The cerebral cortex or brain is a complex organ because millions of circuits involving various neuronal subtypes give rise to complex behavior or specific function. This process of neuronal circuit formation involved a complex network of transcriptional control of specification and plasticity of neurons. FEZF2 is one such transcription factor that is essential for the specification of sub-cerebral projection neuron (SCPN), which is part of layer 5 cortical layer. Factors such as SOX4, SOX5, SOX11, and TBR1 are upstream regulators and bind to enhancer (E4) and non-coding regions of the FEZF2. Levels of these factors and timing of expression are crucial for cortical layer formation. This along with chromatin regulation remains to be explored. A research study by Muralidharan and colleagues explores how transcription factor LHX2 regulates SOX11 and FEZF2. This helps understand the cortical neurogenesis and spatiotemporal dynamics during early cortical development.
The research group performed loss of LHX2 function. This causes an increase in the number of neurons expressing FESF2, altering the fate of SCPN. They performed techniques like ChIP-Seq, mass spectrometry, and nucleosome remodeling, and histone deacetylase (NuRD) complex of chromatin regulators that could potentially bind to LHX2. The transcription start sites (TSS) and LHX2 binding sites of both FEZF2 and SOX11 are epigenetically modified and display histone marks.
Techniques:
ChIP-Seq: This technique helps in analyzing the interaction of proteins with DNA. Chromatin immunoprecipitation and parallel DNA sequencing help in the identification of binding sites of the DNA-associated proteins. It can also be used for creating a global map of DNA binding sites. This is primarily used for determining how transcription factors and chromatin-associated proteins influence behavior, phenotype, or hereditary traits.
Mass Spectrometry: This analytical technique is used to obtain mass-to-charge ratios of ions, where a sample (solid, liquid, or gaseous) is bombarded with a beam of electrons. This leads to the fragmentation of the sample into positively charged molecules. These molecules or ions are separated based on the charge-to-mass ratio. These molecules are subjected to an electric or magnetic field after which the molecules are detected with the help of an electron multiplier. This detection is represented as the signal intensity of the ions as a function of the charge-to-mass ratio. Hence, each sample will display a characteristic pattern.
Nucleosome remodeling or chromatin remodeling is a dynamic process of chromatin modification that allows condensed parts of the chromatin to open to regulatory proteins (such as transcription factors). This is achieved by histone modifications using specific enzymes such as deacetylases, methyltransferases, and kinases. This not only helps in identifying the pattern and extent of gene expression but also epigenetic regulation and control mechanisms of these genes through DNA replication, repair, apoptosis, or cell fate determination (like in the case of the paper under discussion). This is the basic concept that’s being explored in this paper using techniques such as ChIP-Seq and mass spectrometry.
This paper provides an extensive analysis of how LHX2 epigenetically controls the cellular subtype identity of cortical neurons. This study helps us understand how the transcription factor network influences gene expression leaving epigenetic marks during brain development. Such studies will be useful to understand genetic disorders associated with brain development in human beings and possible treatments.
PS: The basic concepts based on this article are provided as links in the first paragraph. Learn the basics of epigenetics here.