Bernat John A, Crawford Gregory E, Ogurtsov Aleksey Y, Collins Francis S, Ginsburg David, Kondrashov Alexey S
Department of Human Genetics, Howard Hughes Medical Institute, USA.
Hum Mol Genet. 2006 Jul 1;15(13):2098-105. doi: 10.1093/hmg/ddl133. Epub 2006 May 24.
The transcriptional regulation of genes is a complex process, particularly for genes exhibiting a tissue-specific pattern of expression. We studied 28 genes that are expressed primarily in endothelial cells, another 28 genes that are expressed highly, but not exclusively, in cultured endothelial cells, and three control sets, consisting of genes not expressed in endothelium, genes expressed in neural tissues and housekeeping genes. For each gene, we identified conserved non-coding sequences (CNSs) of lengths 50 to >1000 nucleotides, located within the upstream intergenic region (from 500 to as far as 200 000 nucleotides upstream from the transcription start) or within the first intron. As a functional test, we assayed the CNSs from the set of endothelial cell-specific genes (EC-CNSs) for DNase hypersensitivity. Among 262 distant EC-CNSs, 33% are hypersensitive (HS) in endothelial cells, whereas only 16% are HS in control fibroblasts. A search for short sequence patterns revealed a number of motifs which are over-represented in EC-CNSs relative to CNSs from the control gene sets. In particular, the motif SAGGAAR is strongly and consistently over-represented among EC-CNSs, and is more over-represented in HS CNSs than in non-HS CNSs. CNSs which contain this motif are no closer to the promoter than an average CNS. This motif contains the core element of binding sites from the Ets family of transcription factors. Thus, one or several factors from this family may play a key role in the regulation of endothelial gene expression.
基因的转录调控是一个复杂的过程，对于呈现组织特异性表达模式的基因而言尤其如此。我们研究了28个主要在内皮细胞中表达的基因、另外28个在培养的内皮细胞中高表达但并非仅在内皮细胞中表达的基因，以及三个对照组，包括在内皮细胞中不表达的基因、在神经组织中表达的基因和管家基因。对于每个基因，我们确定了长度在50至1000多个核苷酸之间的保守非编码序列（CNSs），这些序列位于上游基因间区域（转录起始点上游500至200000个核苷酸处）或第一个内含子内。作为一项功能测试，我们检测了内皮细胞特异性基因组（EC-CNSs）中的CNSs对DNA酶超敏感性。在262个远距离的EC-CNSs中，33%在内皮细胞中具有超敏感性（HS），而在对照成纤维细胞中只有16%具有超敏感性。对短序列模式的搜索揭示了一些在EC-CNSs中相对于对照基因组的CNSs而言过度富集的基序。特别是，基序SAGGAAR在EC-CNSs中强烈且一致地过度富集，并且在HS CNSs中比在非HS CNSs中更过度富集。包含该基序的CNSs与启动子的距离并不比平均CNS更近。该基序包含Ets转录因子家族结合位点的核心元件。因此，该家族中的一个或几个因子可能在内皮基因表达的调控中起关键作用。
