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closeC3H genome sequence
Posted by wfrankel on 03 Mar 2008 at 14:02 GMT
Would be really interesting to see the extent of new insertions in one of the C3H substrains, should this sequence become available, since as you know IAPs have often been seen replicate in C3H and cause mutations. What would be your guess as to the number unique IAP's that C3H would have?
RE: C3H genome sequence
yzhang replied to wfrankel on 13 Mar 2008 at 23:59 GMT
We agree that it would be extremely interesting to determine the number of unique IAPs in C3H since we expect it to be much higher than most other strains, based on the frequency of new IAP-induced mutations in this genetic background. A very limited number of Whole Genome Shotgun C3H/HeJ sequence traces are available and we detected 74 IAPs in those sequences. However, among these 74, we found only 3 IAPs unique to C3H (4%), which is a percentage similar to the other four strains used in the paper. This result is unexpected and we do not yet have a good explanation. Do you have any ideas? It is possible that the small C3H dataset may not be representative, so we are also planning to experimentally measure the relative numbers of active IAPs (the 1delta1 subtype) in the C3H genome compared with other strains.
RE: RE: C3H genome sequence
wfrankel replied to yzhang on 20 Mar 2008 at 11:46 GMT
Other than sampling, which is an issue both for strains and sequence, the only thing I can think of at the moment is that since the survey so far was limited to a few strains, perhaps the 4% that you saw for the four strains were not quite novel insertions but rather polymorphisms (as you correctly claimed) and not yet fixed in the four strains (but would be present in others). A survey of more strains might have knocked this % down somewhat. However, maybe in C3H those 3 proviruses were more recent insertions. From my postdocdom, with similar numbers of MLVs proviruses sampled (but most of them since they were fewer) C3H did not have any new MLVs that were not in other strains. This is consistent with their history as being derived from Bagg's albino (which became BALB/c) and DBA strains. So, the bet would be that most of the novel IAP's in C3H would be unique. Will be interesting to see if more C3H gets sequenced.