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Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach
Qingqing Yan1, Emily J Shields2, Roberto Bonasio3
1Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Cell Reports
|October 31, 2019
Summary
MapR is a new method to detect DNA:RNA hybrids called R-loops, which are linked to diseases. This sensitive technique requires low input material and identifies R-loops at regulatory elements.
Area of Science:
- Molecular Biology
- Genomics
Background:
- R-loops are three-stranded DNA:RNA hybrids involved in nuclear processes.
- Aberrant R-loops are associated with neurological disorders and cancers.
- Existing methods for R-loop detection have limitations including high input requirements and low sensitivity.
Purpose of the Study:
- To develop a sensitive and efficient method for genome-wide R-loop detection.
- To overcome the limitations of current R-loop assessment techniques.
Main Methods:
- MapR utilizes RNase H to guide micrococcal nuclease to R-loops.
- R-loops are cleaved, released, and identified by sequencing.
- The method is designed for low input material and rapid processing.
Main Results:
- MapR detects R-loops at promoters and active enhancers.
- The method is highly sensitive and specific, comparable to existing techniques.
- MapR enables genome-wide R-loop coverage with significantly reduced input requirements and time.
Conclusions:
- MapR provides a sensitive, low-input method for genome-wide R-loop detection.
- This technique facilitates the study of R-loops in various biological contexts, including disease.
- MapR enhances the ability to study dynamic R-loops at regulatory elements.
