Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma

Abstract

BackgroundMYC is a key transcription factor involved in central cellular processes such as regulation of the cell cycle, histone acetylation and ribosomal biogenesis. It is overexpressed in the majority of human tumors including aggressive B-cell lymphoma. Especially Burkitt lymphoma (BL) is a highlight example for MYC overexpression due to a chromosomal translocation involving the c-MYC gene. However, no genome-wide analysis of MYC-binding sites by chromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-Seq) has been conducted in BL so far.Methodology/Principal FindingsChIP-Seq was performed on 5 BL cell lines with a MYC-specific antibody giving rise to 7,054 MYC-binding sites after bioinformatics analysis of a total of approx. 19 million sequence reads. In line with previous findings, binding sites accumulate in gene sets known to be involved in the cell cycle, ribosomal biogenesis, histone acetyltransferase and methyltransferase complexes demonstrating a regulatory role of MYC in these processes. Unexpectedly, MYC-binding sites also accumulate in many B-cell relevant genes. To assess the functional consequences of MYC binding, the ChIP-Seq data were supplemented with siRNA- mediated knock-downs of MYC in BL cell lines followed by gene expression profiling. Interestingly, amongst others, genes involved in the B-cell function were up-regulated in response to MYC silencing.Conclusion/SignificanceThe 7,054 MYC-binding sites identified by our ChIP-Seq approach greatly extend the knowledge regarding MYC binding in BL and shed further light on the enormous complexity of the MYC regulatory network. Especially our observations that (i) many B-cell relevant genes are targeted by MYC and (ii) that MYC down-regulation leads to an up-regulation of B-cell genes highlight an interesting aspect of BL biology.

MINCR is a MYC-induced lncRNA able to modulate MYC’s transcriptional network in Burkitt lymphoma cells

“…Furthermore, five of them were also bound by MYC in at least one of the BL cell lines analyzed in ref. 42. These data suggest that some of the identified lncRNAs may be direct MYC target transcripts.…”

“…To address this point, we analyzed 13 lncRNAs at the genomic and transcriptomic levels to find out if (i) the promoters of these transcripts are bound by MYC in ChIP experiments, (ii) the promoters of these transcripts are characterized by other chromatin marks associated with active transcription, and (iii) there is a positive correlation between MYC expression and the expression of 13 lncRNAs. To answer the first question, we analyzed available data from MYC ChIP-sequencing (ChIP-seq) experiments performed with P493-6 cells under MYC low or MYC high expression (16) as well as MYC ChIP-seq experiments performed in BL cell lines (42). We found that 7 of 13 lncRNAs were bound by MYC under MYC high conditions in the region around the transcriptional start site (TSS) (Fig.…”

“…Using this approach, we found 63 MYC binding sites (defined as in ref. 42) in these promoter regions. To check for significance, we analyzed the number of MYC-bound regions in a background set of cell cycle genes created by randomly selecting 125 of 1,324 genes belonging to the cell cycle functional category (Gene Ontology ID GO:0007049).…”

Myc-induced SUMOylation is a therapeutic vulnerability for B-cell lymphoma

“…These data were confirmed in P493-6 cells cultured in media 6Tet in a Myc-on or Myc-off state ( Figure 1B To test if Myc directly binds to SUMOylation genes via identified E-boxes, we assessed 2 ChIP-seq data sets used to identify genome-wide Myc target genes. 35,36 There was a marked and specific enrichment for Myc and Max binding to the promoter-regulatory regions in these SUMOylation genes in P493-6 B lymphoma cells, and in 5 different BL cell lines. Furthermore, Myc binding occurred at E-boxes in the promoter regions of the majority of these genes; thus, these are direct Myc target genes ( Figure 1D and supplemental Figure 1).…”

Understanding MYC-driven aggressive B-cell lymphomas: pathogenesis and classification

“…31 Interestingly, TCF3 induces its own negative inhibitor, ID3, that is also a target of MYC. 32 These elements may create an autoregulatory loop controlling the transition of cells between the dark and light zones. ID3 expression promoted by TCF3 may contribute to the attenuation of the TCF3 program allowing the cell to move from the dark to the light zone (Figure 2A).…”