Generation of an integrated transcription map of the BRCA2 region on chromosome 13q12-q13
Generation of an integrated transcription map of the BRCA2 region on chromosome 13q12-q13
复制标题
DOI：
10.1006/geno.1996.0428
复制
发表时间：
1996-08-15
期刊：
影响因子：
4.4
通讯作者：
Simard, J
中科院分区：
文献类型：
--
作者：
Couch, FJ;Rommens, JM;Simard, J
一个综合的方法，包括物理映射，转录序列的识别，和基因组序列的计算分析，用于生成一个详细的转录图的1.0 Mb区域含有乳腺癌易感基因BRCA 2的染色体13 q12-q13。该区域包含在由D13 S1444和D13 S310界定的遗传区间内。从外显子扩增或杂交选择程序检索的序列被分组为物理间隔，随后通过克隆重叠分组为转录单位。通过直接杂交、cDNA文库筛选、PCR cDNA连接（岛跳跃）和/或序列比对建立重叠。进行广泛的基因组测序以努力理解转录单位组织。总共完成了大约500 kb的基因组序列。通过与来自一系列人类组织的RNA杂交，进一步表征转录单位。七个基因，两个假定的假基因，和九个额外的假定转录单位的证据。其中一个转录单位最近被鉴定为BRCA 2，但所有其他的都是未知功能的新基因，因为只观察到与公共数据库中序列的有限比对。一个大基因的转录本大小为10.7 kb，与秀丽隐杆线虫基因组和酿酒酵母基因组测序工作预测的基因具有显着的相似性，而另一个包含与人2 '，3'环核苷酸3'磷酸二酯酶基因相似的基序序列。几个检索到的转录序列没有对齐到转录单位中，因为在筛选文库时没有获得相应的cDNA，或者因为缺乏剪接信号或基于计算分析的推定编码序列的明确证据。然而，在BRCA 2区间中存在额外的基因被认为是假定的外显子组和以一致方向转录的杂交选择的克隆可以定位于共同的物理区间。(C)出版社：Academic Press，Inc.
An integrated approach involving physical mapping, identification of transcribed sequences, and computational analysis of genomic sequence was used to generate a detailed transcription map of the 1.0-Mb region containing the breast cancer susceptibility locus BRCA2 on chromosome 13q12-q13. This region is included in the genetic interval bounded by D13S1444 and D13S310. Retrieved sequences from exon amplification or hybrid selection procedures were grouped into physical intervals and subsequently grouped into transcription units by clone overlap. Overlap was established by direct hybridization, cDNA library screening, PCR cDNA linking (island hopping), and/or sequence alignment. Extensive genomic sequencing was performed in an effort to understand transcription unit organization. In total, approximately 500 kb of genomic sequence was completed. The transcription units were further characterized by hybridization to RNA from a series of human tissues. Evidence for seven genes, two putative pseudogenes, and nine additional putative transcription units was obtained. One of the transcription units was recently identified as BRCA2 but all others are novel genes of unknown function as only limited alignment to sequences in public databases was observed. One large gene with a transcript size of 10.7 kb showed significant similarity to a gene predicted by the Caenorhabditis elegans genome and the Saccharomyces cerevisiae genome sequencing efforts, while another contained a motif sequence similar to the human 2', 3' cyclic nucleotide 3' phosphodiesterase gene. Several retrieved transcribed sequences were not aligned into transcription units because no corresponding cDNAs were obtained when screening libraries or because of a lack of definitive evidence for splicing signals or putative coding sequence based on computational analysis. However, the presence of additional genes in the BRCA2 interval is suggested as groups of putative exons and hybrid selected clones that were transcribed in consistent orientations could be localized to common physical intervals. (C) 1996 Academic Press, Inc.