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Meeting Notes for July 29, 2003

Attendance: Dr. Lenwood Heath, Dr. Ruth Grene, Dr. John Paul Vergara, John Archie

In this meeting we primarily discussed two papers on identifying regulatory elements in genes's upstream regions. (Both papers are linked to in the papers section.)

• Rombauts S, Florquin K, Lescot M, Marchal K, Rouze P, Van De Peer Y.
  Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes.
  Plant Physiol. 2003 Jul;132(3):1162-76.

• Helden JV, Andre B, Collado-Vides J.
  Extracting Regulatory Sites from the Upstream Region of Yeast Genes by Computational Analysis of Oligonucleotide Frequencies.
  J Mol Biol. 1998 Sep 4;281(5):827-42.

The accuracy of promoter detection can be improved by looking for promoters within a specific context.

• The sequence of base pairs determines the chemical properties of the DNA molecule which, in turn, effects the shape of the molecule. The shape of the DNA molecule may not allow for regulatory enzymes to bind to the DNA.
• We can classify regions of DNA by counting di- and tri-nucleotide sequences with known chemical properties.
• Histones are also thought to play a role in gene regulation.
• CpG islands are often methylated suppressing the transcription of a gene.
• CpG islands are more susceptible to mutation than typical DNA. So, by their existence, we can assume that they play a biological role.

There are two approaches to identify regulatory elements.

• If we do not know the regulatory element, we can use analogous genes (or other sets of genes that we think are controlled by identical regulatory elements) and perform alignments on their upstream regions. Sequences that are similar might be involved in gene regulation.
• If we know the motif of the regulatory element, we can simply search for the pattern in the DNA sequence.

Another approach to find biologically significant sequences is to count the number of every possible k-mer. k-mers that are found frequently are probably biologically significant by their presence, and k-mers that are not found are probably significant by their absence. The paper by Helden et. al. did this sort of analysis with yeast.

Papers on yeast are of interest to Dr. Grene, as yeast (a fungi) has many characteristics in common with plants.

Dr. Grene was interested in specific software packages, so we will research several and report our findings in the next meeting.