一個(gè)基因組序列含有制造和運(yùn)行一個(gè)生物體所需的全部信息,。但對(duì)了解生物體是如何工作的來說重要的是決定每個(gè)基因何時(shí)何地處于激發(fā)狀態(tài)的編碼體系,。這就是基因組的轉(zhuǎn)錄調(diào)節(jié)編碼體系,，是DNA結(jié)合受體用來控制基因組表達(dá)的序列?，F(xiàn)在,，酵母（Saccharomyces）的這種編碼體系草圖首次編纂完成,。該編碼體系是通過將關(guān)于在不同條件下生長的酵母細(xì)胞中的轉(zhuǎn)錄調(diào)節(jié)因子的基因組結(jié)合位置的數(shù)據(jù)與關(guān)于基因組序列保留情況的知識(shí)及以前關(guān)于調(diào)節(jié)因子-DNA相互作用的證據(jù)結(jié)合起來獲得的,。所得到的調(diào)節(jié)編碼體系圖在一定程度上反映了基因組中所含的調(diào)節(jié)潛力在活細(xì)胞中是怎樣被利用的。

Transcriptional regulatory code of a eukaryotic genome

DNA-binding transcriptional regulators interpret the genome's regulatory code by binding to specific sequences to induce or repress gene expression1. Comparative genomics has recently been used to identify potential cis-regulatory sequences within the yeast genome on the basis of phylogenetic conservation2-6, but this information alone does not reveal if or when transcriptional regulators occupy these binding sites. We have constructed an initial map of yeast's transcriptional regulatory code by identifying the sequence elements that are bound by regulators under various conditions and that are conserved among Saccharomyces species. The organization of regulatory elements in promoters and the environment-dependent use of these elements by regulators are discussed. We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators.
 
 
Figure 1 Discovering binding-site specificities for yeast transcriptional regulators. a, Cis-regulatory sequences likely to serve as recognition sites for transcriptional regulators were identified by combining information from genome-wide location data, phylogenetically conserved sequences and previously published evidence, as described in Supplementary Methods. The compendium of regulatory sequence motifs can be found in Supplementary Table 3. b, Selected sequence specificities that were rediscovered and were newly discovered are shown. The total height of the column is proportional to the information content of the position, and the individual letters have a height proportional to the product of their frequency and the information content30. 

 
 
Figure 2 Drafting the yeast transcriptional regulatory map. a, Portions of chromosomes illustrating locations of genes (grey rectangles) and conserved DNA sequences (coloured boxes) bound in vivo by transcriptional regulators. b, Combining binding data and sequence conservation data. The diagram depicts all sequences matching a motif from our compendium (top), all such conserved sequences (middle) and all such conserved sequences bound by a regulator (bottom). c, Regulator binding site distribution. The red line shows the distribution of distances from the start codon of open reading frames to binding sites in the adjacent upstream region. The green line represents a randomized distribution. 

 
 
Figure 3 Yeast promoter architectures: single regulator architecture, promoter regions that contain one or more copies of the binding site sequence for a single regulator; repetitive motif architecture, promoter regions that contain multiple copies of a binding site sequence of a regulator; multiple regulator architecture, promoter regions that contain one or more copies of the binding site sequences for more than one regulator; co-occurring regulator architecture, promoters that contain binding site sequences for recurrent pairs of regulators. For the purposes of illustration, not all sites are shown and the scale is approximate. Additional information can be found in Supplementary Tables 4–6. 

 
 
Figure 4 Environment-specific use of the transcriptional regulatory code. Four patterns of genome-wide binding behaviour are depicted on the left, where transcriptional regulators are represented by coloured circles and are placed above and below a set of target genes/promoters. The lines between the regulators and the target genes/promoters represent binding events. Specific examples of the environment-dependent behaviours are depicted on the right. Coloured circles represent regulators and coloured boxes represent their DNA binding sequences within specific promoter regions. We note that regulators might exhibit different behaviours when different pairs of conditions are compared.