71.6  Saturday, Jan. 5  Single-cell RNA-seq and cell-specific DNA methylation profiling for comparative and integrative biology: Toward genomic portraits of individual blastomeres and identified neurons KOHN, A.B.*; MOROZ, L.L.; University of Florida, Whitney lab abkohn@msn.com

Considering the enormous heterogeneity of cell populations, methodology for single-cell RNA-seq (transcriptome) and unbiased epigenomic analysis of individual cells is essential for biology in general, and for development and neuroscience in particular. Here we present novel approaches that allow fast and cost-efficient transcriptome sequencing from ultra-small amounts of tissue or even from individual cells across phyla. Specifically, the developed protocols not only can perform single-cell transcriptome profiling but also capture nascent RNAs (nRNAs) following a developmental program or experience-dependent plasticity (e.g. following learning and memory consolidation). We implemented and validated these protocols using identified molluscan neurons (Aplysia californica ) and developmental stages down to the 1 cell stage of the ctenophore Pleurobrachia bachei. As a result of initial mapping to the reference genomes, we estimated that the majority of the genome is expressed in a given cell, generating on the order of 100,000 unique transcripts (including large and small non-coding RNAs) supporting unique cell phenotypes. Furthermore, these RNAseq protocols can be integrated with DNA methylation from the very same cell and miRNA profiling. Because homologous cells and cell populations can be recognized across classes and phyla, both in early development and in nervous systems, it is now possible to follow dynamic reorganization of the specific cellular genomes in evolution to reveal the molecular bases underlying origins of complex phenotypes and novelties. Integrating this type of resolution to comparative biology has enormous evolutionary implications to deciphering the logic of gene regulation and the full scale integrative activity of genomes across phyla.