Harris Group: Mechanisms of transcriptional activation downstream of DNA methylation

Jake Harris

 

 

A recently discovered a complex reads DNA methylation and activates nearby genes. In this project, the student will investigate the molecular mechanisms by which this activation occurs.

 

 

Crop genomes are often full of methylated and silenced transposable elements. However, coding genes nearby must remain available for expression during development or in response to stimuli. Understanding how cells are able to protect genes from silencing is critically important for unlocking and modulating agricultural traits.

 

 

DNA methylation has a complex relationship with transcription. It is normally associated with repression, but in certain contexts, DNA methylation is required for transcription. We previously identified the first molecular complex that directly links DNA methylation to transcriptional activation. This complex consists of the DNA methylation reader proteins SUVH1 and SUVH3, and the transcriptional activator proteins DNAJ1 and DNAJ2. Because transposable elements are marked by methylation for silencing, this complex is thought to help protect the expression of genes if a transposon inserts nearby. Crop genomes often have unusually high transposable element content, and so this complex could help to ‘unlock’ genomic regions from silencing, leading to novel avenues for agricultural improvement. However, major questions remain. How does DNAJ1/2 induce transcriptional activation? Where do DNAJ1/2 exist in the nucleus and what do they interact with? How does DNAJ1/2 differentiate between transposons (which must remain silent) and important genes (which must remain active)?

 

 

The student will examine the subcellular localization of DNAJs by high resolution microscopy. Forward and reverse genetic approaches will be used to identify the machinery involved in transcriptional activation. In vitro approaches will be used to examine DNAJ domain function. Genomic and computational approaches will be used to discover chromatin features that may license DNAJ for activation.

 

 

The student will gain expertise in a range standard molecular biology techniques (cloning, genotyping, qRT-PCR, western blots). In addition the student will learn biochemical (protein purifications, binding assays) and genomic (both wet lab and computational) approaches.