The MuvB Complex Binds and Stabilizes Nucleosomes Downstream of the Transcription Start Site of Cell-Cycle Dependent Genes

Abstract

The chromatin architecture in promoters is thought to regulate gene expression, but it remains uncertain how most transcription factors (TFs) impact nucleosome position. The MuvB TF complex regulates cell-cycle dependent gene-expression and is critical for differentiation and proliferation during development and cancer. MuvB can both positively and negatively regulate expression, but the structure of MuvB and its biochemical function are poorly understood. Here we determine the overall architecture of MuvB assembly and the crystal structure of a subcomplex critical for MuvB function in gene repression. We find that the MuvB subunits LIN9 and LIN37 function as scaffolding proteins that arrange the other subunits LIN52, LIN54 and RBAP48 for TF, DNA, and histone binding, respectively. Biochemical and structural data demonstrate that MuvB binds nucleosomes through an interface that is distinct from LIN54-DNA consensus site recognition and that MuvB increases nucleosome occupancy in a reconstituted promoter. We find in arrested cells that MuvB primarily associates with a tightly positioned +1 nucleosome near the transcription start site (TSS) of MuvB-regulated genes. These results support a model that MuvB binds and stabilizes nucleosomes just downstream of the TSS on its target promoters to repress gene-expression.

Coordinating gene expression during the cell cycle

“…However, the MuvB complex has a key role in DREAM-mediated repression. LIN37 is essential for DREAM-dependent gene repression, but its mode of action remains unknown [58,64,[112][113][114]. Interestingly, it is dispensable for the integrity of DREAM and transcriptional activation mediated by MMB:FOXM1 [58,64].…”

“…Interestingly, it is dispensable for the integrity of DREAM and transcriptional activation mediated by MMB:FOXM1 [58,64]. LIN37 and RBBP4 interact with the N terminus of LIN9, while LIN54 and LIN52 bind to the C terminus of LIN9 [33,44,113] indicating that LIN9 forms a central scaffold within the MuvB core (see Figure 1 in the main text). Recent analyses showed that the LIN9 N terminus contacts RBBP4, creating a binding surface for LIN37.…”

“…When bound to LIN9, the binding site of RBBP4 for histone H3, but not H4, is accessible, and a reconstituted LIN9-LIN37-RBBP4 complex was found to bind nucleosomes. In quiescent cells, DREAM primarily associates with the +1 nucleosome near TSS, offering an explanation for gene repression by stabilizing the +1 nucleosome [113]. Interestingly, PAF/PCLAF was recently reported to bind to RBBP4, thereby inhibiting DREAM formation and function [115].…”

Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling

“…The DNA-binding domain of LIN54 recruits MuvB to its target genes at a specific sequence termed the cell cycle homology region (CHR) 7,8 . MuvB target promoters are TATA-less and the CHR is located directly upstream of the transcription start site (TSS) and the +1 nucleosome 8,9 . The presence of the +1 nucleosome generates a barrier for the assembly of the basal transcriptional apparatus 10 , and its positioning and dynamics are finely regulated to define the transcriptional status of each gene.…”

DREAM Interrupted: Severing LIN-35-MuvB association in Caenorhabditis elegans impairs DREAM function but not its chromatin localization

“…Extensive biochemical analyses have demonstrated how the DREAM complex assembles on chromatin (Figure 1A) (LITOVCHICK et al 2007;PILKINTON et al 2007;SCHMIT et al 2007;GUILEY et al 2015;ASTHANA et al 2022). E2F-DP and LIN54, a MuvB component, direct site-specific chromatin localization (ZWICKER et al 1995;SCHMIT et al 2009;MULLER AND ENGELAND 2010;MULLER et al 2012;MARCEAU et al 2016).…”