Determining the Role of KZFPs in Modulating Chromatin Accessibilityand Gene Expression in Mouse Embryonic Stem Cells

Document Type


Publication Date

Summer 2021

JAX Location

In: Student Reports, Summer 2021, The Jackson Laboratory


The purpose of this study is to determine the impact that genetic variation has on chromatin accessibility and gene expression in phenotypic variation and differentiation of mouse embryonic stem cells (mESCs). Prior work in the Baker Laboratory has identified a set of DNA binding proteins that are variable between B6 and D2 mice which regulate chromatin accessibility and gene expression. Our hypothesis is thatKZFPs are responsible for the variation in chromatin accessibility and gene expression underlying a QTL locus on Chr 4. The approach we utilized to test our hypothesis involved guide cloning, transfection of ESCs, FAC sorting, harvesting of RNA, and the completion of a qRTPCR. Our goal is to silence the expression of three of these KZFPs individually, and determine the effects on gene expression of potential targets of the Chr4 QTL using RNA sequencing. This data will contribute to our understanding of these QTL regions and more broadly the role of chromatin accessibility on gene regulation. Our qRTPCR results confirmed successful knockdown of 2 out of 3 KZFPs, as well as a corresponding increase in two predicted distal target genes.

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