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ENCODE meeting at UCSC furthers understanding of gene transcription

Saturday, November 12, 2005

Scientists from Europe, Asia, and throughout the United States attended a working meeting of two ENCODE project teams at UCSC in November, hosted by the UCSC Genome Bioinformatics Group.

The ENCODE (ENCyclopedia Of DNA Elements) project aims to discover all regions of the human genome that are crucial to biological function. The two project teams that met here focus on genes and transcription and on transcription regulation. During the meeting, they reviewed data, discussed key findings, and outlined papers for publication.

The genes and transcription team searches the genome computationally for regions that are likely to be transcribed into RNA. They validate the findings experimentally, then add annotations to the online UCSC genome browser to point the way for researchers. This team is led by Tom Gingeras of Affymetrix and Roderic Guigo from the Centre de Regualci'n'a in Barcelona, Spain.

Their research so far indicates that as much as 50 percent of the genomic regions outside of genes are subject to transcription. This finding suggests that alternative splicing and gene regulation may explain a large part of species variation.

The transcription regulation team explores how genes are expressed and what controls the expression. Cross-species analysis greatly aids this discovery process. The means for this exploration is a process called "ChIP/chip" for Chromatin Immunoprecipitation arrays on a microarray chip. This effort is led by Mike Snyder from Yale and Zhiping Weng from Boston University with assistance from Kevin Struhl from Harvard. To ensure the usefulness of their output, this team hopes to standardize the ChIP/chip method for determining gene expression so that data collection becomes more uniform.