Huntingtin and Huntington's Disease


This website was produced as an assignment for Genetics 677 at UW-Madison Spring 2009

Gene Analysis


DNA Motifs

In order to search for any DNA motifs present in the Htt sequence, I used the Motif Search program and the MEME program (MEME).  The results are described below for each. 

MotifSearch

I used the full DNA sequence of human huntingtin for this program.  Initially, with the cutoff score set at 85, I did not retrieve any motifs.  I reran the program with the cutoff score set at 100 and still did not retrieve any results.  I switched to using the mRNA with the two cutoff settings.  I found 189 motifs at a cutoff of 85, and at a cutoff 100 found 10 motifs.  These 10 motifs follow.

     

Motif Name

Description

HSF

heat shock factor (Drosophila)

HSF

heat shock factor (yeast)

CRE-BP1/c-Jun        

CRE-binding protein 1/c-Jun heterodimer

GCR1         

GCR1

ADR1   

alcohol dehydrogenase gene regulator 1

CdxA

CdxA

CF1

chorion factor 1

SRY

sex-determining region Y gene product

AML-1

arunt-factor AML-1

CF1

chorion factor 1

 

MEME



Because of the size of the gene (17.5 kb) exceeded the maximum sequence size, I had to use the shorter mRNA sequence for the analysis.  The program identified 3 motifs, with the first one appearing the most highly conserved, with a pattern of [AT]GC[AT]GCAGCAGCAG[CG].  The full MEME results follow this paragraph.  While I was impressed with the graphical nature of the program, I am not sure I gained a good understanding of the actual motifs, at least so far as how they might indicate a certain function of the protein.  Click on the images to the right to enlarge the images. 

Motif 3

Motif 1

Motif 2

Created by Eric Nickels enickels@wisc.edu       3/13/2009      Genetics 677 Webpage