The use of genomic imprinting to investigate the relationship between subnuclear localisation and gene expression

• Applicant: Dr. Lisa Hülsmann
• Subject Area: General Genetics and Functional Genome Biology ; Evolutionary Cell and Developmental Biology (Zoology)
• Term: from 2014 to 2017
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 262543100

Transcriptional regulation has been extensively studied through the analysis of cis-acting genomic features, transcription factor control and epigenetic modifications. In addition, several lines of evidence support a role for three-dimensional organisation of the chromatin within the nucleus in regulation. However, the impact of subnuclear localisation on genome function is not understood. I will use genomic imprinting, a process that leads to parental-origin-specific gene expression, as a model to investigate the relationship between subnuclear localisation and gene expression. Preliminary experimental results suggest a preferential localisation of one allele of the imprinted Dlk1-Dio3 region to the nuclear periphery. Since different genes are expressed from both parental chromosomes this raises a number of important questions with wider implications for our understanding of subnuclear localisation. My aim is therefore, to analyse the relationship of the differential transcriptional regulation of imprinted genes and their subnuclear localisation. With this model system I will ask the following questions: 1. Can peripheral localisation be used as a regulatory mechanism for the control of monoallelic expression and/or gene dosage?2. How do genes interact with the nuclear periphery?3. What are the functional implications of such interactions?To answer my questions, I will use 3D RNA and DNA Fluorescence in situ hybridisation (FISH) and DamID-Seq on normal and mutant mouse cells and comparative interpretation of the results. By sequential FISH detection of imprinted genes on the level of nascent RNA and DNA I will determine the position of expressed and non-expressed genes in the nucleus and measure the distance of signals to the chromatin border by fluorescence microscopy. In addition, interactions of imprinted regions with the nuclear lamina and with nuclear pore complexes will be analysed using the DamID technology and next generation sequencing. Subsequently, a wide range of existing mouse mutants available in the host lab and from our collaboration partner will be considered to use for comparative manipulation of the outlined experiments in order to uncover functional relationships.I hope that with this imprinting-based model system I will develop a useful tool with wider applications in nuclear organisation research.

• DFG Programme: Research Fellowships
• International Connection: United Kingdom
• Host: Professorin Dr. Anne C. Ferguson-Smith