Research

The small Proteome


Chromatin and Epigenetics

Epigenetic states determine gene expression patterns during differentiation and organismal development. These heritable states are layered on top of the genetic information, which is the same in every cell irrespective of the differentiation program it follows. Epigenetic states are, while usually established by a DNA sequence-specific signal (such as the action of a transcription factor), maintained or propagated in the absence of DNA-sequence specific factors. The molecular basis of such cellular memory has remained elusive, yet histones, the proteins that package DNA into chromatin, have been recognized as a prime candidate for epigenetic regulation. The wealth of known histone posttranslational modifications (marks) and combinations thereof highlight the verbose coding potential of chromatin for epigenetic information. With the advent of epigenomics, histone modifications have been studies in many aspects of human disease – pre and postnatal development, behaviour, memory and neurodegeneration, genome stability and cancer, diabetes and cardiovascular diseases, AIDS, stem cells and reprogramming. However, it has been noted that our current, descriptive methodologies do not rule out the possibility that histones are mere bystanders rather than culprits in many pathologies. For example, it is disputed that histone marks, and ultimately the underlying histone moiety, have a long lifetime, and are inherited faithfully during DNA replication. In the absence of unequivocal proof of locus-specific histone inheritance, the epigenetic nature of their marks remains debatable. It is therefore a major challenge of our field to devise experiments that can directly and conclusively test this hypothesis.

Epigenetic Networks

 

Living cells as a test tube

We are developing a chemical biology technique called amber suppression or unnatural amino acid mutagenesis in mammalian cells. Unnatural amino acids with a variety of chemical functionalities can be inserted site-specifically into a target protein within a living cells in response to a recoded stop codon. Such strategy for genetic code expansion holds great potential for engineering proteins in vivo, but its applicability to basic biology and human disease research has been hampered by the limited biological systems it could be established in. We have developed an optimized system that allows highly efficient amber suppression in mammalian cells (read more). Using this system, we aim to do biochemistry in a living cell, controlling and observing proteins ‘at work’ in their in vivo environment.

Amber Suppression

 

Stem cell chromatin

Gene expression plasticity is thought to be an essential feature of germ line and pluripotency. Yet, transcriptionally permissible chromatin poses a severe challenge for maintaining heterochromatin. ERVs and other interspersed repeats are particularly vulnerable to reactivation, as their integration sites are not part of large repressed domains (such as telomeric and centromeric heterochromatin). The repressed state of ERVs can be inherited across generations in mice despite global chromatin reorganization in the germline, underpinning the epigenetic basis of silencing . In mESC, the repressive histone mark H3K9me3, established by the methyltransferease SETDB1, is essential for ERV silencing. In addition, the corepressor KAP1 is required, orchestrating the silencing machinery around the characteristic long terminal repeats (LTRs) that are recognized by DNA-sequence specific transcription factors. We have recently uncovered a role for histone variant H3.3 amplifying H3K9me3-mediated silencing (read more). Intriguingly, in more differentiated cell types, such as neuronal precursors, DNA CpG methylation becomes necessary and sufficient for silencing. Thus, ERVs provide an ideal study system to dissect the dynamic interplay between DNA-sequence-dependent and epigenetic silencing pathways.

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