Conference reports
Daniela Raijman, TAU
Michal Ozery-Flato, TAU
Daniela will report on the Otto Warburg International Summer School and
Workshop on Evolutionary Genomics 2006.
She will present the work "Functionality of Intergenic Transcription:
An Evolutionary Comparison" by P. Khaitovich, J. Kelso, et al.
Abstract:
Although a large proportion of human transcription occurs outside the
boundaries of known genes, the functional significance of this
transcription remains unknown. We have compared the expression patterns
of known genes as well as intergenic transcripts within the ENCODE
regions between humans and chimpanzees in brain, heart, testis, and
lymphoblastoid cell lines. We find that intergenic transcripts show
patterns of tissue-specific conservation of their expression, which
are comparable to exonic transcripts of known genes. This suggests
that intergenic transcripts are subject to functional constraints that
restrict their rate of evolutionary change as well as putative positive
selection to an extent comparable to that of classical protein-coding
genes. In brain and testis, we find that part of this intergenic
transcription is caused by widespread use of alternative promoters.
Further, we find that about half of the expression differences between
humans and chimpanzees are due to intergenic transcripts.
Michal will report on the 4th RECOMB Comparative Genomics
Satellite Workshop (2006).
She will present the study "Inferring Gene Orders from Gene Maps
Using the Breakpoint Distance" by G. Blin, E. Blais, et al.
Abstract:
Preliminary to most comparative genomics studies is the annotation of
chromosomes as ordered sequences of genes. Unfortunately, different genetic
mapping techniques usually give rise to different maps with unequal gene
content, and often containing sets of unordered neighboring genes. Only partial
orders can thus be obtained from combining such maps. However, once a total
order O is known for a given genome, it can be used as a reference to order
genes of a closely related species characterized by a partial order P. In this
paper, the problem is to find a linearization of P that is as close as possible
to O in term of the breakpoint distance. We first prove an NP-complete
complexity result for this problem. We then give a dynamic programming
algorithm whose running time is exponential for general partial orders, but
polynomial when the partial order is derived from a bounded number of genetic
maps. A time-efficient greedy heuristic is then given for the general case,
with a performance higher than 90% on simulated data. Applications to the
analysis of grass genomes are presented.