Fisher S E, Ciccodicola A, Tanaka K, Curci A, Desicato S, D'urso M, Craig I W
Department of Biochemistry, Oxford University, South Parks Road, Oxford, OX1 3QU, United Kingdom.
Genomics. 1997 Oct 15;45(2):340-7. doi: 10.1006/geno.1997.4941.
The human Xp11.23-p11.22 interval has been implicated in several inherited diseases including Wiskott-Aldrich syndrome; three forms of X-linked hypercalciuric nephrolithiaisis; and the eye disorders retinitis pigmentosa 2, congenital stationary night blindness, and Aland Island eye disease. In constructing YAC contigs spanning Xp11. 23-p11.22, we have previously shown that the region around the synaptophysin (SYP) gene is refractory to cloning in YACs, but highly stable in cosmids. Preliminary analysis of the latter suggested that this might reflect a high density of coding sequences and we therefore undertook the complete sequencing of a SYP-containing cosmid. Sequence data were extensively analyzed using computer programs such as CENSOR (to mask repeats), BLAST (for homology searches), and GRAIL and GENE-ID (to predict exons). This revealed the presence of 29 putative exons, organized into three genes, in addition to the 7 exons of the complete SYP coding region, all mapping within a 44-kb interval. Two genes are novel, one (CACNA1F) showing high homology to alpha1 subunits of calcium channels, the other (LMO6) encoding a product with significant similarity to LIM-domain proteins. RT-PCR and Northern blot studies confirmed that these loci are indeed transcribed. The third locus is the previously described, but not previously localized, A4 differentiation-dependent gene. Given that the intron-exon boundaries predicted by the analysis are consistent with previous information where available, we have been able to suggest the genomic organization of the novel genes with some confidence. The region has an elevated GC content (>53%), and we identified CpG islands associated with the 5' ends of SYP, A4, and LMO6. The order of loci was Xpter-A4-LMO6-SYP-CACNA1F-Xcen, with intergenic distances ranging from approximately 300 bp to approximately 5 kb. The density of transcribed sequences in this area (>80%) is comparable to that found in the highly gene-rich chromosomal band Xq28. Further studies may aid our understanding of the long-range organization surrounding such gene-enriched regions.
人类Xp11.23 - p11.22区间与多种遗传性疾病相关，包括威斯科特-奥尔德里奇综合征；三种X连锁高钙尿性肾结石症；以及眼部疾病色素性视网膜炎2型、先天性静止性夜盲症和阿兰岛眼病。在构建跨越Xp11.23 - p11.22的酵母人工染色体（YAC）重叠群时，我们先前已表明，突触素（SYP）基因周围区域难以在YAC中克隆，但在黏粒中高度稳定。对后者的初步分析表明，这可能反映了编码序列的高密度，因此我们对一个含SYP的黏粒进行了全序列测定。使用诸如CENSOR（用于屏蔽重复序列）、BLAST（用于同源性搜索）以及GRAIL和GENE - ID（用于预测外显子）等计算机程序对序列数据进行了广泛分析。这揭示了除完整SYP编码区的7个外显子外，还存在29个推定外显子，它们被组织成三个基因，所有这些都定位在一个44kb的区间内。两个基因是新发现的，一个（CACNA1F）与钙通道的α1亚基具有高度同源性，另一个（LMO6）编码的产物与LIM结构域蛋白具有显著相似性。逆转录聚合酶链反应（RT - PCR）和Northern印迹研究证实这些基因座确实被转录。第三个基因座是先前描述但未定位的A4分化依赖性基因。鉴于分析预测的内含子-外显子边界与现有信息一致，我们能够有一定把握地推测新基因的基因组结构。该区域的GC含量升高（>53%），并且我们鉴定出与SYP、A4和LMO6的5'端相关的CpG岛。基因座的顺序为Xpter - A4 - LMO6 - SYP - CACNA1F - Xcen，基因间距离从约300bp到约5kb不等。该区域转录序列的密度（>80%）与基因高度丰富的染色体带Xq28中的密度相当。进一步的研究可能有助于我们理解围绕此类基因丰富区域的长程结构。
