DNA Demethylation and non-coding RNA in stem cells and neural memory
1 PhD project offered in the IPP summer call 2019
Epigenetic gene regulation is of central importance in stem cells, in development, and in disease. Despite dramatic progress in epigenetics during the past decade, DNA demethylation remains one of the last big frontiers and little is known about it. DNA demethylation is a widespread phenomenon that occurs in plants as well as in animals, during development, in adults, and during somatic cell reprogramming of pluripotency genes. In 2007 we showed that Growth Arrest and DNA Damage 45 a (GADD45a) is a key player in active DNA demethylation (Barreto et al.), which opened new avenues in the study of this elusive process. GADD45a is an RNA binding protein and our results indicate a regulatory role for non-coding RNA in this context (Arab et al. 2014). More recently we found that mice mutant for Gadd45a show a defect in stress-induced neural memory, affecting expression of key players regulating synaptic plasticity.
The goal of the projects is to analyze the function of DNA demethylation in different projects focusing on stem cells, Xenopus embryos, and mice to unravel both the mechanism of action and the biological role played by demethylation factors in development as well as neural memory and synaptic plasticity. We will focus on the role played by noncoding RNAs in this context.
We strongly recommend applicants to familiarize themselves with the following cited references prior to interview:
Schäfer A, Mekker B, Mallick M, Vastolo, V, Karaulanov E, Sebastian D, von der Lippen C, Epe B, Downes DJ, Scholz C, Niehrs C (2018). Impaired DNA demethylation of C/EBP sites causes premature aging. Genes Dev. 32:742-762
Niehrs, C. and Schäfer, A. (2012) Active DNA demethylation by Gadd45 and DNA repair. Trends Cell Biol. 22, 220-227
PhD project proposal: Role of GADD45A in regulating RNA processing in neural memory and synaptic plasticity
Understanding how we learn and store memory is of fundamental interest for basic research, but also carries important translational significance in the context of brain dysregulations, such as mental retardation, cognitive decline with age, and post-traumatic stress disorder. The formation of a new memory includes the crucial phase of memory consolidation, which requires behaviorally induced alterations in the availability of functional mRNAs. We found Gadd45a regulates aversive memory formation by specifically regulating mRNAs coding for synaptic plasticity proteins. The majority of Gadd45a-regulated transcripts contain an extended 3´ untranslated region (3´UTR), which is considered a central hub for post-transcriptional regulation. In this project, we aim to investigate the mechanisms underlying the regulation of mRNA stability in memory consolidation. We will investigate the physical interaction between Gadd45a and neuronal target RNAs and their consequences for target mRNA/protein localization within the neuron using RNA-immunoprecipitation. We will apply RNA-seq and Omics approaches for analysis of Gadd45a targets, followed by comprehensive bioinformatics analysis of the target RNAs identified. Using neuronal cultures, we will analyze the role of 3’UTR length in synaptic mRNA localization and transport using luciferase-reporter assays. We will test whether the localization of synaptic mRNAs and their encoded proteins are affected in Gadd45a deficient neurons using confocal fluorescence microscopy.
Gadd45a regulates hippocampal synaptic plasticity.
(A) Nissl stained slice (left) and corresponding section from brain atlas (right). Left panel shows hippocampus and position of the stimulating (left) and recording (right) electrode. (B) LTP protocol was applied to slices of Gadd45a-WT and Gadd45a-KO mice, resulting in lowered induction of LTP in Gadd45a-KO mice.