The role of G-density in switch region repeats for immunoglobulin class switch recombination

• Published in: Nucleic acids research Vol. 42; no. 21; pp. 13186 - 13193
• Main Authors: Zhang, Zheng Z., Pannunzio, Nicholas R., Hsieh, Chih-Lin, Yu, Kefei, Lieber, Michael R.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.12.2014
• Subjects: Animals; Cell Line; DNA - chemistry; Genome Integrity, Repair and; Immunoglobulin Class Switching; Immunoglobulin Switch Region; Mice; Recombination, Genetic; Repetitive Sequences, Nucleic Acid
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gku1100

The boundaries of R-loops are well-documented at immunoglobulin heavy chain loci in mammalian B cells. Within primary B cells or B cell lines, the upstream boundaries of R-loops typically begin early in the repetitive portion of the switch regions. Most R-loops terminate within the switch repetitive zone, but the remainder can extend a few hundred base pairs further, where G-density on the non-template DNA strand gradually drops to the genome average. Whether the G-density determines how far the R-loops extend is an important question. We previously studied the role of G-clusters in initiating R-loop formation, but we did not examine the role of G-density in permitting the elongation of the R-loop, after it had initiated. Here, we vary the G-density of different portions of the switch region in a murine B cell line. We find that both class switch recombination (CSR) and R-loop formation decrease significantly when the overall G-density is reduced from 46% to 29%. Short 50 bp insertions with low G-density within switch regions do not appear to affect either CSR or R-loop elongation, whereas a longer (150 bp) insertion impairs both. These results demonstrate that G-density is an important determinant of the length over which mammalian genomic R-loops extend.