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High-resolution expression map of the arabidopsis root reveals alternative splicing and lincRNA regulation

Item Type:Article
Title:High-resolution expression map of the arabidopsis root reveals alternative splicing and lincRNA regulation
Creators Name:Li, S. and Yamada, M. and Han, X. and Ohler, U. and Benfey, P.N.
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.
Keywords:RNA-seq, Arabidopsis, Alternative Splicing, lincRNA, Transcriptome, Proteome, PacBio Sequencing, Root Development, Intron Retention, Co-Expression Network
Source:Developmental Cell
ISSN:1534-5807
Publisher:Cell Press / Elsevier (U.S.A.)
Volume:39
Number:4
Page Range:508-522
Date:21 November 2016
Official Publication:https://doi.org/10.1016/j.devcel.2016.10.012
PubMed:View item in PubMed

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