This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
MECP2 Gene
Human MECP2 DNA Sequence Accession Number: NC_000023.9
The human MECP2 gene is located on the long (q) arm of X chromosome in band 28. It is oriented on the minus strand, starting at 152,940 kb from the end. MECP2 is 76,189 bases long and has 4 exons. (1)
Human MECP2 MRNA Sequence Accession Number: NM_004992
Homologs
Pan troglodytes (Chimpanzee) |
Mus musculus (Mouse) |
I used homologene to identify 6 homologs in different organisms. (2) This resource was very easy to use and each homolog had links to the DNA and Protein sequences in entrez. However, even though results were given back rapidly, they were limited to the 6 most similar homologs. One weakness of homologene is that it doesn't give the E-value. So, I used BLAST to determine the E-value for each individual homolog. (3)
I also used BLAST to search for homologs in other organisms, such as Drosophila melanogaster, C. elegans, and Arabidopsis thaliana but found no significant similarities to the Human MECP2 sequence. (3)
DNA Motifs
To determine the motifs in the MECP2 gene, I used MOTIF with the full length of the gene and several different cut off scores. (4)
Cut of Score Total Motifs
85 184
90 107
95 42
100 16
Figure 1: The 16 motifs found with a cut off score of 100 found in MOTIF. (4)
I also used the full DNA sequence in MEME to find motifs in the MECP2 gene. I used default parameters, except I used 10 for the maximum number of motifs. MEME identified 10 motifs with e-values ranging from 3.0e-001 to 6.5e+005. The 3 motifs with the lowest e-value, representing the highest accuracy, are described below.(5)
Figure 2: The first motif had an e value of 3.0e-001 and a log likelihood ratio of 137. It had a width of 29 nucleotides and occured at 5 different sites. (5)
Figure 3: The second motif had an e value of 6.7e+002 and a log likelihood ratio of 158. It had a width of 41 nucleotides and occured at 5 different sites. (5)
Figure 4: The third motif had an e value of 4.0e+004 and a log likelihood ratio of 161. It had a width of 41 nucleotides and occured at 5 different sites. (5)
The two programs I used to identify DNA motifs produced very different results and provided very different information about the motifs identified. MOTIF found 16 motifs and provided information on the name, a brief description, consensus sequence, and the number of positions it occurred in. I found it useful that the cut off score could be changed. It worked well to start off the default cutoff score of 85 and increase the cut off score to narrow the results down to a reasonable number of motifs. The classification (all, vertebrate, insects, plants, fungi, nematodes, bacteria) of motifs that the sequence will be compared to could also be changed. I chose to search in the "all" classification. The motif that had occurred the most was the Heat Shock Factor motif. The biggest weakness of MOTIF was that it provided only very brief descriptions of the function or significance of the motifs identified. This makes it difficult to determine which motifs are involved in the general function of the gene and which may be more necessary to the specific function of MECP2.
MEME identified 3 motifs and provided information on the e-value, log likelihood ratio, the number of nucleotides, and how many sites it occurred in. MEME had several parameters that could be changed depending on the query. These parameters include the optimum (minimum and maximum) number of sites, how it is expected that a motif will be distributed among the sequence, and the optimum (minimum and maximum) width of the motif, and the maximum number of motifs to find. MEME gives even less information about the function of the motifs identified but it gives a good visual representation motif sequence and uses very specific statistical measures.
Microarrays
I used GEO to search for microarray experiments in patients with Rett Syndrome. I was able to find one experiment in humans comparing gene expression in the frontal cortices of wildtype patients and patients with Rett Syndrome. A limitation to this study in performing the microarray analysis designed for this class was that the samples were pooled by age group in both the control patients and those with Rett Syndrome. Therefore it was not feasible to look at patterns in gene expression between the control and experimental groups. Expression seems to vary greatly with age. Interestingly, MECP2 expression did not vary significantly between wildtype patients and Rett Syndrome patients in this study.
The main finding of this study was that the gene FXYD1 is targeted my MECP2 and is overexpressed in mice with Rett Syndrome, where MECP2 is not present. FXDY1 encodes a small membrane protein controls cell excitability by modulating Sodium/Potassium ATPase activity. The authors suggest that this leads to a decrease in complexity of the neural dendritic tree and a loss of dendritic spines in the frontal cortex. (7)
Figure 5: Heatmap for microarray experiment showing MECP2 expression in wildtype patients and patients with Rett Syndrome. (6)
This study identified several other genes that have increased expression in MECP2 null individuals, but the Princeton GO term finder did not come up with any results. (8)
List of 16 genes with the largest difference in gene expression in MECP2 patients: ATP1A2, NTRK2, ALDH6A1, EHMT2, IDS, SLC681, PPPIR3C, IL17REL, CYP4B1, SNTA1, CDA, PRODH, MYO10, PTN, HTRA1, ADD3.
Click here for a complete list.
References
1. Gene Cards - http://www.genecards.org/
2. Homologene - http://www.ncbi.nlm.nih.gov/homologene
3. BLAST (nucleotide) - http://blast.ncbi.nlm.nih.gov/Blast.cgi
4. MOTIF - http://motif.genome.jp/
5. MEME - http://meme.sdsc.edu/meme4/intro.html
6. GEO - http://www.ncbi.nlm.nih.gov/geo/
7. Deng V, Matagne V, Banine F, Frerking M et al. FXYD1 is an MeCP2 target gene overexpressed in the brains of Rett syndrome patients and Mecp2-null mice. Hum Mol Genet 2007 Mar 15;16(6):640-50. PMID: 17309881.
8. Princeton GO Term Finder: http://go.princeton.edu/cgi-bin/GOTermFinder
Jessica Connor
[email protected]
Last Updated: 3/1/09