An early Myc‐dependent transcriptional program orchestrates cell growth during B‐cell activation

Abstract

Upon activation, lymphocytes exit quiescence and undergo substantial increases in cell size, accompanied by activation of energy‐producing and anabolic pathways, widespread chromatin decompaction, and elevated transcriptional activity. These changes depend upon prior induction of the Myc transcription factor, but how Myc controls them remains unclear. We addressed this issue by profiling the response to LPS stimulation in wild‐type and c‐myc‐deleted primary mouse B‐cells. Myc is rapidly induced, becomes detectable on virtually all active promoters and enhancers, but has no direct impact on global transcriptional activity. Instead, Myc contributes to the swift up‐ and down‐regulation of several hundred genes, including many known regulators of the aforementioned cellular processes. Myc‐activated promoters are enriched for E‐box consensus motifs, bind Myc at the highest levels, and show enhanced RNA Polymerase II recruitment, the opposite being true at down‐regulated loci. Remarkably, the Myc‐dependent signature identified in activated B‐cells is also enriched in Myc‐driven B‐cell lymphomas: hence, besides modulation of new cancer‐specific programs, the oncogenic action of Myc may largely rely on sustained deregulation of its normal physiological targets.

Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription

“…2G): as a consequence, the extended residence time of the transcription factor on DNA may increase the probability of activation. In line with this scenario, Myc-induced transcriptional programs in diverse cell types correlated with the relative gain in Myc binding at promoters (de Pretis et al, 2017, Lorenzin et al, 2016, Tesi et al, 2019, Walz et al, 2014, as confirmed in our experiments ( Fig. S6A): moreover, and consistent with the proposed mechanism, DNA binding and activation by either form of MycER were associated with enrichment of the cognate DNA motif (Fig.…”

“…EV5A,B): hence, as previously proposed (Baluapuri et al, 2019, de Pretis et al, 2017, repression by either MycER WT or MycER HEA may be largely indirect. Moreover, MycER HEArepressed loci included known Myc-dependent genes (Lorenzin et al, 2016, Muhar et al, 2018, Perna et al, 2012, Tesi et al, 2019 (Fig. EV5C): we surmise that by binding these loci without being able to recognize the E-box, MycER HEA may impair their sustained activation by endogenous Myc.…”

“…Functional annotation analysis to determine enriched Gene Ontology categories was performed using the online tool at http://software.broadinstitute.org/gsea/index.jsp. Gene set enrichment analysis (GSEA) was performed using the Desktop tool of the Broad Institute (http://software.broadinstitute.org/gsea/index.jsp) with custom gene lists (Tesi et al, 2019).…”

“…The transcription factor Myc orchestrates complex gene expression programs that foster cell growth and proliferation, in both normal and cancer cells (Kress et al, 2016, Kress et al, 2015, Muhar et al, 2018, Tesi et al, 2019, Walz et al, 2014. Myc dimerizes with Max (Blackwood & Eisenman, 1991) to bind DNA with a preference for the E-box consensus sequence CACGTG (Blackwell et al, 1993, Solomon et al, 1993, through which it activates transcription (Amati et al, 1992, Kretzner et al, 1992.…”

“…consequently, when expressed at high levels, Myc can be detected on virtually all active promoters and enhancers in the genome (Guo et al, 2014, Lin et al, 2012, Nie et al, 2012, Walz et al, 2014. Hence, while Myc-activated promoters tend to show overrepresentation of E-box motifs (Tesi et al, 2019) and stronger Myc recruitment (de Pretis et al, 2017, Lorenzin et al, 2016, Walz et al, 2014, the role of DNA sequence recognition in Myc activity remains to be clarified.…”