Three-Dimensional Reorganization of the Genome During B Cell Affinity Maturation

Abstract 279

B cell affinity maturation is fundamental to the development of humoral immunity. To create a diverse antibody repertoire, B cells activated in the germinal centre (GC) must undergo a profound change in phenotype. This unique phenotypic change, which features simultaneous proliferation and somatic hypermutation and which can predispose to the development of lymphoma, requires radically altered gene expression programming in GC B cells. However, the way that this gene expression program is coordinated is unknown. Emerging evidence suggests that the higher-order organization of chromatin plays a role in the co-regulation of genes. We hypothesised that the three-dimensional organization of genes and chromosomes in the nucleus of B cells plays a key role in the epigenetic and transcriptional reprogramming that underlies acquisition of the GC B cell phenotype during B cell maturation. Using genome-wide mapping of chromatin interactions (Hi-C), combined with genome-wide profiles of gene expression (RNA-seq), histone modifications and transcription factor binding (ChIP-seq) in human naïve B (NB) and GC B cells, we have discovered that the three-dimensional structure of the genome undergoes widespread reorganization during B cell maturation to coordinate the GC transcriptional programme. Conformational maps of chromosome folding in these cells reveal a novel and profound loss of inter-arm interactions, reflecting lower chromosome compaction in GC B cells. Remarkably, we observed extensive differential partitioning of genes into NB- and GC B cell-specific compartments, and demonstrate for the first time that coordinated changes in histone modifications (H3K4Me2: P=3×10⁻³⁵; H3K27Ac: P=3×10⁻³³; Fisher's exact test) and transcription (P=1×10⁻⁹) required for cell type specification is mediated by the de novo formation of precisely delimited chromosome neighbourhoods. Most strikingly, we find that remodelling of the GC B cell genome involves the specific structural unlocking of genes that drive the GC transcriptional programme, such as AICDA, MTA3, and BCL6. Coordinate activation of these genes is mediated by the expansion of gene interaction neighbourhoods, increased promoter interactivity (P=3×10⁻³⁵), engagement of long-range enhancer-promoter interactions (>2-fold increase), and the formation of gene body loops (P=3.18×10⁻¹⁵). Intriguingly, the master regulator of GC B cell differentiation, BCL6, shows a high propensity for all of these different types of interactions, suggesting that regulation of this gene in the context of chromatin is highly complex. Integration with genome-wide binding data for the structural organizing proteins, CTCF and cohesin, as well as the cell-specific factor, PU.1, supports a specific role for these proteins in the repositioning of activated promoters and enhancer regions during B cell maturation. This study shows for the first time that the architecture of the genome is critical for specification of cellular phenotype, and that epigenetic and transcriptional reprogramming in GC B cells is functionally linked to the structural reorganization of genes in the nucleus. Importantly, the higher-order organization of chromatin could represent a novel mechanism by which GC B cell gene expression is dysregulated in lymphoma.