Computational Biology Seminars

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA

Transcription factors control cell fate decisions by binding to specific short DNA sequences to activate or repress their target genes. A typical mammalian transcription factor binds to thousands of sites across the genome forming a complex transcription network. Despite significant progress in mapping the binding sites of transcription factors across the genome, outstanding questions still remain. How does transcription factor binding relate to activity of the target gene? How do individual transcription factor binding sites contribute to specific cellular phenotypes? We will present how precision and programmability of CRISPR-based tools can be used to identify functional interactions in complex transcription networks. We will show how CRISPR-based tools can be used to understand the biological function of the stem cell pluripotency transcription network. Finally, we present how CRISPR activation of 2-3 elements in the pluripotency network leads to generation of distinct 2D and 3D spatial patterns similar to those found in periimplantation mammalian embryos.