Epigenetics, broadly defined as heritable changes in gene expression independent of changes to the DNA sequence itself, is tightly associated with how one genome can give rise to multiple phenotypes. Social insects are an ideal model system for epigenetics, as their colonies contain individuals with highly similar genomes but divergent behaviors and phenotypes. Harpegnathos saltator in particular provides opportunities for studying epigenetic control over gene expression, as typically non-reproductive workers can be induced to activate their ovaries and reproduce in the absence of a dominant reproductive, a transition accompanied by substantial changes in gene expression. Long untranslated transcripts (lncRNAs), are one means by which epigenetics asserts control over gene regulation in a variety of organisms, including Harpegnathos. Technologies for better annotation and functional classification of lncRNAs have provided insight into biochemical mechanisms, while studying lncRNAs in a variety of model systems has illuminated aspects of their biological impact. Here, we investigate how caste-specific gene expression in ant brains affects phenotype and develop a method to study R-loops, a potential mechanism of lncRNAs. The first section describes how we improved the contiguity of the Harpegnathos genome using PacBio long-read sequencing technology, enabling the annotation of lncRNAs and identification of caste-, brain-, and developmental stage-specific lncRNAs. The biochemically focused second section discusses development of a method called MapR to detect R-loops, DNA:RNA hybrids that form co-transcriptionally at many loci and, in some examples, contribute to lncRNA function. The third section covers our investigation of cellular plasticity between brains of Harpegnathos ants of different castes and ages using single-cell sequencing, aided by the new genome assembly. Along with establishing a map of cell types in the social insect brain, we identified a caste-specific role for phagocytic ensheathing glia that persists throughout aging, indicating a potential contribution of these neuroprotective cells to the extended lifespan of gamergates. Overall, my thesis work explores the function of lncRNAs from the perspective of both biochemical mechanism and general biological function, revealing a complex repertoire of lncRNAs in a non-model organism and their finely tuned expression profiles on the levels of the whole organism and in single-cells.