Abstract A23: High mobility group N proteins modulate chromatin regulatory sites and gene expression during LPS-induced B-cell activation

The features of chromatin which allow cells to alter gene expression in response to various environmental or endogenous cues are regulated by dynamic interactions between DNA elements and numerous chromatin-associated factors including the ubiquitous HMGN proteins. Resent research established a direct link between over-expression of HMGN protein and acute lymphoblastic leukemia. However, the functions of HMGN proteins in B lymphocytes during their transition from a resting to an activated state has been unclear. Here we use B cells from wild type and genetically altered mice lacking HMGN variants to examine the function of HMGN proteins in B cell activation. We find that HMGN proteins affect the DNase I hypersensitivity patterns of chromatin and modulate the fidelity of transcriptional profiles during B-cell activation. Our ChIP-seq results reveal that both HMGN1 and HMGN2, the two major HMGN variants are highly enriched at CpG-containing promoters of transcriptionally active genes. Comparison of ChIP-seq and DNase-seq data shows a strong correlation between HMGN binding sites and DNase I hypersensitivity sites in resting B cells. Loss of HMGN proteins induced significant changes in chromatin structure: the normalized DNase I hypersensitivity at promoter regions was reduced by ~40% in Hmgn1-/n2-/- double knockout cells compared with wt control. Interestingly, activation of B cells with LPS lead to a global disruption in the binding of HMGN proteins on chromatin. Only 10% HMGN binding sites identified in resting B cells are retained after B-cell activation. Correspondingly, in activated B cells, loss of HMGNs did not lead to significant changes in DHS. However, genome-wide mapping of nucleosomes indicates that loss of HMGN proteins did increase the nucleosomal occupancy at promoters of active genes in both resting and activated B cells. To investigate whether the global changes in chromatin structure affect the regulation of gene expression, we examined the transcriptomic profiles in Hmgn1-/n2-/- double knockout cells in resting, 1h-, 4h-, 24h- and 72h-activated B cells. We found that loss of both HMGN1 and HMGN2 proteins affects gene expression throughout B-cell activation process. The most remarkable changes were observed 72 hour after activation, when the expression of more than one thousand genes was significantly affected. GO analysis identifies the immune system processes as the top category affected by loss of HMGN proteins at all time points tested. Our study demonstrates a role for HMGN proteins in maintaining the chromatin regulatory landscape and in modulating gene-regulatory networks. Given the ubiquitous presence of HMGN1 and HMGN2 in all vertebrate cells, it is likely that similar roles of HMGN proteins are widely spread in vertebrate cells. Citation Format: Shaofei Zhang, Iris Zhu, Tao Deng, Takashi Furusawa, David Landsman, Michael Bustin. High mobility group N proteins modulate chromatin regulatory sites and gene expression during LPS-induced B-cell activation. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr A23.