Chromatin Regulation in Complex Brain Disorders

Abstract

Chromatin-related phenomena regulate gene expression by altering the compaction and accessibility of DNA to relevant transcription factors, thus allowing every cell in the body to attain distinct identities and to function properly within a given cellular context. These processes occur not only in the developing central nervous system, but continue throughout the lifetime of a neuron to constantly adapt to changes in the environment. Such changes can be positive or negative, thereby altering the chromatin landscape to influence cellular and synaptic plasticity within relevant neural circuits, and ultimately behavior. Given the importance of epigenetic mechanisms in guiding physiological adaptations, perturbations in these processes in brain have been linked to several neuropsychiatric and neurological disorders. In this review, we cover some of the recent advances linking chromatin dynamics to complex brain disorders and discuss new methodologies that may overcome current limitations in the field.

Figure 1.. Epigenetic regulation of gene expression.

Chromosomes are comprised of chromatin fibers that contain nucleosomes: DNA (~146 bp) wrapped around the histone octamer (four core histone proteins, with two copies each of H2A, H2B, H3 and H4). Stretches of chromatin can either be open (i.e., euchromatic) or closed (i.e., heterochromatic) to transcriptional regulation. Enzymes and chromatin-interacting proteins that deposit (i.e., “writers”), remove (i.e., “erasers”) and “read” chemical modifications on DNA and histone tails alter the compaction of chromatin. DNA methylation is typically associated with heterochromatin, while depending on the type of chemical modification and residue, histone PTMs can either be associated with eu- or hetero-chromatin formation.

Figure 2.. Techniques for assessing cell-type specific chromatin states in brain.

Alterations in chromatin following environmental stimuli/experiences underlie the development of several complex brain disorders. Accurate assessments of these changes can be achieved by using neural cell-type specific reporter lines where neurons are fluorescently tagged (can even be achieved following “activation” by environmental stimuli). Cells/nuclei can be sorted using INTACT or FACS/FANS and used for several downstream analyses: 1. RNA-seq can measure relative levels of transcripts. 2. ChIP-seq utilizes antibodies specific for histone PTMs and/or transcription factors to examine alterations in their genomic enrichment in response to experience. 3. Hi-C can be used to discover contacts between proximal and distal genomic loci that may affect gene expression and/or chromatin structure. 4. ATAC-seq can be used to access chromatin accessibility and for transcription factor foot printing. 5. Histone MS can be used to identify and quantify single and combinatorial histone PTMs simultaneously. 6. Global MS can be used to characterize the entire proteome within a given set of cells. INTACT = isolation of nuclei tagged in specific cell types; FACS/FANS = fluorescent-activated cell/nuclear sorting; seq = high-throughput sequencing; ChIP = chromatin immunoprecipitation; TSS = transcriptional start site; PTM = post-translational modification; ATAC = assay for transposase-accessible chromatin; MS = mass spectrometry.

Figure 3.. The potential use of trans-splicing inteins for synthesis of modified histone proteins in brain.

Specific populations of neurons in vivo could be transduced to express truncated versions of histone proteins lacking segments of their tails fused to an intein fragment (e.g., Int^N). Then, using temporal delivery of a synthetic cargo in brain–via a cell-penetrating peptide (CPP) conjugated to the other intein fragment (e.g., Int^C)–modified histone tails could theoretically be delivered and fused to the truncated histone protein in a traceless manner. On the cellular level, the synthetic peptide would be taken-up by the endocytic pathway, after which it would be released to the cytosol following endosomal rupture. The naturally reducing environment of the cytosol would promote the release of the intein peptide from the CPP. The free intein containing the modified histone tail would then diffuse into the nucleus where it would splice with its intein counterpart, thereby leaving a site-specific modified histone incorporated in neuronal chromatin.