Zooming into the 3D Genome Architecture and Gene Regulation

Tuesday, March 3, 2015 -
4:00pm to 5:00pm
Wisconsin Institutes for Discovery Building, H.F. DeLuca Forum, 330 N. Orchard St.

Speaker Name: 

Wenxiu Ma, PhD

Speaker Institution: 

University of Washington




This is a Computational Biology Seminar featuring Wenxiu Ma, PhD, a Postdoctoral Fellow in the Department of Genome Sciences, University of Washington.

Abstract: The genome is tightly packaged in the cell nucleus. High-throughput methods based on chromosome conformation capture have greatly advanced our understanding of the 3D organization of genomes and demonstrated that genome architecture strongly influences gene expression. In this talk, I will present two of my recent projects looking into the interplay between genome architecture and gene expression in mammalian cells.

First, I will present a novel method called DNase Hi-C, which uses DNase I instead of restriction enzymes for chromatin fragmentation, to comprehensively map global chromatin contacts. Coupling DNase Hi-C with DNA capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture. We applied targeted DNase Hi-C to characterize the 3D organization of ~1000 lincRNA promoters in two human cell lines and revealed cell type-specific 3D organization of lincRNA genes.

Next, I will talk about our study of the allele-specific transcriptional regulation, gene expression and chromatin structure in a hybrid mouse system, with an emphasis on understanding the X chromosome inactivation. Applying high-throughput sequencing assays and new computational approaches, we surveyed allelic gene regulation in various mouse tissues and identified that CTCF plays an important role in shaping escape and silenced domains on the inactive X chromosome.