Modeling and predicting the structure of transmembrane proteins
Speaker: Elizabeth Thomas , Bauer Center for Genomics, Harvard
Date: March 14 2005
Time: 11:30AM to 1:00PM
Location: 32-G575
Host: P Clote/ BC & B Berger/ MIT, MIT- Dept of Mathematics, CSAIL & HST
Contact: Kathleen Dickey, 617 253-3037, kvdickey@mit.edu
Relevant URL: http://www-math.mit.edu/compbiosem/Mammalian genomes are densely populated with long duplicated sequences. In this work, we demonstrate the existence of doublets, short duplications between 25 and 100 bp, distinct from previously described repeats. Each doublet is a pair of exact matches, separated by some distance. The distribution of these inter-match distances is strikingly nonrandom. An
unexpectedly high number of doublets have matches either within 100 bp (adjacent) or at distances tightly concentrated ~1,000 bp apart (nearby). We focus our study on these proximate doublets. First, they tend to have both matches on the same strand. By comparing nearby doublets shared in human and chimpanzee, we can also see that these doublets seem to arise by an insertion event that produces a copy without markedly affecting the surrounding sequence. Most doublets in humans are shared with chimpanzee, but many new pairs arose after the divergence of the species. Doublets found in human but not chimpanzee are most often composed of almost tandem matches, whereas older doublets (found in both species) are more likely to have matches spaced by {approx}1 kb, indicating that the nearly tandem
doublets may be more dynamic. The spacing of doublets is highly conserved.
So far, we have found clearly recognizable doublets in the following genomes: Homo sapiens, Mus musculus, Arabidopsis thaliana, and Caenorhabditis elegans, indicating that the mechanism generating these doublets is widespread. A mechanism that generates short local duplications
while conserving polarity could have a profound impact on the evolution of regulatory and protein-coding sequences.
MIT
Department of Mathematics
& The Theory of
Computation Group
At CSAIL
****please note that there won't be a talk the week of March 21st.****
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