Gene regulatory mechanisms underlying neuronal function

2 PhD projects offered in the IPP summer call 2020

PhD Project 1: Molecular mechanisms of contrast- and luminance sensitivity

Scientific Background

We are interested to understand the molecular and circuit mechanisms behind neural computations. We study this in the fly visual system, where the anatomy and connectivity of the ~100 cell types are known with exquisite details, and powerful genetic tools exist to measure and manipulate. The identity and contribution of many cell types to specific visual processing steps has been worked out. Any given cell type achieves a functional state based on the expression of specific sets of genes. We for example recently identified a single transcription factor that determines fundamentally different processing strategies in first order interneurons of the fly visual system, namely luminance vs. contrast sensitivity. We are now broadly interested to understand how gene regulatory mechanisms specify and maintain neuronal function. Neurons also maintain their functional properties longer than their subcellular components. This suggests cell intrinsic mechanisms that keep the cell in a transcriptional state that is critical for maintenance of the neuron’s properties. The key determinant of this transcriptional state is the control of gene expression via correlated action of transcription factors and chromatin proteins. Thus, understanding the molecular mechanism behind gene expression control reveals the relationship between the gene expression and functional state.

Project Description

The goal of this project aims to obtain a comprehensive understanding of cell-type specific gene expression and its effect on functional properties of cells involved in visual-processing circuits. Specifically, we recently found that two first interneurons  in the fly visual system show fundamentally different physiological properties (Ketkar et al. 2020). This depends on the activity of a single transcription factor (unpublished), and we next want to understand how this transcription factor mediates neuronal function. The lab has also recently developed an ultra-low input ChIP-Seq approach on cells isolated though Fluorescence Activated Cell Sorting (FACS) to investigate epigenetic marks and transcription factor binding (Akthar et al. 2019). We plan to leverage this approach as well as low amount RNA-seq to identify genes that are differentially expressed between cell types.
We will then combine this approach with neuroscience techniques and test the functional role of candidate genes using of in vivo two photon calcium imaging in the living fly brain, or by using behavioral assays. This will allow us to link differences in gene expression to neuronal function (see e.g. Molina-Obando et al. 2019, Ketkar et al. 2020).
We are looking for a motivated student with a strong intrinsic drive to make exciting discoveries in an interdisciplinary field, bridging molecular biology and neuroscience.

PhD Project 2: Measuring, modeling, and manipulating spontaneous-activity during visual system development

Scientific Background

To perform neural computations with flexibility and robustness, sensory centers need to be correctly wired during development. Although circuit development has been largely considered to be hard-wired in Drosophila, there is evidence of activity-dependent refinement of cellular and synaptic properties that may influence circuit function. Spontaneous activity (SA) has recently been reported in the developing visual system of Drosophila (Akin et al. Neuron 2019), which stands to be an excellent system to test causal relationships between such developmental SA and adult circuit function.
The optic lobe is further ideal to combine theoretical modeling and experimental approaches to explain the functional relevance of SA. The vast Drosophila molecular genetic toolkit offers an unparalleled opportunity to link developmental activity and adult function. Previous efforts on modeling the spontaneous activity in the mouse visual system provide a basis for model design and comparison.

Project Description

In Drosophila, adult visual system development starts in the larva and continues throughout the pupa. SA appears during the second half of the pupa. To characterize regular features within SA, we will establish a protocol for calcium imaging in the developing visual system, and quantitatively describe spatial and temporal features of SA. With these data in hand, we aim to build a network model based on the architecture of the optic lobe to describe and test the role of plasticity driven by SA on circuit development. Based on this model, we aim to identify cellular mechanisms that could influence receptive fields and contrast selectivity.
We will then experimentally probe how spontaneous activity influences adult visual system function. The Drosophila genetic toolkit allows to acutely, decrease or increase electrical activity, using genetic silencing or optogenetics. Following such perturbations, we will measure spatial receptive fields and temporal filters in the adult. Together, computational and experimental approaches will clarify the role of SA in the development of sensory circuits in Drosophila and open an avenue to find cellular properties influencing network formation.

Publications relevant to the projects

Ketkar M D, Sporar K, Gür B, Ramos-Traslosheros G, Seifert M, Silies M (2020) Luminance Information Is Required for the Accurate Estimation of Contrast in Rapidly Changing Visual Contexts. Current Biology, 30: 657-669 Link

Molina-Obando S, Vargas-Fique J F, Henning M, Gür B, Schladt T M, Akhtar J, Berger T K, Silies M (2019) ON selectivity in Drosophila vision is a multisynaptic process involving both glutamatergic and GABAergic inhibition. eLife, pii: e49373. doi: 10.7554/eLife.49373. Link

Akhtar J, More P, Albrecht S, Marini F, Kaiser W, Kulkarni A, Wojnowski L, Fontaine J F, Andrade-Navarro MA, Silies M, Berger C (2019) TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay. Life Sci Alliance: e201900318. doi: 10.26508/lsa.201900318 Link

Peng J, Santiago IJ, Ahn C, Gur B, Tsui CK, Su Z, Xu C, Karakhanyan A, Silies M, Pecot MY (2018). Drosophila Fezf coordinates laminar-specific connectivity through cell-intrinsic and cell-extrinsic mechanisms. eLife 7: e33962. doi: 10.7554/eLife.33962 Link

Fisher YE, Leong JCS, Sporar K, Ketkar MD, Gohl DM, Clandinin TR and Silies M (2015) A class of visual neurons with wide field properties is required for elementary motion detection. Current Biology, 22: 3178 – 3189 Link




Marion Silies