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 cannot be traced back to 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 are working as multi-histone complexes and forming a backbone for the DNA to be wound around. The termini of those nucleosomes are hanging out of the nucleosome. These protein tails are target for a lot of different modifications, determining the state of the chromatin.

One very prominent modification is the methylation at histone 3, lysin 9 (H3K9me). These methylations are a hallmark of repression.

One interesting fact about histone modification is the capability to spread the state via reader proteins on the surrounding chromatin. So the information of e.g. "repressed state" may be spreaded over a locus, once introduced.

This is the point where the uniCAS system gets interesting. By introducing specific histone modification at several loci we should be able to regulate several genes at once, using a dCas9 fusion with a specific methyltransferase that is known to specificly methylate histones.

for our device we have been using a part of the murine EHMT2 gene, the G9a. It is descirbed in literature, that, when targeted to an open locus via zinc finger proteins, it is able to repress expression from this locus. [9]

This is a system we can improve by using the dCas9. So we fused the 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 into 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. These plates were transfected with our constructs, and targeted to open regions [10] of the VEGF locus. By specific histone modificaiton by G9a we should repress VEGF secretion into the medium. After 24 hours after medium change we harvested the supernatant and performed VEGF measurments by ELISA. Additionally we co-transfected a constitutive reporter (SEAP) as an internal standard to reduce mistake of non-transfected cells and cell number. A major problem of working with endogenous loci is the background of non-transfected cells which will display VEGF secretion, even though we have strong repression in other cells.

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 be due to the G9a targeted to this locus. [11] As we can see in the graph, we see a strong reduction in VEGF expression, especially in the -475 locus. This is in line with literature results and makes sense, when having in mind the fact, that the promoter region is targeted here and dense chromatin in prooters leads to repression.

Figure 3: 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

This results in a valuable tool, that is able to specifically change histone states and can change transcriptional states. This leads to many possible applications as cancer research, fundamental epigenetical science or even tissue engineering.