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Genetic mechanisms and signaling pathways in the developing brain:  from epigenetic control of cell fate to neurocircuitry and behaviour

The cerebral cortex is the most complex brain structure and responsible for higher functions such as sensory perception, motor control, language, learning and memory.  How this structure is formed from a simple sheet of tissue in the embryo is one of the most important areas of exploration in neurobiology.  We use multiple approaches aimed at answering different aspects of the fundamental question of how the cortex is formed.

Genetic approaches:

We use knockout mice, conditional gene inactivation, in utero perturbation, RNAi, and gene overexpression to test the function of different genes, and to test the interaction between different signaling pathways.  The “readouts” we employ are changes in cell fate, morphogenesis, cell signaling, cell migration, and axon outgrowth.  Some projects are aimed at examining specific behaviors in mature animals.

Reference: Mangale et al., Science, 2008; Subramanian et al., PNAS, 2011

Biochemical and Molecular Biological approaches:

We focus on known regulators of cell identity, cell migration, and axon outgrowth, and examine the protein complexes they participate in.  For example, we recently reported that transcription factor Lhx2 binds members of the NuRD complex of chromatin modifiers in the developing cerebral cortex (Muralidharan et al., 2016).  These NuRD complex members were identified by Mass-spectrometry, and validated by protein immunoprecipitation and western blotting.  Furthermore, using chromatin immunoprecipitation followed by sequencing (ChIP-seq), we identified several targets of Lhx2 in the developing cerebral cortex and hippocampus.  Future projects in the lab are aimed at exploring these targets and how they control the development of specific brain structures.

Reference: Muralidharan et al., Journal of Neuroscience, 2016

Epigenetic approaches:

We identified that specific regulators of cerebral cortical development, Fezf2 and Sox11, are epigenetically modified by Lhx2 (Muralidharan et al., 2016).  Future projects in the lab are aimed at what types of epigenetic modifications are predominant in the presence and absence of Lhx2.  Since this transcription factor is a fundamental regulator of the development of the cortex, hippocampus, olfactory bulb, amygdala, and hypothalamus, this exploration will begin with epigenetics and molecular biology, and lead into an examination of the development of each of these brain structures.

Reference: Muralidharan et al., Journal of Neuroscience, 2016

Examining Neurocircuitry: 

We are interested in the mechanisms governing the connectivity of critical in the brain, that bring olfactory, visual, sensory, and auditory information to the cerebral cortex, the tracts that connect the two hemispheres together, and the tracts that carry information to and from the hippocampus, which is critical in learning and memory.  These projects use tissue culture, in vivo tract tracing using advanced microscopic techniques, CLARITY-based whole brain imaging, gene misexpression or perturbation, immunohistochemistry and tissue sectioning.  The insights we hope to gain are in the fundamental question of how the “hardware” of the brain is set up so that the “software” may operate, and enable our complex brain functions.  Ultimately, we will examine the behavior of the animal with specific perturbations, to examine how the altered development of a particular tract affects the behavior of the animal.

Reference:  Saha et al., Journal of Neuroscience, 2007; Shetty et al., PNAS, 2013.

Electrophysiological approaches

Specific projects are aimed at asking how the function of individual neurons in a circuit is controlled by genetic mechanisms.  These projects are motivated by an interest in disorders such as autism, and the genes we target are well established or novel candidates that may play a role in this disorder. The molecular datasets we obtained from the ChIP-seq projects form the basis of these questions.

Behavioural Neuroscience

Ultimately, the gene disruption or epigenetic perturbations we study regulate specific developmental phenomena, such as neurogenesis/gliogenesis/cell fate/cell identity/cell migration/axon outgrowth/circuit formation.  These directly control the behavior of the animal.  Therefore, many projects are aimed at testing setting up specific behavioral paradigms to extend our studies from gene to behavior.