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

包括人类在内的温血脊椎动物的基因组由G+C%(GC%)的长程镶嵌结构组成，被认为与染色体带有关。我们以前报道了在MHC II类和III类之间的连接区有一个百万碱基大小的GC%马赛克结构域的边界的例子，提出它可能是一个染色体带边界。然后，我们在结构域边界上发现了一个与人类性染色体的伪常染色体边界(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阶段，带状边界包含DNA复制时间的转换点。为了确定复制转换点，我们确定了MHC II和III类的精确DNA复制时间，重点放在连接区。复制时间在两侧相差2小时的边界区域发生了精确的变化，表明该区域是染色体带的边界。在开关区域，复制叉运动似乎终止(暂停)或显著减慢，该区域包含密集的Alu簇和多嘌呤/多嘧啶束。在转换区及其周围发现了三个与支架相关的区域(SARS/MARS)。在GC%边界附近发现了小鼠乳腺肿瘤基因Int3的人类对应物。我们将这个III类基因命名为NOTCH4。将预测的氨基酸序列与其他已知的Notch同源物进行比较，揭示了哺乳动物Notch的四个亚家族。在人类NOTCH4中，我们发现(CTG)n重复序列对不同的人类白细胞抗原单倍型具有可变数目串联重复序列(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多数定位在9q33-q34上的基因具有相似的结构和功能，这表明进化过程中染色体的节段性复制。染色体1、6、9、19上的基因也有相似性。

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.