Differential Nucleosome Spacing in Neurons and Glia. Differential Nucleosome Spacing in Neurons and Glia

Eukaryotic chromosomes are composed of chromatin, in which regularly spaced nucleosomes containing ~147 bp of DNA are separated by linker DNA. Most eukaryotic cells have a characteristic average nucleosome spacing of ~190 bp, corresponding to a ~45 bp linker. However, cortical neurons have a shorter average spacing of ~165 bp. The significance of this atypical global chromatin organization is unclear. We have compared the chromatin structures of purified mouse dorsal root ganglia (DRG) neurons, cortical oligodendrocyte precursor cells (OPCs) and cortical astrocytes. DRG neurons have short average spacing (~165 bp), whereas OPCs (~182 bp) and astrocytes (~183 bp) have longer spacing. We measured nucleosome positions by MNase-seq and gene expression by RNA-seq. Most genes in all three cell types have a promoter chromatin organization typical of active genes: a nucleosome-depleted region at the promoter flanked by regularly spaced nucleosomes phased relative to the transcription start site. In DRG neurons, the spacing of phased nucleosomes downstream of promoters (~178 bp) is longer than expected from the genomic average, whereas phased nucleosome spacing in OPCs and astrocytes is similar to the global average (~183 bp). Thus, the atypical nucleosome spacing of neuronal chromatin does not extend to promoter-proximal regions. Overall design: Three different mouse cell types (purified primary cultures): dorsal root ganglia (DRG) neurons, oligodendrocyte progenitor cells (OPCs) and astrocytes. Two biological replicate experiments for each.

真核染色体由染色质（chromatin）构成，其中包含约147 bp DNA的规则间隔核小体（nucleosome）由连接DNA（linker DNA）分隔。大多数真核细胞具有典型的平均核小体间隔约190 bp，对应约45 bp的连接区。但皮层神经元的平均间隔较短，约为165 bp。这种非典型的整体染色质组织的生物学意义尚不明确。本研究对纯化的小鼠背根神经节（dorsal root ganglia, DRG）神经元、皮层少突胶质前体细胞（oligodendrocyte precursor cells, OPCs）以及皮层星形胶质细胞（astrocytes）的染色质结构进行了比较分析。其中DRG神经元的平均间隔较短（约165 bp），而OPCs（约182 bp）与星形胶质细胞（约183 bp）的间隔更长。研究人员通过微球菌核酸酶测序（micrococcal nuclease sequencing, MNase-seq）检测核小体定位，通过RNA测序（RNA sequencing, RNA-seq）分析基因表达水平。三种细胞类型中的绝大多数基因均具有活跃基因典型的启动子染色质组织模式：启动子区域存在核小体缺失区（nucleosome-depleted region），其两侧为相对于转录起始位点（transcription start site, TSS）形成相位排列的规则间隔核小体。在DRG神经元中，启动子下游相位排列核小体的间隔（约178 bp）高于基因组平均水平预期值，而OPCs与星形胶质细胞的相位核小体间隔则与整体平均水平（约183 bp）相近。由此可见，神经元染色质的非典型核小体间隔模式并不延伸至启动子近端区域。实验整体设计：选取3种不同的小鼠原代纯化培养细胞——背根神经节神经元、少突胶质前体细胞（OPCs）以及星形胶质细胞，每种细胞设置2次生物学重复实验。