Developing Integrated Single-Cell Epigenome and Transcriptome Sequencing Technologies to Understand Cellular Heterogeneity
ONLINE CBE SEMINAR
All Spring 2020 CBE Seminars will be hosted online via Zoom. Zoom will open after the host has joined at the start of each seminar. You can ask questions through the chat forum and by raising your "hand" and the speaker will call on you. Zoom link here: https://ucsb.zoom.us/j/943297219
Speaker
Siddharth Dey
Assistant Professor, Department of Chemical Engineering
University of California, Santa Barbara
Abstract
A fundamental question in biology is to understand how heterogeneity in the epigenome drives cell-to-cell variability in gene expression and cell fate specification. In this talk, I will discuss three recent single-cell multiomics technologies our group has developed to study the role of different epigenetic marks and features in regulating gene expression during mammalian development. First, I will discuss a single-cell method that enables us to simultaneously quantify cellular lineages and mRNA to understand how symmetric and asymmetric cell divisions regulate the dynamics of tissue development. Next, I will present another method to detect DNA methylation strand-specifically in single cells. I will show that strand-specific quantification of DNA methylation allows us to uncover the molecular mechanisms responsible for the global erasure of the methylome during preimplantation mammalian development. Most recently, we have developed a method for simultaneous quantification of protein-DNA interactions and mRNA from the same cell. Specifically, we have used this technology to understand how cell-to-cell heterogeneity in the 3D organization of the genome tunes gene expression variability. Thus, while single-cell genomics has led to the discovery of a vast catalog of diverse cellular states, development of integrated single-cell sequencing technologies is enabling us to understand the dynamics and causal mechanisms responsible for producing these varied states.
BIO
Siddharth Dey is an Assistant Professor in the Department of Chemical Engineering at the University of California, Santa Barbara. He graduated from the Institute of Chemical Technology (Formerly: UDCT), Mumbai in 2006 with a B.S. in Chemical Engineering. Thereafter, he worked with Professor David Schaffer and Professor Adam Arkin and received his Ph.D. in 2012 from the University of California, Berkeley. Next, he conducted post-doctoral research in Professor Alexander van Oudenaarden's group at the Hubrecht Institute, The Netherlands before moving to UC Santa Barbara in 2017. Dr. Dey’s group develops novel single-cell sequencing technologies to study how variability in the epigenome regulates gene expression heterogeneity and cell fate decisions during mammalian development.
