Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior

Abstract

Examining the role of chromatin modifications and gene expression in neurons is critical for understanding how the potential for behaviors are established and maintained. We investigate this question by examining Drosophila melanogaster fru P1 neurons that underlie reproductive behaviors in both sexes. We developed a method to purify cell-type-specific chromatin (Chromatag), using a tagged histone H2B variant that is expressed using the versatile Gal4/UAS gene expression system. Here, we use Chromatag to evaluate five chromatin modifications, at three life stages in both sexes. We find substantial changes in chromatin modification profiles across development and fewer differences between males and females. We generated cell-type-specific RNA-seq data sets, using translating ribosome affinity purification (TRAP), and identify actively translated genes in fru P1 neurons, revealing novel stage- and sex-differences in gene expression. We compare chromatin modifications to the gene expression data and find patterns of chromatin modifications associated with gene expression. An examination of the genic features where chromatin modifications resides shows certain chromatin modifications are maintained in the same genes across development, whereas others are more dynamic, which may point to modifications important for cell fate determination in neurons. Using a computational analysis to identify super-enhancer-containing genes we discovered differences across development, and between the sexes that are cell-type-specific. A set of super-enhancer-containing genes that overlapped with those determined to be expressed with the TRAP approach were validated as expressed in fru P1 neurons. Author SummaryDifferences in male and female reproductive behaviors are pervasive in nature and important for species propagation. Studies of sex differences in the fruit fly, Drosophila melanogaster, have been ongoing since the early 1900s, with many of the critical molecular and neural circuit determinates that create sexually dimorphic behavior identified. This system is a powerful model to understand fundamental principles about the underpinnings of complex behavior at high resolution. In this study, we examine the gene expression and chromatin modification differences specifically in a set of neurons that direct male and female reproductive behaviors in Drosophila. We describe differences across development and between the sexes with the goal of understanding how the potential for behavior is created and maintained.