Beyond the Identification of Transcribed Sequences:
Functional, Evolutionary and Expression Analysis
12th International Workshop
October 25-28, 2002
Washington, DC

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Big Genes: What? Where? Why?

Lee Rowen, Brian Birditt, Ryan Nesbitt, Amardeep Kaur, Gustavo Glusman, and Lee Hood
Institute for Systems Biology, Seattle WA 98103
Telephone: 206-732-1272
Fax: 206-732-1299

As more of the human genome is represented in multimegabase-sized contigs and genomes of other vertebrates get drafted and scaffolded, features of overall genomic architecture can be investigated with more specificity.   Of interest to us are the big genes, that is, genes whose primary transcripts (pre-mRNA) span over 500 kilobases.  To date, we have identified about 200 such genes accounting for about 5% of the human genome.

The big genes fall into several functional classes, the most noteworthy being their involvement in the development or physiology of the central nervous system.  Examples include glutamate receptors and neurexins.  Many big genes are loci of chromosomal instabilities -- trinucleotide repeat expansions, large deletions, and translocations.  The alternative splicing of some of the big genes is highly complex, and it is not obvious how cryptic splicing within the introns is avoided or detected and repaired.

Gene size may be an important mechanism for controlling the expression of some genes -- if the time required for transcription is longer than the cell division time, then the proteins will presumably not be made.  On the other hand, gene size could simply be an outcome of vertebrate evolution and there may be little functional significance to intron size.  Interestingly, the trivial explanation that big genes are big because the introns are full of transposable elements (interspersed repeats) is not true, unless the repeats are so old that their sequences have diverged far away from the consensus sequences.  We will analyse a selected subset of big genes in the mouse and pufferfish genomes to address the issue of whether genes that are big in human are also big in other species.

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