Department of Biology

Event Information

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Title: GCDB Seminar Series: "Defining the transcriptional regulatory structure of plant genomes." Roger Deal.
Start Time: Thursday September 21, 2017 04:00 PM
End Time: Thursday September 21, 2017 05:00 PM
Location: Myers Hall 130  
Contact: Biology Seminar Coordinator
Description:

Compared to animal genomes, the cis-regulatory structure of plant genomes remains poorly defined. It is currently unclear how many enhancer elements exist in plant genomes, where these elements lie in relation to their target promoters, and how many elements are typically used to regulate each gene. To address these issues, we have employed the assay for transposase accessible chromatin (ATAC-seq) in four different plant species (Arabidopsis, Medicago, Tomato, and Rice) to delineate open chromatin regions and transcription factor binding sites across each genome. Despite major variations in genome size and evolutionary divergence, we find that the distribution of open chromatin sites is highly similar across species. The majority of intergenic open chromatin sites occur within 3 kb upstream of a transcription start site (TSS) in all four species. Nearly 70% of genes in Arabidopsis, Medicago, and Rice have a single putative enhancer region upstream of the TSS, while a similar percentage of Tomato genes have 2-5 such elements. We have also used ATAC-seq profiling of specific cell types in Arabidopsis to address the differential utilization of regulatory elements during cell differentiation. We find that while closely-related cell types often have qualitatively indistinguishable open chromatin profiles, quantitative analysis of chromatin accessibility reveals functionally relevant differences between cell types. Furthermore, by combining chromatin accessibility data with transcription factor (TF) expression and genomic binding data, we can identify TF networks acting at a high level to control transcriptional output in specific cell types. These putative regulatory networks then inform further experimentation and hypothesis testing. In this talk I will discuss the key findings of this work and future goals for deciphering transcriptional control in plants. 

Contact Email: biotalk@indiana.edu
More Contact Info: Host: Gabe Zentner
Other Info: Refreshments served prior to seminar.
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