Comparative Genomics of Non-Model Invertebrates

ESR Project 13: Computational identification of major gene regulation modules in development and cell differentiation

Supervisor: Kristian Vlahovicek (University of Zagreb), Co-supervisor Alexandros Stamatakis (HITS Heidelberg)

Student: Juan Antonio Ruiz Santiesteban

Objectives: Spatiotemporal data on gene expression and chromatin structure during the development and differentiation of different metazoan clades is important for detecting regulatory modules common for all multicellular organisms. It also has the potential to reveal clade-specific differences in these processes. This project will focus on genomic mechanisms for environmental adaptation to light and circadian rhythm. We will use two freshwater demosponges, Ephydatia muelleri and Eunapius subterraneus as models. Both are closely related and share their adaptation to freshwater, yet inhabit completely different ecosystems, above ground vs. subterranean, respectively.

O1: Collect novel NGS data on the developmental time course of these two species, specifically targeting small and noncoding RNA complement.

O2: Combine them with other data collected in IGNITE and compare with data we have already collected and analyzed in rodents.

O3: Identify putative common developmental and differentiation gene expression modules and (if they exist) basal metazoan specifics deviating from the common metazoan regulome.

O4: Corroborate this data with the computational search for transcription factor binding motifs in co-expressed loci in order to further describe the developmental and differentiation regulome.

Secondments: Michael Schrödl (Munich), Denis Tagu (Rennes), Andreas Hejnol (Bergen).


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