Class switch recombination (CSR) is the somatic DNA rearrangement process by which B lymphocytes change their heavy chains from IgM to IgG, IgA or IgE. This DNA recombination process is distinctive among all eukaryotic (and prokaryotic) recombination mechanisms because it is the only one in which the recombination occurs within long repetitive regions in a manner that is dependent on transcription through the region such that a G-rich transcript is generated. Understanding of the mechanism of this process is important for immunologic reasons (infection, allergy, autoimmunity) and for its cancer-relevance (neoplastic translocations that occur within the class switch sequences, such as the t(8;14)). In the previous funding cycle, we showed that class switch regions assume a distinctive structure within the chromosomes of appropriately stimulated B cells. This structure is an R-loop in which the G-rich (nontemplate) strand of the repetitive switch regions is single-stranded for lengths exceeding 1 kb. The G-rich RNA that is generated by transcription through the switch region remains annealed to the C-rich (template) strand of the switch region. These results explain the in vivo orientation-dependence of the transcription requirement, which we documented in our earlier switch recombination work. In the current proposal, Aim 1 examines whether the chromosomal R-loop is limited to the switch repeats and whether it is affected by splicing.
Aim 2 examines the mechanism of R-loop formation, and this is optimally done in vitro where we probe the structure with enzymes; study the repeat length and sequences needed for R-loop formation; vary the rate of RNA polymerase movement; and vary the number of hybrogen bonds in the R-loop.
Aim 3 examines the interface between AID enzyme activity and R-loops. Can purified AID deaminate both DNA strands in the R-loop? Is the proximity of WRC sequence motifs on the two DNA strands critical for double-strand break formation? Aim 4 tests whether DNA ligase IV is required for CSR.
This aim i s directed at providing some clarification of what end joining pathway is used for class switch recombination. Hence, this proposal tests in vivo substrate structure, its mechanism of formation, the action of AID enzyme on that structure, and the pathway for rejoining the ends after breakage has occurred.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM056984-06
Application #
6995201
Study Section
Cellular and Molecular Immunology - B (CMI)
Program Officer
Portnoy, Matthew
Project Start
1998-09-01
Project End
2010-12-31
Budget Start
2007-01-01
Budget End
2008-12-31
Support Year
6
Fiscal Year
2007
Total Cost
$262,338
Indirect Cost
Name
University of Southern California
Department
Pathology
Type
Schools of Medicine
DUNS #
072933393
City
Los Angeles
State
CA
Country
United States
Zip Code
90089
Pannunzio, Nicholas R; Lieber, Michael R (2016) RNA Polymerase Collision versus DNA Structural Distortion: Twists and Turns Can Cause Break Failure. Mol Cell 62:327-334
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Lu, Zhengfei; Pannunzio, Nicholas R; Greisman, Harvey A et al. (2015) Convergent BCL6 and lncRNA promoters demarcate the major breakpoint region for BCL6 translocations. Blood 126:1730-1
Zhang, Zheng Z; Pannunzio, Nicholas R; Han, Li et al. (2014) The strength of an Ig switch region is determined by its ability to drive R loop formation and its number of WGCW sites. Cell Rep 8:557-69
Zhang, Zheng Z; Pannunzio, Nicholas R; Hsieh, Chih-Lin et al. (2014) The role of G-density in switch region repeats for immunoglobulin class switch recombination. Nucleic Acids Res 42:13186-93
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Lu, Zhengfei; Tsai, Albert G; Akasaka, Takashi et al. (2013) BCL6 breaks occur at different AID sequence motifs in Ig-BCL6 and non-Ig-BCL6 rearrangements. Blood 121:4551-4
Greisman, Harvey A; Lu, Zhengfei; Tsai, Albert G et al. (2012) IgH partner breakpoint sequences provide evidence that AID initiates t(11;14) and t(8;14) chromosomal breaks in mantle cell and Burkitt lymphomas. Blood 120:2864-7
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Roy, Deepankar; Zhang, Zheng; Lu, Zhengfei et al. (2010) Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site. Mol Cell Biol 30:146-59

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