Age-associated chromatin re-organization in progenitor B cells

Three-dimensional (3D) organization of the genome is essential for precise patterns of gene expression required for biological processes, however its role in physiological aging is not known.Here we show that large scale chromatin re-organization distinguishes bone marrow progenitor (pro-) B cells of old mice from that of young mice.These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs).One genomic region that transitions from compartment A to B with age contains the gene encoding Ebf1, a key regulator of normal B cell development.Genetically reducing Ebf1 recapitulates some features of old pro-B cells.TADs that are most reduced with age also harbor genes important for function and development of pro-B cells, including the immunoglobulin heavy chain (IgH) gene locus.Weaker intra-TAD interactions at IgH correlate with reduced utilization of distally located variable gene segments in VDJ recombination.Our observations implicate 3D chromatin re-organization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age. Overall design: Hi-C, capture Hi-C, ChIP-seq, HiChIP and RNA-seq were used to study the changes of chromatin structures in progenitor B cells during aging.

基因组的三维（3D）构象对于生物过程所需的精准基因表达模式至关重要，但其在生理性衰老中的作用尚未明确。本研究证实，大规模染色质重塑可区分老年小鼠与年轻小鼠的骨髓祖（pro-）B细胞。此类重塑使得区室层面的染色质互作增强，而拓扑关联结构域（TAD）内部的互作则减弱。随着衰老由A区室向B区室转变的一个基因组区域，携带着编码Ebf1的基因——Ebf1是正常B细胞发育的关键调控因子。通过遗传学手段下调Ebf1的表达，可复现老年pro-B细胞的部分特征。随衰老而出现互作减弱最为显著的TAD，还包含对pro-B细胞功能与发育至关重要的基因，其中包括免疫球蛋白重链（IgH）基因座。IgH位点处TAD内部的较弱互作，与VDJ重组中远端可变基因片段的使用效率降低存在相关性。本研究结果表明，3D染色质重塑是导致衰老过程中pro-B细胞表型异常、进而损害B细胞生成的主要驱动因素。实验设计概述：本研究采用Hi-C、捕获Hi-C（capture Hi-C）、染色质免疫沉淀测序（ChIP-seq）、HiChIP与RNA测序（RNA-seq）技术，探究衰老过程中祖B细胞的染色质结构变化。