Transcription factor binding motif analyses in two biological systems
Embargo until
2015-05-01
Date
2014-04-25
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Publisher
Johns Hopkins University
Abstract
The mechanism of gene regulation is a crucial problem in current computational biology. Chromatin-immunoprecipitation microarray (ChIP-chip) is a technique used to study transcriptional regulation by identifying the binding regions of specific transcription factors. In this thesis, we focus on the binding of transcription factors to upstream region motifs to understand the mechanism of gene regulation.
Sonic hedgehog (Shh) signals direct digit number and identity in the vertebrate limb via Gli transcription factors. We sought to identify key Gli binding motifs in Gli binding regions through whole-genome ChIP-chip in the developing mouse limb. Through de novo motif discovery method, we found that there were specific DNA motifs enriched in different expression domains of the developing limb. A novel motif in Gli binding regions is highly likely to be a functional element. In addition, we noted that there was no statistically significant difference of quality of Gli motifs in Gli binding regions associated with genes expressed in different domains. The quality of Gli motif might not be a factor that influences the expression of genes in different domains.
Myc transcription factor, produced by the MYC oncogene, has the ability to activate and repress gene transcription. Elevated expression of Myc transcription factor is frequently found in cancers. We conducted antibody-specific motif analysis with application to human MYC transcription factor by using high-throughput genomic approaches. Chromatin immunoprecipitation was performed using two different anti-Myc antibodies in human P493-6 B cells, Santa Cruz (SC) antibody and Epitomics (Epit) antibody. Intersection of the two peak lists from SC antibody and Epit antibody identified 885 common Myc binding regions in both data sets. With the average probe intensities of the ChIP samples, we found no statistically significant difference between the binding intensity of probe with ChIP sequences immunoprecipitated by SC antibody and Epit antibody. There was linear increasing relationship between Epit antibody and SC antibody. Furthermore, we identified that Sfpi1 motif might be specifically bound to Myc-SC antibody and involved in differentiation or activation of B-cells.
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Keywords
Transcription factor, Motif, ChIP-chip, MYC, Sonic hedgehog.