708, USA.
authors.forename: Xinwei
authors.initials: X
authors.lastname: Han
authors.affiliation: Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27710, USA; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany. Electronic address: uwe.ohler@mdc-berlin.de.
authors.forename: Uwe
authors.initials: U
authors.lastname: Ohler
authors.affiliation: Department of Biology and HHMI, Duke University, Durham, NC 27708, USA. Electronic address: philip.benfey@duke.edu.
authors.forename: Philip N
authors.initials: PN
authors.lastname: Benfey
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics*; D002454:Cell Differentiation / Q000235:genetics; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D007438:Introns / Q000235:genetics; D018517:Plant Roots / Q000235:genetics*; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D040901:Proteomics; D020871:RNA Stability / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D020033:Protein Isoforms; D062085:RNA, Long Noncoding; D018749:RNA, Plant
keywords: Arabidopsis; PacBio sequencing; RNA-seq; alternative splicing; co-expression network; intron retention; lincRNA; proteome; root development; transcriptome