Lubin Lab at UAB

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Dr. Lubin’s page on UAB Department of Neurobiology website

UAB Graduate Biomedical Sciences

Epigenetics

Dr. Lubin’s research interest is focused on understanding the cellular and molecular mechanisms underlying transcriptional regulation of genes to mediate changes in synaptic connections between neurons in the central nervous system. Our research is primarily directed at characterizing the role of epigenetic mechanisms, such as histone modifications, DNA methylation, and the interaction of the NF-kB signaling pathway with chromatin to determine how these participate in the regulation of gene expression related to learning and memory and cognitive deficits.

Our research program focuses on neurons and synapses in the hippocampus, an area of the brain that plays an important role in learning and memory and the development of epilepsy in humans. We are investigating the epigenetic regulation of brain derived neurotrophic factor (BDNF) transcripts during memory formation. This has lead to the discovery that exon-specific gene regulation of BDNF transcripts are dynamically regulated by DNA methylation and specific histone modifications (acetylation and methylation) in hippocampus during memory consolidation. Current work also includes an assessment of DNA and Histone demethylating agents that may be promising in the mitigation or disruption of cognitive disorders.

Our laboratory uses interdisciplinary methods ranging from systems to molecular neuroscience: Behavior (learning and memory tasks for rats and mice); Kainate Epilepsy rodent model; Acute hippocampal slice preparations for pharmacological bath applications; Rodent brain surgeries (e.g., Cannula and electrode implantations); Cell and molecular biology [immunohistochemistry, quantitative real-time PCR, Methyl Specific Bisulfite PCR (MSP), Bisulfite sequencing PCR (BSP), Methyl-DNA immunoprecipitation (MeDIP), Western blotting (e.g., Histone modifications, NF-kB, p65), Electrophoretic Mobility Shift assays (EMSAs), Chromatin Immunoprecipitation (ChIP) assays, Laser-capture microdissections (LCM, e.g. cell-type specific changes in DNA methylation and gene expression (e.g. BDNF, Zif268)]; Neurophysiology (long-term potentiation) and Genomic analyses (Direct Bisulfite Sequencing and Pyrosequencing) (via collaborations with other neuroscience laboratories and Core facilities at UAB).

Figure 1. Nuclear factor-kappa-light-chain-enhancer of activated B cells (NF-kB) signaling mediates histone H3 post-translational modification in hippocampus during memory reconsolidation (Adapted from Neuron 2007).

Figure 2. Covalent post-translational modifications of histones. Schematic of the covalent histone modifications observed in histone H3, which include acetylation, phosphorylation and methylation. Lysine methylation is catalyzed by histone methyltrasferases (HMT) and the reverse reaction is catalyzed by histone demethylases (HDM). Methylation of lysine residue can result in gene activation or repression. Histone H3 Lysine acetylation is catalyzed by histone acetyl transferase (HAT) and deacetylated by histone deacetylases (HDAC). Histone deacetylase inhibitors (HDI) target HDACs resulting in de-compaction of chromatin. Serine phosphorylation is catalyzed by protein kinases (PK) and reversed by protein phosphatase (PP). H3, Histone-3; K, Lysine; S, Serine.

Figure 3. Covalent DNA modifications. A) DNA methylation occurring at cytosine residues of CpG sites, renders the DNA inaccessible to transcription. B) Mechanism of DNA methylation; the enzyme DNA methyltransferase (DNMT) catalyzes the conversion of cytosine to 5-methylcytosine. The methyl group is donated by S-adenosylmethionine (SAM). DNMT inhibitors block DNA methylation.