Sequence specificity incompletely defines the genome-wide occupancy of Myc

Abstract

BackgroundThe Myc-Max heterodimer is a transcription factor that regulates expression of a large number of genes. Genome occupancy of Myc-Max is thought to be driven by Enhancer box (E-box) DNA elements, CACGTG or variants, to which the heterodimer binds in vitro.ResultsBy analyzing ChIP-Seq datasets, we demonstrate that the positions occupied by Myc-Max across the human genome correlate with the RNA polymerase II, Pol II, transcription machinery significantly better than with E-boxes. Metagene analyses show that in promoter regions, Myc is uniformly positioned about 100 bp upstream of essentially all promoter proximal paused polymerases with Max about 15 bp upstream of Myc. We re-evaluate the DNA binding properties of full length Myc-Max proteins. Electrophoretic mobility shift assay results demonstrate Myc-Max heterodimers display significant sequence preference, but have high affinity for any DNA. Quantification of the relative affinities of Myc-Max for all possible 8-mers using universal protein-binding microarray assays shows that sequences surrounding core 6-mers significantly affect binding. Compared to the in vitro sequence preferences, Myc-Max genomic occupancy measured by ChIP-Seq is largely, although not completely, independent of sequence specificity.ConclusionsWe quantified the affinity of Myc-Max to all possible 8-mers and compared this with the sites of Myc binding across the human genome. Our results indicate that the genomic occupancy of Myc cannot be explained by its intrinsic DNA specificity and suggest that the transcription machinery and associated promoter accessibility play a predominant role in Myc recruitment.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0482-3) contains supplementary material, which is available to authorized users.

An early Myc-dependent transcriptional program underlies enhanced macromolecular biosynthesis and cell growth during B-cell activation

“…Altogether, in line with previous observations in either B-cells (Guccione, Martinato et al, 2006, Lin et al, 2012, Nie et al, 2012, Sabò et al, 2014 or others (Guo, Li et al, 2014, Kress et al, 2016, Lin et al, 2012, Soufi, Donahue et al, 2012, Walz et al, 2014, Zeid et al, 2018, acute accumulation of Myc upon LPS treatment led to its widespread association with pre-existing promoters and enhancers: this phenomenon, also termed "invasion" (Lin et al, 2012, Nie et al, 2012, Sabò et al, 2014, most probably occurs through low affinity, non sequence-specific interactions with genomic DNA. Together with the findings that Myc deletion only impacts a subset of the genes regulated by either LPS (this work) or serum , we infer that chromatin association cannot be systematically equated with productive regulatory engagement of the transcription factor onto genomic DNA (de Pretis et al, 2017, Muhar et al, 2018.…”

Learning from mistakes: Accurate prediction of cell type-specific transcription factor binding

“…As TAF1 (TATA-Box Binding Protein Associated Factor 1) is associated with transcriptional initiation at the TATA box, one explanation might be that binding sites of these TFs are enriched at core promoters. Indeed, binding to proximal promoters has been reported for MYC/MAX (Guo et al ., 2014), CREB1 (Zhang et al ., 2005), YY1 (Li et al ., 2008), and E2F factors (Rabinovich et al ., 2008).…”

Miz-1 and Max compete to engage c-Myc: implication for the mechanism of inhibition of c-Myc transcriptional activity by Miz-1

“…11,12,15 In fact, it was also demonstrated that the location of c-Myc on chromatin correlates more closely with the location of Pol II rather than that of E-Box sequences. 16 As discussed elsewhere, 15 this is explained by the fact that dimeric b-HLH-LZs bind to nonspecific DNA with significant affinities only one to two order of magnitude lower than for E-box sequences. 16,17 This invasion was further shown to a steady recruitment of the pauserelease factor P-TEFb by c-Myc at the newly bound promoters and enhancers and to the linear amplification of the expression of active transcriptional programs.…”

“…16 As discussed elsewhere, 15 this is explained by the fact that dimeric b-HLH-LZs bind to nonspecific DNA with significant affinities only one to two order of magnitude lower than for E-box sequences. 16,17 This invasion was further shown to a steady recruitment of the pauserelease factor P-TEFb by c-Myc at the newly bound promoters and enhancers and to the linear amplification of the expression of active transcriptional programs. 10,15 This nonspecific binding and transcriptional amplification are believed to play a key role in the carcinogenesis processes and to cause to the so-called addiction to c-Myc.…”