Deciphering the cis-regulatory logic of plant genomes at single-cell resolution

Significant progress has been made in recent years in plant genome assembly and gene annotation. However, the systematic identification of plant cis-regulatory DNA elements remains a challenge. A comprehensive and well-curated data set of plant cis-regulatory DNA elements is instrumental to understanding transcriptional regulation during development and/or in response to external stimuli. In addition, cis-regulatory DNA elements are also hotspots for genetic variations underlying key agronomical traits. We have discovered a plant-specific chromatin signature that is indicative of cis-regulatory DNA elements. We are using this newly identified signature in combination with high-throughput validation assays to systematically identify, analyze and functionally validate cis-regulatory elements in important crop species. In parallel, we are discovering cell-type-specific cis-regulatory elements using single-cell ATAC-seq (scATAC-seq) across a range of crop species. Data from maize revealed that cell-type-specific cis-regulatory elements are sequenced constrained, yet the sequence variation that does occur is important for expression and phenotypic variation. We discovered breeders have been unknowingly selecting genetic variants within cis-regulatory elements in modern maize breeding schemes. We also learned that scATAC-seq data is useful for predicting presence/absence expression of genes and used this to map transcription factors and their binding sites in a cell-type-specific manner. In this presentation I will discuss how we are using single-cell genomics to map the genetic basis for gene expression and chromatin accessible variation across the maize germplasm and present future goals to decode the cis-regulatory landscape of crop genomes using single-cell genomics through time, across environments and by genotype.

講者: Dr. Robert J. Schmitz (Professor, UGA Foundation Professorship of Plant Sciences & Georgia Research Alliance Lars G. Ljungdahl Distinguished Investigator, University of Georgia, Athens, GA, USA)

主持人: Dr. Jer-Young Lin

時間:2020/11/18 11:00 AM

地點:農業科技大樓1樓A134演講廳