哺乳动物启动子结构与进化的全基因组分析。

Genome-wide analysis of mammalian promoter architecture and evolution.

作者信息

Carninci Piero, Sandelin Albin, Lenhard Boris, Katayama Shintaro, Shimokawa Kazuro, Ponjavic Jasmina, Semple Colin A M, Taylor Martin S, Engström Pär G, Frith Martin C, Forrest Alistair R R, Alkema Wynand B, Tan Sin Lam, Plessy Charles, Kodzius Rimantas, Ravasi Timothy, Kasukawa Takeya, Fukuda Shiro, Kanamori-Katayama Mutsumi, Kitazume Yayoi, Kawaji Hideya, Kai Chikatoshi, Nakamura Mari, Konno Hideaki, Nakano Kenji, Mottagui-Tabar Salim, Arner Peter, Chesi Alessandra, Gustincich Stefano, Persichetti Francesca, Suzuki Harukazu, Grimmond Sean M, Wells Christine A, Orlando Valerio, Wahlestedt Claes, Liu Edison T, Harbers Matthias, Kawai Jun, Bajic Vladimir B, Hume David A, Hayashizaki Yoshihide

机构信息

Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

出版信息

Nat Genet. 2006 Jun;38(6):626-35. doi: 10.1038/ng1789. Epub 2006 Apr 28.

DOI:10.1038/ng1789

PMID:16645617

Abstract

Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.

摘要

哺乳动物启动子可分为两类

富含保守TATA盒的启动子，其在一个明确界定的位点起始转录；以及更具可塑性、宽泛且可进化的富含CpG的启动子。我们已对小鼠和人类基因组中对应数十万个转录起始位点（TSS）的标签进行了测序，从而能够对不同类型启动子的序列结构和进化进行精确分析。不同组织和基因家族对不同类型启动子的使用存在差异。我们的标签方法可对不同组织中启动子的使用情况进行定量分析，并表明差异调节的可变TSS是蛋白质编码基因的一个常见特征，且通常会产生可变的N端。在这些TSS中，我们鉴定出了与大多数外显子以及3'UTR相关的新起始位点。这些数据使得在全基因组范围内鉴定组织特异性启动子以及分析与之相关的顺式作用元件成为可能。