Bernardi Giorgio
Science Department, Roma Tre University, Viale Marconi 446, 00146 Rome, Italy.
Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.
Life (Basel). 2021 Apr 13;11(4):342. doi: 10.3390/life11040342.
The chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two "gene spaces" were found many years ago: A GC-rich, gene-rich "genome core" and a GC-poor, gene-poor "genome desert", the former corresponding to open chromatin centrally located in the interphase nucleus, the latter to closed chromatin located peripherally. This bimodality was later confirmed and extended by the discoveries (1) of LADs, the Lamina-Associated Domains, and InterLADs; (2) of two "spatial compartments", A and B, identified on the basis of chromatin interactions; and (3) of "forests and prairies" characterized by high and low CpG islands densities. Chromatin compartments were shown to be associated with the compositionally different, flat and single- or multi-peak DNA structures of the two, GC-poor and GC-rich, "super-families" of isochores. At the second, sub-compartment, level, chromatin corresponds to flat isochores and to isochore loops (due to compositional DNA gradients) that are susceptible to extrusion. Finally, at the short-sequence level, two sets of sequences, GC-poor and GC-rich, define two different nucleosome spacings, a short one and a long one. In conclusion, chromatin structures are moulded according to a "genomic code" by DNA sequences that pervade the genome and leave no room for "junk".
在三个DNA大小水平上对人类基因组的染色质进行了分析。首先，在区室水平上，多年前发现了两个“基因空间”：一个富含GC、富含基因的“基因组核心”和一个GC含量低、基因稀少的“基因组荒漠”，前者对应于位于间期细胞核中心的开放染色质，后者对应于位于外周的封闭染色质。这种双峰性后来通过以下发现得到证实和扩展：（1）发现了LADs（核纤层相关结构域）和InterLADs；（2）基于染色质相互作用鉴定出两个“空间区室”，A和B；（3）发现了以高低CpG岛密度为特征的“森林和草原”。染色质区室与两种等密度区（GC含量低和GC含量高）的组成不同、扁平且单峰或多峰的DNA结构相关。其次，在亚区室水平上，染色质对应于扁平的等密度区和等密度区环（由于DNA组成梯度），它们易于被挤压。最后，在短序列水平上，两组序列，GC含量低的和GC含量高的，定义了两种不同的核小体间距，一种短间距和一种长间距。总之，染色质结构是由遍布基因组且不留“垃圾”空间的DNA序列根据“基因组密码”塑造而成的。
