Team:Freiburg/Project/effector

Introduction

Effectors

Activation

Repression

Epigenetics

Effector Control

Targeting

uniBAss

Manual

Modeling

Activation

Repression

Krüppel-associated Box (KRAB) repressor domains are highly conserved polypeptide motifs and were first functionally characterized in 1991 [1]. Their occurence in about one third of all human zinc finger transcription factors suggests key regulatory features in higher eukaryotic transcriptomics [2]. In terms of tetrapod evolution, the role of their great abundance has been extensively discussed [3]. Even though KRAB minimal domains are usually no longer than ~ 50-75 amino acids, their mechanism of function remains complex. Common biochemical models suggest a key role in epigenetic silencing, by recruiting a scaffold of diverse proteins to the zinc fingers‘ binding site - amongst others histone deacetylases and histone methyltransferases [4]. Til date, KRAB domains were attached to several DNA binding proteins such as lacR and tetR, thereby silencing gene expression downstream of designed reporter targets.

In this work, KRAB was fused to enzymatically inoperable dCas9. Thus, a transcriptional repressor with the flexibility to target almost any DNA sequence of interest was yielded. Transient SEAP expression could thus be reduced by almost 60 %. In a second attempt, CMV-driven expression of the signaling scaffold protein CNK1 was targeted over 36h - being partially knocked down to background amounts [5]. Furthermore, GFP reporter expression was shown to be drastically reduced by dCas9-KRAB in both Fluorescence Microscopy and Flow Cytometry data. Endogenous levels of VEGF-A, a key factor in hypoxic tumor angiogenesis [6], were also successfully reduced and quantified through an Enzyme-Linked Immunosorbent Assay.

Epigenetics

Histone modification by dCas9-G9a

Introduction

For organisms it is crucial to have a tight control over their transcriptional machinery. As every cell has basically the same genetic information, different tissues have to be formed by differentially regulating the expression of this information. One of the most prominent mechanisms that give rise to this differential expression of genes are epigenetic modifications. Epigenetics are, by definition, inheritable changes in gene expression, that are not accompanied by changes in the nucleotide sequence [7].

There are several types of epigenetic modifications that may have severe impact on gene expression [8]. Basically there are two main types of modifications. The first type are the chemical modification of cytosine residues of nucleotides, better known as DNA methylation. At so-called CpG islands, that can be found clustered in front of promoters the nucleotides can be altered by methylation. This methylation is a hallmark of repressive transcriptional states. But not only the DNA may be altered, but also the protein-nucleotide complex, called the chromatin, that forms the highly variable system that has massive impact on the differential regulation of expression. The probably most prominent epigenetic modifications are histone modifications.

Histones are proteins that work as multi-histone complexes and form a backbone for the DNA to be wound around. The termini of these nucleosomes are protruding from the histone core complex and can be targets for a lot of different modifications, which influence the chromatin state. One very prominent modification is methylation at lysine 9 of histone 3 (H3K9me) which renders before-open chromatin inactive. Such methylations are a hallmark of gene repression. One interesting fact about histone modification is the capability to spread the activity state over the surrounding chromatin via reader proteins. So the information of e.g. "repressed state" can, once specifically introduced, be propagated over a whole locus.

This is the point where the uniCAS system becomes interesting. By introducing specific histone modifications at several loci we should be able to regulate several genes at once using a dCas9 fusion with a methyltransferase that is known to specifically perform certain histone tail methylations.

For our device we used a part of the murine EHMT2 gene, the G9a. It is described in literature that, when targeted to an open locus via zinc finger proteins, G9a is able to repress expression of this locus [9].

We sought to test and improve the zinc finger system by fusing G9a to dCas9 and assayed the function as an epigenetic repressor. As a test subject we chose the VEGF locus, as it is

1. well characterized
2. easy to measure by ELISA methods
3. VEGF is known to be involved in tumorgenesis and therefore an interesting target for testing our system
4. HEK293T cells have an open VEGF locus, so we do not have to artificially open the locus, before testing the system

Results

HEK293T cells were seeded into 24-well plates and transfected with our constructs, that were targeted to open regions [10] of the VEGF locus.

Figure 3: Target sites on the VEGF locus. As the VEGF locus offers several accessible regions we chose four loci around the promoter. Arrows mark the regions. Numbers indicate position of the PAM sequence relative to the starting point of transcription.

For having a control, that our protein does not sterically block the transcription we designed a mutated version of the G9a (dG9a), that has no catalytic activity. So every detectable difference is due to the G9a targeted to this locus. [11] As we can see in the graph, we achieved a strong reduction in VEGF expression, especially when targeting the -8 and -573 loci. This is in line with literature results and plausible, when having in mind the fact, that the promoter region is targeted here and dense chromatin in promoters leads to repression.

Figure 4: Endogenous, stable repression by dCas9-G9a Chromatin remodeling, resulting in repression of endogenous genes, is possible by fusing the histone methyltransferase G9a to dCas9.

Discussion

Our results obviously show a strong repression of VEGF expression around 50%, depending on the locus targeted. We can conclude from our results and literature data that we were able to specifically methylate histones and change the transcriptional state of the VEGF locus. Off-target controls do not display differences in VEGF expression, which supports the specificity of our protein.
As we always show the diference to the Cas9 protein without effector. This leads to the point that we only observe the catalytic activity of G9a. This results in a valuable repressor tool that is able to specifically change histone methylation patterns and can change transcriptional states. This leads to many possible applications such as cancer research, fundamental epigenetical science or even tissue engineering.