YIn Shen, PhD

Core

We study the fundamental mechanisms of transcriptional control.  By investigating how genetic and epigenetic variations contribute to cis-regulatory elements function, we will develop a detailed understanding how cis-regulatory elements contribute to cell fate determination and health. These studies will lead to a better comprehension of development, and will facilitate the improvement and advancement of preventive methods, diagnoses, and treatments for diseases.

1. High-throughput functional characterization of regulatory elements with targeted single-sgRNA CRISPR/Cas9 mediated genetic screening

In order to fully assess the contribution of a candidate element to gene expression it is necessary to delete or modify the element in its endogenous location. We are utilizing a high throughput CRISPR/Cas9 mediated genetic screening system to interrogate the biological significance of a large number of non-coding regulatory sequences in the mammalian genome.

2. Unlocking cell type-specific mechanisms of gene regulation.

A remarkable feature of multi-cellular organisms is that they develop a distinct set of highly specialized cells from the same genetic blueprint. This is achieved by precise transcriptional regulation involving the interplay of multiple components including transcription factors and cis-regulatory elements in the genome. The NIH Roadmap Epigenome and ENCODE projects have mapped millions of putative cis-regulatory elements across more than one hundred different cell types and tissues. While these maps have significantly expanded our knowledge of non-coding sequences, there are still large gaps between having these maps of cis-regulatory elements and understanding how cis-regulatory elements function in gene regulation. We are utilizing integrative, unbiased, and high-throughput genomic and genetic tools to identify and functionally characterize cis-regulatory elements.

3. Determining functional consequences of neurological disease-associated genetic variation at cis-regulatory elements.

Putative regulatory regions harbor a disproportionally large number of sequence variants associated with human traits and diseases, leading to the notion that genetic lesions in the cis-regulatory elements contribute substantially to common human diseases. However, we know little about the consequences of such disease-associated genetic variations in cis-regulatory elements, especially for their function in the central nervous system. To begin to address these issues, we will focus on complex neurological disorders, such as Parkinson’s disease (PD), to address the important challenge of moving forward from the identification of disease- associated SNPs by GWAS to a more thorough understanding of the functional consequences of specific variants that cause or contribute to human disease.