Structure and function of chromosome band boundaries of warm-blooded vertebrates

温血脊椎动物（包括人类）的基因组是由G+C% （GC%）的长链镶嵌结构组成的，这被认为与染色体带有关。我们之前报道了一个在MHC II类和III类之间的连接区域的兆级大小的GC%镶嵌结构域边界的例子，提出它可能是染色体带边界。然后，我们在结构域边界中发现了与人类性染色体的假常染色体边界（PAB）序列非常相似的序列。我们将其命名为“PABL”，并在人类基因组中发现了许多PABL。据预测，在S期，带边界包含DNA复制定时的开关点。为了确定复制开关点，我们确定了MHC II类和III类的精确DNA复制时间，重点是连接区域。边界区复制时间发生精确变化，两侧相差2小时，表明该区域为染色体带边界。在包含密集Alu簇和多嘌呤/多嘧啶束的开关区域，复制叉运动似乎终止（暂停）或显著减慢。在开关区及其周围发现了三个支架相关区（SARs/MARs）。在GC%边界附近发现了与小鼠乳腺肿瘤基因Int3相对应的人类基因。我们将这一III类基因命名为NOTCH4。将预测的氨基酸序列与其他已知的Notch同源物序列进行比较，揭示了哺乳动物Notch的4个亚家族。在人类NOTCH4中，我们发现（CTG）n个重复序列在不同HLA单倍型中表现出可变数串联重复（VNTR）多态性。我们还发现，定位在6p21.3上的10个基因，包括NOTCH4，在结构和功能上与大部分定位在9q33-q34上的基因相似，表明进化过程中存在染色体片段复制。在第1、6、9和19号染色体上也发现了基因的相似性。

The genomes of warm-blooded vertebrates, including humans, are composed of long-range mosaic structures of G+C% (GC%), which are thought to be related to chromosome bands. We previously reported an example of a boundary of megabase-sized GC% mosaic domains at the junction area between MHC classes II and III,proposing it to be a possible chromosome band boundary. We then found in the domain boundary a sequence very similar to pseudoautosomal boundary (PAB) sequences of human sex chromosomes. We designated it "PABL" and found many PABLs in the human genome. Band boundaries have been predicted to contain a switch point for DNA replication timing during S phase. To identify the replication swich point, we determined the precise DNA replication timing for MHC classes II and III,focusing on the junction area. The replication timing changed precisely in the boundary region with 2-hours difference between both sides, showing this region to be a chromosome band boundary. Replication fork movement appears to terminate(pause) or significantly slow down in the switch region, which contains dense Alu clusters and polypurine/polypyrimidine tracts. Three scaffold-associated regions (SARs/MARs) were found in and around the switch region. The human counterpart of the mouse mammary tumor gene Int3 was found near the GC% border. We designated this class III gene as NOTCH4. The comparison of the predicted amino acid sequence with those of other known Notch homologues revealed four subfamilies for mammalian Notch. In the human NOTCH4, we found (CTG)n repeats showing variable number tandem repeat (VNTR) polymorphism for different HLA haplotypes. We show also that ten genes mapped on 6p21.3, including NOTCH4, have counterparts structurally and functionally similar to those mostly mapped on 9q33-q34, indicating segmental chromosome duplication during evolution. Similarity of genes on chromosome 1,6,9 and 19 was also found.