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Genomic targets of the human c-Myc protein
Paula C Fernandez1, Scott R Frank, Luquan Wang
1DNAX Research Institute, Palo Alto, California 94304, USA.
Abstract:
The transcription factor Myc is induced by mitogenic signals and regulates downstream cellular responses. If overexpressed, Myc promotes malignant transformation. Myc modulates expression of diverse genes in experimental systems, but few are proven direct targets. Here, we present a large-scale screen for genomic Myc-binding sites in live human cells. We used bioinformatics to select consensus DNA elements (CACGTG or E-boxes) situated in the 5' regulatory region of genes and measured Myc binding to those sequences in vivo by quantitative chromatin immunoprecipitation. Strikingly, most promoter-associated E-boxes showed selective recovery with Myc, unlike non-E-box promoters or E-boxes in bulk genomic DNA. Promoter E-boxes were distributed in two groups bound by Myc at distinct frequencies. The high-affinity group included an estimated 11% of all cellular loci, was highly conserved among different cells, and was bound independently of Myc expression levels. Overexpressed Myc associated at increased frequency with low-affinity targets and, at extreme levels, also with other sequences, suggesting that some binding was not sequence-specific. The strongest DNA-sequence parameter defining high-affinity targets was the location of E-boxes within CpG islands, correlating with an open, preacetylated state of chromatin. Myc further enhanced histone acetylation, with or without accompanying induction of mRNA expression. Our findings point to a high regulatory and biological diversity among Myc-target genes.
Insights
The transcription factor Myc binds to specific DNA sequences in human cells, revealing distinct high-affinity targets and regulatory diversity. This study identifies key Myc-binding sites, crucial for understanding gene regulation and cancer development.
Area of Science:
- Molecular Biology
- Genetics
- Cancer Biology
Background:
- The transcription factor Myc is a key regulator of cell growth and proliferation, often overexpressed in various cancers.
- While Myc's role in malignant transformation is known, the precise set of its direct genomic targets remains incompletely defined.
Purpose of the Study:
- To conduct a large-scale screen for genomic Myc-binding sites in live human cells.
- To identify direct Myc target genes and characterize the features of high-affinity binding sites.
Main Methods:
- Bioinformatic selection of consensus DNA elements (E-boxes) in gene regulatory regions.
- Quantitative chromatin immunoprecipitation (ChIP) to measure in vivo Myc binding.
- Analysis of DNA sequence, CpG island location, and chromatin state (histone acetylation) in relation to Myc binding.
Main Results:
- Most promoter-associated E-boxes were selectively recovered with Myc, indicating specific binding.
- Myc-binding sites were categorized into high- and low-affinity groups, with high-affinity sites conserved and bound independently of Myc levels.
- High-affinity binding correlated with E-box location within CpG islands and an open chromatin state; Myc enhanced histone acetylation.
Conclusions:
- Myc exhibits regulatory and biological diversity among its target genes.
- The study identified a significant set of direct Myc targets and characterized factors influencing binding affinity.
- Findings provide insights into Myc's role in gene regulation and potential therapeutic strategies in cancer.