534B Poster - 07. Chromatin, epigenetics and genomics
Friday April 08, 2:00 PM - 4:00 PM

Authors:
Timothy Stanek ^1,2; Rohan Mehra ¹; Weihuan Cao ¹; Christopher Ellison ¹

Affiliations:
1) Department of Genetics, Rutgers University, Piscataway, NJ; 2) Department of Pathology, Robert Wood Johnson Medical School, Piscataway, NJ

Keywords:
a. chromatin structure; h. sex-specific traits and molecules

R-loops are three-stranded nucleotide structures consisting of a DNA:RNA hybrid and a displaced ssDNA non-template strand. Originally viewed as byproducts of transcription, R-loops are now recognized as important regulators of gene expression and genomic stability. Persistent dysregulation of R-loop maintenance can result in replication stress, DNA double-strand breaks, and chromosomal rearrangements that contribute to diseases such as neurological disorders and cancer. Although R-loops are conserved across cell types in mammals, little is known about natural variation in R-loop formation between individuals.

Using DNA:RNA immunoprecipitation followed by high-throughput sequencing (DRIP-seq), we have mapped the R-loop profiles of two D. melanogaster individuals from the Drosophila Genetic Reference Panel (DGRP) in both males and females. R-loops are largely conserved across individuals and between sexes. Consistent with previous studies, R-loops are found at 5’UTRs of protein-coding genes and across many classes of noncoding RNA. R-loops are also enriched at Polycomb response elements and topologically associating domain boundaries. More broadly, R-loops are enriched in both the active RED and Polycomb Group BLUE chromatin states and depleted from GREEN heterochromatin and BLACK repressive states. Differential enrichment analysis reveals a small number of sex-specific R-loops: while non-differentially enriched and male-enriched R-loops form at similar genetic features and chromatin states and contain similar sequence motifs, female-enriched R-loops are enriched at unique genetic features, chromatin states, and sequence motifs. Male-enriched R-loops are most abundant on the dosage-compensated X chromosome, where R-loops appear stronger compared to autosomal R-loops. However, where most R-loop-containing genes exhibit higher levels of expression compared to R-loop-absent genes, male-enriched R-loops on the X chromosome do not correspond to increased gene expression. These male-enriched R-loops also show lower MOF binding and reduced H4K16ac, suggesting that canonical marks of hypertranscription associated with dosage compensation are antagonistic to R-loop formation. Collectively, these results reveal a series of sex-specific characteristics of R-loop formation in vivo and suggest that these hybrid structures can act to the benefit or detriment of specific cellular processes.