Abstract
- Nucleosomes Positioning - Existing algorithms can only predict the rotational setting of 65% of human nucleosomes. To uncover novel factors responsible for nucleosome positioning, we reconstituted H2A/H4 N-tailless nucleosomes in vitro. The H2A N-tail displayed an interaction with the AT content at SuperHelical Locations (SHL) ±4 and the H4 N-tail at SHL ±1 and SHL ±2, suggesting the importance of the tails in selecting nucleosome positions. Nucleosomes may reposition in cancer - Using high-resolution nucleosome maps in breast cancer patients, we detected 20-fold enrichment of nucleosome repositioning at CpG islands and a 5-10 bp decrease in the nucleosome repeat length (NRL), the latter being qualitatively similar to the differences between pluripotent and differentiated cells, as well as correlated with gene activity, differential DNA methylation and changes in local occupancy of linker histones. 2. Single-Cell Exon Profiling with scCHyMErA-Seq - To systematically investigate the role of alternative splicing in cell fate determination, we developed a scalable CRISPR-based exon deletion screening platform able to simultaneously capture Cas9/Cas12a guides and polyadenylated transcripts at single-cell resolution. Applying scCHyMErA-Seq to high-throughput profiling of alternative cassette exons, we identified numerous exons with pronounced regulatory effects on gene expression and cell cycle progression. For instance, the alternative NRF1 exon-7 demonstrates that its inclusion modulates NRF1’s regulatory function by influencing its recruitment to the promoters of target genes. scCHyMErA-Seq represents a versatile platform for systematically unraveling the functional impact of alternative splicing by directly linking specific splicing variants to transcriptional phenotypes.
Bio
Bachelor of Science: Biology – Biochemistry. University of Nantes. France; Master of Science: Biology. University of Puerto Rico, Mayagüez. Advisor: Taras Oleksyk; Ph.D. in Bioinformatics and Genomics: The Pennsylvania State University. Advisors: Kateryna Makova and Anton Nekrutenko; Postdoctoral fellowship at the National Cancer Institute. Laboratory of Cell Biology. Advisors: Victor Zhurkin and Pedro Batista; Currently: Computational Scientist at the Frederick National Laboratory for Cancer Research.