DR. STEPHEN MONDO
Staff Data Scientist,
Fungal & Algal Genomics Program, Functional Genomics Work Lead
DOE Joint Genome Institute
WHEN: Nov. 13th, 2020 at Noon
WHERE: Seminar will be presented via Zoom
Zoom Meeting
https://ucdenver.zoom.us/j/91048440693
Meeting ID: 910 4844 0693
Data mining reveals new approaches to gene regulation across fungi
The fungal kingdom is extremely old and diverse. Owing to their relatively small genomes (for eukaryotes), massive amounts of -omics data have been collected already. With these data in hand, we can now ask evolutionary questions at scale across fungi. To this end, I will discuss to two studies conducted using data available at the DOE Joint Genome Institute. Using PacBio genome sequencing, we performed a kingdom-wide exploration of epigenetic modifications upon DNA and discovered that early-diverging fungi (EDF) are heavily utilizing a non-canonical modification, N6-methyldeoxyadenine (6mA), to mark actively expressed genes. This trait was not present in the Dikarya. EDF display the highest 6mA levels of any eukaryote and these modifications are found in dense clusters at promoters/gene starts. Methylated clusters denote the start of gene expression and we observed shifts in nucleotide composition associated with these clusters. Exploring these nucleotide shifts surrounding other genomic features led us to another interesting observation - a DNA signature possibly related to nucleosome organization. While the distribution of this signal was variable across lineages, through conducting in-vitro chromatin assembly for several fungi we were able to confirm these patterns provide a map of positions favorable to nucleosome formation. Through in-vivo chromatin assembly and other methods we were able to confirm that these sites are meaningful in-vivo. Using this information, we are beginning to develop methods for predicting nucleosome favorable DNA signatures.
Everyone is welcome to join the seminar, please see the Zoom link above.