Bioinformatics Seminars

Current Bioinformatics Seminar

29 May 2018

Functional genomics of seeds, tissues and cells

Mat Lewsey
La Trobe University

Seed germination and early growth is an excellent model with which to investigate functional genomics. The seed goes through a developmental progression from complete metabolic dormancy to a highly active, growing seedling in a period of 48 to 96 h. At the start of this, the genome is compacted into heavily methylated heterochromatin, which must be rapidly reactivated. Germination is regulated by many factors, including environmental sensing, hormone signalling and transcription factor activity. These interact extensively with one-another, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression on a genome-wide scale during germination is limited currently, as is our knowledge of the dynamic changes in the epigenome and small RNAs (sRNAs). I will discuss a study of whole seeds in which we used time-series transcriptome data and binding site maps for hundreds of transcription factors to identify key genome regulators, and charted dynamic changes in the DNA methylome. However, the seed is a complex structure composed of tissues with distinct roles, each requiring their own genome regulatory program. We are investigating how these programs differ using tissue and cell-specific gene expression analyses. Moreover, events occurring at genes are regulated by signal transduction pathways to condition responses appropriate for the environment. We have studied how gene expression fits into a broader hormone signalling pathway and developed methods to link genotype with phenotype in high-throughput, which I will describe lastly.


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