Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation

Abstract

50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially-regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input. Single-molecule imaging shows that this step lowers transcription factor residence time and non-specific collisions during sampling for DNA targets. Third, chromatin interactions shift from long-range to predominantly short-range, and CTCF-mediated loops and contact domains double in numbers. This architectural change facilitates cognate promoter-enhancer contacts and also requires Myc and continual ATP production. Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells.

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

“…However, our results and others [4,8,28,31] provide no formal support for this model: instead, when observed, RNA amplification is most consistently interpretable as a late, indirect consequence of Myc action, mediated by a selective-yet complex-set of target genes [24,32]. In stimulated primary B-cells in particular, Myc was needed for ATP production, which in turn supported widespread chromatin remodeling and decompaction [5], in line with the delayed increase in bulk RNA synthesis reported here. Finally, the Myc-dependent program that we identified in activated B-cells was constitutively deregulated during lymphomagenesis in El-myc transgenic mice [4].…”

“…Ncl and Pus7, another Myc-dependent mRNAs previously identified in fibroblasts [8], responded to LPS in B-cells and required Myc for maximal accumulation, from 4 h onward ( Fig 1A). While global RNA levels also increased in a Myc-dependent manner [3,4], this occurred later (24 h, Fig EV1E) concomitant with increases in bulk RNA synthesis and nuclear size ( Fig 1B), overall cell size [2,4,5], and Sphase entry ( Fig EV1F) [4]. As expected [4,5,14,15], all of the above effects were lost in c-myc Δ/Δ cells, accompanied by a reduced proliferative response ( Fig EV1F and G), residual expansion at 48-72 h resulting from the selection of non-deleted c-myc f/f cells ( Fig EV1H).…”

“…A key regulator in this overall process is the Myc transcription factor, encoded by the c-myc proto-oncogene: indeed, Myc is directly induced by mitogenic signals and, in turn, is thought to orchestrate the plethora of transcriptional changes that foster cell growth and proliferation, as exemplified in cultured mouse fibroblasts [7,8]. In either B or T lymphocytes, c-myc serves as a direct sensor of activating signals [3,[9][10][11][12][13] and is required for multiple facets of cellular activation, including metabolic reprogramming, ATP production, ATP-dependent chromatin decompaction, RNA and biomass accumulation, and cell growth [3][4][5]11,[13][14][15][16][17][18]. However, how Myc activity impacts on those diverse cellular features remains largely unclear.…”

“…Myc binds DNA and activates transcription as a dimer with its partner protein Max [19][20][21], but its precise contribution to transcriptional programs in cells has been subject of an intense debate in the field in recent years: while multiple studies indicated that Myc can either activate or repress select target genes [8,[20][21][22][23][24], others concluded that it acts instead as a general activator-or amplifier-of all expressed genes [3,[25][26][27]. However, careful scrutiny of the available data [3][4][5]8,[25][26][27][28][29][30][31] lends no formal support to this model, suggesting instead that RNA amplification-when present-is one of the consequences of the metabolic and genomic changes that occur during cellular activation and/or transformation [30,32]. Hence, understanding the precise contribution of Myc to global changes in RNA biology will require a fine mapping of direct, Myc-dependent transcriptional programs.…”

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

“…Mature splenic B-cells can be activated ex vivo to re-enter the cell cycle and differentiate into antibody-producing cells, accompanied by massive increases in cell size and RNA content (Kieffer-Kwon, Nimura et al, 2017, Kouzine, Wojtowicz et al, 2013, Nie, Hu et al, 2012, Pogo, Allfrey et al, 1966, Sabò, Kress et al, 2014. This implies a concomitant intensification of the metabolic pathways needed to provide energy and building blocks for macromolecular biosynthesis and cell growth and, in turn, the necessity for the cells to adapt their transcriptional and translational outputs to the augmented cell size and metabolic activity (Marguerat, Schmidt et al, 2012).…”