ArticleMolecular bioSystems2009
A c-Myc regulatory subnetwork from human transposable element sequences.
Article in Molecular bioSystems, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 21 citations in OpenAlex.
- MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia.Nature communications · 2022Article
- A KRAS-responsive long non-coding RNA controls microRNA processing.Nature communications · 2021Article
- An atlas of transposable element-derived alternative splicing in cancer.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.Biology · 2016Review
- Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.Mobile DNA · 2014Article
- Constraint and opportunity in genome innovation.RNA biology · 2014Review
- The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors.BMC genomics · 2012Article
- Measuring the evolutionary rewiring of biological networks.PLoS computational biology · 2011Article
- CpG deamination creates transcription factor-binding sites with high efficiency.Genome biology and evolution · 2011Article
- Effect of the transposable element environment of human genes on gene length and expression.Genome biology and evolution · 2011Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Transposable elements (TEs) can donate regulatory sequences that help to control the expression of human genes. The oncogene c-Myc is a promiscuous transcription factor that is thought to regulate the expression of hundreds of genes. We evaluated the contribution of TEs to the c-Myc regulatory network by searching for c-Myc binding sites derived from TEs and by analyzing the expression and function of target genes with nearby TE-derived c-Myc binding sites. There are thousands of TE sequences in the human genome that are bound by c-Myc. A conservative analysis indicated that 816-4564 of these TEs contain canonical c-Myc binding site motifs. c-Myc binding sites are over-represented among sequences derived from the ancient TE families L2 and MIR, consistent with their preservation by purifying selection. Genes associated with TE-derived c-Myc binding sites are co-expressed with each other and with c-Myc. A number of these putative TE-derived c-Myc target genes are differentially expressed between Burkitt's lymphoma cells versus normal B cells and encode proteins with cancer-related functions. Despite several lines of evidence pointing to their regulation by c-Myc and relevance to cancer, the set of genes identified as TE-derived c-Myc targets does not significantly overlap with two previously characterized c-Myc target gene sets. These data point to a substantial contribution of TEs to the regulation of human genes by c-Myc. Genes that are regulated by TE-derived c-Myc binding sites appear to form a distinct c-Myc regulatory subnetwork.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.