Gene regulatory networks control development via domain-specific gene expression. However, the gene expression patterns in different cell domains are difficult to obtain, especially in plants where cells are glued together by cell walls.
Recently, a team led by Prof. JIAO Yuling from Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, constructed a cell domain-specific gene expression atlas for the Arabidopsis shoot apex that includes shoot apical meristem and leaf primordia.
The researchers used a technology termed translating ribosome affinity purification to isolate translating mRNAs associated with ribosomes, where mRNAs are translated into proteins. By deep sequencing isolated cell domain-specific mRNAs, they quantified expression of each gene in each domain. They also built a user-friendly browser for data visualization, which is implemented in electronic fluorescent pictograph (eFP) browser at
http://jiaolab.genetics.ac.cn/shootapex.html.
The cell domain-specific gene expression atlas provides a community resource for further study of shoot growth and development, including responses to environmental signals.
The researchers identified many domain-specific features, including signature genes and domain-specific alternative splicing, and long non-coding RNAs. As a proof of concept for the use of the data, they identified novel regulators of axillary meristem (AM) initiation through co-expression network analysis. From modules enriched with AM regulatory genes, the researchers showed that RBE and HAN had previously unknown roles in AM initiation.
The paper entitled “A gene expression map of shoot domains reveals regulatory mechanisms” has been published online in
Nature Communications on January 11th, 2019 (
DOI:10.1038/s41467-018-08083-z).
