The Effects of Heterochromatin Formation on 3-D Genome Contacts in Mouse Embryonic Stem Cells


Brooke Wilson

Document Type


Publication Date

Summer 2022



JAX Location

In: Student Reports, Summer 2022, The Jackson Laboratory


Cis regulatory elements (CREs) such as promoters and enhancers direct cell-type specific transcription and in turn cell-type specific function (Catarino & Stark, 2018). Previous work has shown quantitative trait loci (QTL) can regulate biochemical activity at these CREs locally, in cis, or distally, in trans; however, the regulatory mechanisms that exhibit coordinated control on chromatin state and gene expression are not well understood. With the use of CRISPR silencing tools and 3C-qPCR, heterochromatin induction at the Zfp951 locus in mouse embryonic stem cells (mESCs) can be used to further understand regulation of chromatin interactions on 3D genome contacts as well as chromatin accessibility and gene expression. 3C-qPCR was validated in B6 and D2 mESCs with stronger interactions found at the Zfp951 locus in B6, consistent with our hypothesis. These results provide validation that: A) confirms results obtained using another 3D genome assay, HiChIP, and B) more importantly validates that in the absence of histone modifications, we can capture the same differences we previously saw in 3D interactions. Gene editing techniques such as CRISPRi can be used to induce heterochromatin (H3K9me3) in gene regions where it is naturally absent. Furthermore, this tool can be used to test the hypothesis that heterochromatin formation alters 3D genome contacts. Further investigation of these findings is warranted to better understand the trans-regulation of 3D genome contacts and their influence on chromatin accessibility and gene expression, and how variation in transQTL regions affect these mechanisms.

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