Chromatin and Gene Analyses

One of the major objectives of this Center is to define the transcriptome and epigenome of depression and antidepressant treatment within the brain's limbic regions and to use this information as a foundation from which to define novel mechanisms of neural and synaptic plasticity that control mood under health and disease. We use a broad range of genome-wide approaches to map the effects of stress and antidepressant treatments. For example, ChIP-seq (chromatin immunoprecipitation followed by high throughput sequencing) is used to define, genome-wide, the range of chromatin modifications that are induced by stress or antidepressant medications in specific limbic brain regions over the life cycle of the individual, both in animal models and postmortem human brain. WGBS (whole genome bisulfite sequencing) is used to map DNA methylation, including both 5-methylcytosine and 5-hydroxymethylcytosine. ATAC-seq is used to map nucleosome positioning. A host of chromatin conformation capture techniques (3C, 4C, and 5C) are used to map chromosomal loopings—the so-called 3D genome. Finally, RNA-seq is used to identify, genome-wide, all RNAs whose expression levels are altered in these same regions in response to chronic drug exposure. A major feature of this work is the advanced bioinformatic analyses that are required to optimally mine the vast amounts of such data generated by our research. Center investigators have led the field in genome-wide gene and chromatin analyses within depression models, including pioneering these approaches in brain—especially human brain, which offers several unique technical challenges.

Chromatin and Gene Analyses | Conte Center | Mount Sinai

FIGURE. Examples of ChIP-seq data from NAc. Plots show genome-wide binding patterns of several chromatin marks around promoter regions of genes (LEFT) and gene bodies (RIGHT). H3K4me3, H4K16ac, and Pol-II binding are enriched around transcription start sites (TSS); H3K36me3 is more enriched in gene bodies (toward transcription end sites or TES); and H3K9me2 is more evenly distributed across genes - compared to DNA input. These patterns are very similar to genome-wide patterns observed for these marks in cultured neurons and in peripheral tissues, demonstrating our ability to obtain very high quality ChIP-seq data from microdissected brain regions. The y-axis is in arbitrary units, allowing the plotting of multiple marks on the same graph.