Two Master Theses / Masterarbeiten, Department of Biotechnology, AG Himmelbauer

The Department of Biotechnology, group Himmelbauer, has two openings for Master thesis projects. We are a multidisciplinary team that combines wet-lab experimentation with bioinformatics. In particular, we have broad experience with strategies for the acquisition of next-generation sequencing (NGS) data, as well as their analysis. An important focus of the group is plant genomics; we recently published a reference sequence of the sugar beet genome (Dohm et al., Nature, 2014). Both Master thesis projects will utilise a well-characterised sugar beet reference genotype to establish wet-lab methods related to the identification of chromatin structure. NGS data generation will be outsourced to a service provider; NGS data will be analysed and interpreted by the students to verify their successful method implementation.

Project 1: Goal of the thesis is the implementation of the “Chromosome Conformation Capture” method to collect information about regions in the genome that interact across large distances. Sequences that are far apart within linear DNA can be closely located within chromatin. The student will reconstitute chromatin from sugar beet DNA together with recombinant histone octamers, followed by preparation of sequencing libraries, and NGS sequencing. The computational analysis of the data will involve mapping of read-pairs against the sugar beet reference genome assembly to verify successful library preparation. The resulting long-range pairs represent a resource to substantially improve the scaffolding process during genome assembly.

Project 2: Goal of the project is to identify regions of open chromatin within the sugar beet genome, and to put this new layer of information into context with already existing beet genome annotation. Open chromatin is a hallmark of regions that are transcriptionally active, and charting them can direct further attention to genome intervals that are of functional importance. The student will set up a protocol to isolate intact nuclei from sugar beet leaves, followed by in situ fragmentation of chromatin using a transposase according to a method referred to as ATAC-seq. Preferred fragmentation will occur within intervals that allow free access to the transposase. The data obtained from these sequencing libraries will be analysed using read mapping. Peaks of read-enrichment will be identified, followed by interpretation of the data.

Preferred starting dates: May or June 2015.

Duration: Six months. It is expected that the work will be well balanced (50% experimental, 50% computational).

Requirements: Essential are basic lab experience and basic experience with computation in a linux environment.

To apply, please send your CV and a summary of your bachelor’s thesis no later than March 31st by e-mail to heinz.himmelbauer@boku.ac.at