R-loop Identification and Mapping Methods

TOPICAL COLLECTIONS

Guest Editor

Elizabeth Tran

Purdue University, Department of Biochemistry

Dr. Elizabeth Tran is a professor at Purdue University in the Department of Biochemistry. She obtained her PhD at North Carolina State University in 2004 under the guidance of Dr. E Stuart Maxwell and subsequently completed postdoctoral training in the laboratory of Dr. Susan Wente at Vanderbilt University Medical Center in 2008. Her research program focused on RNA biology and regulation of gene expression. She is most well known for her work on DEAD-box RNA helicases using classic biochemistry and both budding yeast S. cerevisiae and mammalian cell model systems. These studies formed the groundwork for numerous investigations into the mechanisms for unwinding, the inter-relationship between nucleic acid structure and expression of specific genes, and how defects in these processes can result in the onset of cancer. She has also made significant discoveries regarding the role of R-loops—ubiquitous, non-B-form DNA structures that function in a variety of cellular processes from gene regulation to DNA repair. In addition to research, Dr. Tran is currently the Director of Graduate Studies in the Department of Biochemistry at Purdue University. She has also been heavily involved in the broader scientific community where she has developed new events at international conferences specifically geared to the needs of junior scientists. In 2018, she earned the Showalter University Scholar award for outstanding research at Purdue as well as the RNA Society Lifetime of Service Award for all of her efforts with the international RNA Society during her scientific career.

Collection Overview

R-loops are ubiquitous and prevalent three-stranded nucleic acid structures composed of an RNA-DNA hybrid and a single stranded DNA. These structures have been found in prokaryotes, eukaryotes, and viruses and occur when a single-stranded RNA invades the double-stranded DNA duplex genome. Initially thought to be a detrimental byproduct of failed RNA processing during transcription, R-loops have now been shown to function in a variety of biologically beneficial processes such as genome editing, DNA repair, and both transcriptional and post-transcriptional gene expression steps. Understanding the biochemical mechanisms for R-loop-mediated cellular processes necessitates development and usage of highly efficient and high-resolution methods to identify when and where R-loops form in a variety of different cell types and organisms. Thus far, the vast majority of R-loop identification methods have relied on immunoprecipitation methods using the RNA-DNA hybrid-binding antibody, S9.6. However, issues with length bias and cross-reactivity with double-stranded RNA have led to the development of several new approaches. The purpose of this collection is to gather and showcase the current methods for both low throughput and genome-wide R-loop identification along with helpful tools for downstream bioinformatic analyses.