Detection and characterization of R-loops at the immunoglobulin switch alpha (Sα) region
Date Issued
2011
Date
2011
Author(s)
Kao, Yu-Pu
Abstract
After stimulation with external antigens and coupling with activation of T cell , naïve B cells can differentiate into plasma cells that produce antibodies . External antigens are processed and bound to B cells. That activates the appropriate immune response in B cells and antibody production to protect the body. Antibody can be divided into five main isotypies according to constant regions, namely IgM, IgG, IgA, IgD and IgE; Different antigens stimulate B cells to undergo class switch recombination (CSR) for production of different types of antibodies. Different isotypies of antibodies trigger different immune response so as to enhance the ability of removing different kinds of antigens. class switch recombination is initiated by activation-induced cytidine deaminase (AID), which in two switch (S) regions of the antibody genes so that S region can further generate double-stranded breaks and then two S region are combined by non-homologous end joining (NHEJ) and other mechanisms.
When RNA polymerase transcribes DNA in the S region, RNA is produced and base paired with the template strand DNA, so that another strand of DNA exists in single-stranded form, which is called the R-loop. The target of AID is single-stranded DNA. Therefore, it’s assumed that R-loop structures may provide AID’s substrates, and which makes AID trigger CSR. However, this hypothesis needs to be confirmed with more experiments.
Previous research indicates that R-loop structures exist at the Sμ, Sγ2b and Sγ3 in primary B cells of mice, and which makes it more possible that R-loops structure provide substrates for AID. In order to better apprehend the function of R-loop structures, we test whether R-loop structures existat the Sα in CH12F3-2A cells (a murine B cell line). The CH12F3-2A cell would switch to IgA positive cells through CSR after stimulation. If R-loops exist at the Sα, where are initiation sites and the endpoints of R-loops? In addition, whether the frequency of R-loops is directly proportional to the frequency of CSR? If so, it can further determine that R-loops structure is important to CSR.
In the thesis, results show that R-loop structures also exist at the Sα, and it supports that R-loops are the common features of S regions. Surprisingly, the initiation sites of some R-loops are located in the region upstream of the Sα; this phenomenon is never observed in other acceptor switch regions, and this particular R-loop has a recurring phenomenon, which may be correlated with that fact that the G density of Sα is lower than the other S regions. However, it needs to be confirmed by more experiments. In addition, R-loop with initiation sites in the Sα region are detected in stimulated cells but not in unstimulated cells. With increasing of stimulation time, there is no significant difference of the pattern of R-loops. Moreover, since CSR breakpoints often appear in the core region of Sα, we also detect and analyze R-loops in the core region of the Sα.
Subjects
Class switch recombination
Switch region
R-loops
Activation induced cytidine deaminase
Immunoglobulin
Type
thesis
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