This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison
LDLR Gene Motifs
Using MOTIF, I was able find relevant DNA motifs within the LDLR gene. Initially, the entire DNA sequence was analyzed in MOTIF, however both a cutoff of 85 and 100 did not give any motifs. The mRNA sequence was then analyzed at a cutoff of 85, giving 165 motifs. In order to reduce the amount of motifs, a cutoff of 100 was used. Only 7 motifs were identified at this cutoff, indicating that these motifs are truly found within the LDLR mRNA. The 7 mRNA motifs are listed below.
Motif Name
EGF_1
INTEGRIN_BETA
ANAPHYLATOXIN_1
4FE4S_FERREDOXIN
THIOLASE_3
VWFC_1
2FE2S_FER_1
EGF_1
INTEGRIN_BETA
ANAPHYLATOXIN_1
4FE4S_FERREDOXIN
THIOLASE_3
VWFC_1
2FE2S_FER_1
Description
EGF-like domain signature 1
Integrins beta chain cysteine-rich domain signature Anaphylatoxin domain signature
4Fe-4S ferredoxins, iron-sulfur binding region signature Thiolases active site
VWFC domain signature
2Fe-2S ferredoxins, iron-sulfur binding region signature
EGF-like domain signature 1
Integrins beta chain cysteine-rich domain signature Anaphylatoxin domain signature
4Fe-4S ferredoxins, iron-sulfur binding region signature Thiolases active site
VWFC domain signature
2Fe-2S ferredoxins, iron-sulfur binding region signature
The EGF_1 motif is notable because the LDLR protein has known EGF domains. Further analysis of the EGF sequence and its function in the LDLR protein can be seen here. The LDLR protein is also known to have cysteine-rich domains that are involved in LDL binding, potentially implicating the INTEGRIN_BETA motif as a functional and FH-relevant coding region of the LDLR mRNA (1, 2). Although potentially relevant motifs were found using MOTIF, protein domain analysis gives a more practical visualization of function, and will further our understanding of the LDLR gene and its protein function.
Figure 1-Motif tree generated by STAMP. Click to enlarge.
Analysis
To further analyze LDLR motifs I used MEME and STAMP. Using the mRNA sequence, MEME was able to provide visualization of the motifs. The motif maximum was capped at 3 in order to decrease the amount of information provided by the program. It was difficult to interpret the motifs found by MEME, so STAMP was then utilized. The MEME motif outputs were entered into STAMP for analysis, and the resulting DNA motif tree can be seen above. Unfortunately, it is not clear whether the motifs found in MEME correspond to the similar motifs from MOTIF. MOTIF clearly states the names and general sequence patterns of motifs, while MEME and STAMP present a more visually pleasing motif representation. Ideally, a program that combines the outputs of MOTIF and MEME or STAMP would be the best way to analyze DNA motifs.
References
1. Yamamoto, T., Davis, C. G., Brown, M. S., Schneider, W. J., Casey, M. L., Goldstein, J. L., Russell, D. W. (1984). The human LDL receptor: a cysteine-rich protein with multiple Alu sequences in it mRNA. Cell, 39(1), 27-38. doi:10.1016/0092-8674(84)90188-0
2. Rudenko, G., Henry, L., Henderson, K., Ichtchenko, K., Brown, M. S., Goldstein, J. L., Deisenhofer, J. (2002). Structure of the LDL receptor extracellular domain at endosomal pH. Science, 298(5602), 2353-8.
doi:10.1126/science.1078124
2. Rudenko, G., Henry, L., Henderson, K., Ichtchenko, K., Brown, M. S., Goldstein, J. L., Deisenhofer, J. (2002). Structure of the LDL receptor extracellular domain at endosomal pH. Science, 298(5602), 2353-8.
doi:10.1126/science.1078124
