Single sample sequencing (S3EQ) of epigenome and transcriptome in nucleus accumbens

Area of Science:

• Neuroscience
• Genomics
• Molecular Biology

Background:

• High-throughput sequencing is crucial for understanding neurological and psychiatric disorders.
• Epigenetic mechanisms play a significant role in neurological function.
• Current methods analyze epigenetic and transcriptomic changes in separate cohorts, limiting precise correlation.

Purpose of the Study:

• To introduce Single Sample Sequencing (S3EQ) for analyzing both epigenetic and transcriptomic regulation within a single neuronal sample.
• To overcome the limitations of analyzing separate cohorts for epigenetic and transcriptomic data.

Main Methods:

• Developed and applied Single Sample Sequencing (S3EQ) to analyze chromatin immunoprecipitation (ChIP)- and RNA-sequencing data from the same neuronal sample.
• Utilized S3EQ on nucleus accumbens (NAc) samples from adult mice.

Main Results:

• ChIP-S3EQ reliably identified histone post-translational modification (hPTM) enrichment in adult mouse NAc.
• RNA-S3EQ from cytosolic fractions better recapitulated spliceosome profiles compared to nuclear RNA-seq.
• S3EQ demonstrated increased sensitivity in correlating chromatin modifications with gene expression, particularly for lowly expressed transcripts.

Conclusions:

• S3EQ accurately generates both RNA- and ChIP-seq from a single sample, offering an advantage over existing two-sample methods.
• ChIP-S3EQ performance is comparable to standard ChIP-seq.
• RNA-S3EQ provides expression profiles similar to nuclear-enriched and whole-cell RNA-seq, enabling direct comparison across cellular compartments.