Detection and structural analysis of R-loops.
R-loops are structures where an RNA strand is base paired with one DNA strand of a DNA duplex, leaving the displaced DNA strand single-stranded. Stable R-loops exist in vivo at prokaryotic origins of replication, the mitochondrial origin of replication, and mammalian immunoglobulin (Ig) class switch regions in activated B lymphocytes. All of these R-loops arise upon generation of a G-rich RNA strand by an RNA polymerase upon transcription of a C-rich DNA template strand. These R-loops are of significant length. For example, the R-loop at the col E1 origin of replication appears to be about 140 bp. Our own lab has focused on class switch regions, where the R-loops can extend well over a kilobase in length. Here, methods are described for detection and analysis of R-loops in vitro and in vivo.
Yu
Kefei
K
Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, USA.
Roy
Deepankar
D
Huang
Feng-Ting
FT
Lieber
Michael R
MR
D000818:Animals; D004247:DNA / Q000737:chemistry*; D051379:Mice; D015335:Molecular Probes; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D017422:Sequence Analysis, DNA; D013447:Sulfites / Q000737:chemistry
D015335:Molecular Probes; D013447:Sulfites; D012313:RNA; D004247:DNA; C009279:sodium bisulfite