I have some Rag1-/- zebrafish, and I have primers that target the 3rd and 4th constant region segments of IgM, which should only be transcribed if the B cell is producing sIgM. I also have primers that target various V segments and the 1st constant region. When I do PCR with the V -> C1 primers, in WT fish, I get a band at ~500 bp (expected) and no band in the Rag1-/- fish (expected). However, with the C3 -> C4 primers, I get a band at ~200 bp (expected size) in both WT and Rag1-/- fish. I'm very confused by this result.
I think you may be describing "sterile" transcription, the transcription of gene segments that don't encode a functional protein. This is thought to contribute to accessibility of chromatin for class switch recombination, among other things. Here are some relevant papers: http://www.ncbi.nlm.nih.gov/pubmed/?term=sterile+transcript+constant+region
I've sequenced the 200bp product, it's definitely IgM constant region
I think should be refere any relavent paper...i will inofrm u very soon professor
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