Posts Tagged ‘chromosome’

CoGe

Friday, November 12th, 2010

There is an excellent comparative genomics site at UC Berkeley called CoGe. Check it out!

-- Eric Kofoid

Possible REP Snap-Back in TT24815 Chromosome

Thursday, March 25th, 2010

A read-depth analysis of the TT24815 chromosome is noisy though relatively flat. It has a few interesting spikes, including one near 336000, about 3x higher than the average read depth elsewhere.

tt24815_readdepth

The nearest rrn locus is rrnH, about 41 kb upstream of the spike, so I doubt that rrn’s are involved in the amplification.

I scanned the immediate vicinity and found a REP sequence at position 336899. The feature lies in the intercistronic space between the large (4 kb) rhsD gene and rhsE.

(In the following figures, add 336898 to “stem-loop” addresses and 300000 to plotfold addresses to get correct chromosomal positions.)

stem_loop

I looked for clusters of anomalous read-pairs in the vicinity. There are 23 read-pairs containing convergent joins in the rhsD gene (STM0291), 3 containing divergent joins a little upstream of these, 3 containing deletions in rhsD, and 8 containing tandem duplication join points, also in rhsD.

rep_snap_back

These read pairs are isolated members of the collection of sheared DNA. No single cell carries all of them and most contain none. Many may be uninheritable cast-offs discarded by error correction machinery.

Nevertheless, it appears that the REP could be nucleating snap-backs, which then get fixed in a variety of ways. Some of these may be full-fledged TIDs, some may be remodeled into tandem duplication arrays. My guess is that enough cells are carrying various forms of amplifications arising from this REP that they account for the spike.

-- Eric Kofoid