Dynamics of tissue-specific genome regulatory programs in the germinating barley seed

Liew LC, Chen M, Wang Y, Whelan J and Lewsey MG

AgriBio, La Trobe University, Melbourne, VIC, Australia.

We are studying tissue-specific genome regulatory programs in germinating barley seeds so as to better understand how they are controlled by transcription factors. The roles of transcription factors in genome-wide regulation of gene expression are subject to much attention currently, but determing these roles is complex. Regulatory events occur dynamically over short time scales (minutes to hours), with many transcription factors interacting to regulate the output of any given gene and cascades of interacting factors operating across the wider program. Studies have historically depended on analysis of bulk tissue samples, due largely to the capabilites of available techniques. However, individual cell-types must be specified by distinct regulatory programs. To investigate cell-type specific genome regulation during germination we have applied laser-capture microdissection RNA sequencing to three tissues of barley seeds that have distinct functions (plumules, radicles and scutellum). We analysed complete transcriptomes from samples of 200 cells over a 36 h time series, enabling us to observe the dynamic changes in gene expression. The data allow us to identify modules of gene expression that are unique to and conserved between these three tissues and to identify associated groups of potential cis-regulatory motifs. By extrapolation from the extensive Arabidopsis transcription factor target datasets we are also able to infer likely families of regulatory factors. The outcome is an improved understanding of the direct regulation of gene expression and how this varies between tissues in a crop species with a relatively complex genome.