Cell-type specific profiling of histone post-translational modifications in the adult mouse striatum.
Marco D CarpenterDelaney K FischerShuo ZhangAllison M BondKyle S CzarneckiMorgan T WoolfHongjun SongElizabeth A HellerPublished in: Nature communications (2022)
Epigenetic gene regulation in the heterogeneous brain remains challenging to decipher with current strategies. Bulk tissue analysis from pooled subjects reflects the average of cell-type specific changes across cell-types and individuals, which obscures causal relationships between epigenetic modifications, regulation of gene expression, and complex pathology. To address these limitations, we optimized a hybrid protocol, ICuRuS, for the isolation of nuclei tagged in specific cell-types and histone post translational modification profiling from the striatum of a single mouse. We combined affinity-based isolation of the medium spiny neuron subtypes, Adenosine 2a Receptor or Dopamine Receptor D1, with cleavage of histone-DNA complexes using an antibody-targeted micrococcal nuclease to release DNA complexes for paired end sequencing. Unlike fluorescence activated cell sorting paired with chromatin immunoprecipitation, ICuRuS allowed for robust epigenetic profiling at cell-type specific resolution. Our analysis provides a framework to understand combinatorial relationships between neuronal-subtype-specific epigenetic modifications and gene expression.
Keyphrases
- gene expression
- dna methylation
- single cell
- single molecule
- genome wide
- cell therapy
- randomized controlled trial
- stem cells
- clinical trial
- oxidative stress
- circulating tumor
- mass spectrometry
- resting state
- transcription factor
- dna binding
- brain injury
- functional connectivity
- cerebral ischemia
- high throughput sequencing