September 22, 2019  |  

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

Authors: Li, Song and Yamada, Masashi and Han, Xinwei and Ohler, Uwe and Benfey, Philip N

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. Copyright © 2016 Elsevier Inc. All rights reserved.

Journal: Developmental cell
DOI: 10.1016/j.devcel.2016.10.012
Year: 2016

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