Information content differentiates enhancers from silencers in mouse photoreceptors.
Information content differentiates enhancers from silencers in mouse photoreceptors.
复制标题
DOI：
10.7554/elife.67403
复制
发表时间：
2021-09-06
期刊：
影响因子：
7.7
通讯作者：
White MA
中科院分区：
文献类型：
--
作者：
Friedman RZ;Granas DM;Myers CA;Corbo JC;Cohen BA;White MA
增强子和沉默子通常依赖于相同的转录因子 (TF)，并且在 TF 结合或染色质状态的基因组分析中混为一谈。为了识别区分增强子和沉默子的序列特征，我们分析了小鼠视网膜中光感受器 TF 锥杆同源盒 (CRX) 靶向的基因组序列的大规模平行报告基因库。增强子和沉默子都比非活性序列包含更多的 TF 基序，但相对于沉默子，增强子包含来自更多样化的 TF 集合的基序。我们开发了一种信息内容测量方法，描述序列中基序的数量和多样性，并发现，虽然增强子和沉默子都依赖于 CRX 基序，但增强子具有更高的信息内容。信息内容区分同一 TF 所针对的增强子和沉默子的能力说明了基序上下文如何决定顺式调控序列的活性。不同的细胞类型是通过激活和抑制特定基因组的活性来建立的，这一过程由称为转录因子的蛋白质控制。转录因子通过识别和结合基因组部分（称为顺式调控序列）中的短 DNA 片段来发挥作用。当与转录因子结合时增加基因活性的顺式调节序列称为增强子，而导致基因活性降低的序列称为沉默子。为了建立细胞类型，特定的转录因子将作用于控制不同基因活性的增强子和沉默子。例如，转录因子锥杆同源盒（CRX）对于指定视网膜中不同类型的细胞至关重要，它对增强子和沉默子都起作用。在视杆细胞光感受器中，CRX 通过结合视杆细胞基因的增强子来激活视杆细胞基因，同时通过结合视锥细胞光感受器基因的沉默子来抑制视锥细胞光感受器基因。然而，CRX 总是识别并结合相同的 DNA 序列（称为其结合位点），这使得人们不清楚为什么一些与 CRX 结合的顺式调控序列充当沉默子，而其他序列则充当增强子。弗里德曼等人。试图了解增强子和沉默子（两者均与 CRX 结合）如何对其控制的基因产生不同的影响。由于增强子和沉默子都含有 CRX 结合位点，因此两者之间的差异必定在于这些结合位点周围的 DNA 序列。 Friedman 等人使用从小鼠身上摘除并在实验室中保持活力的视网膜。测试了来自小鼠基因组的数千个 CRX 结合序列的活性。这表明增强子和沉默子都比不活跃的基因组序列具有更多的 CRX 结合位点拷贝。此外，结果表明增强子具有多种其他转录因子的结合位点，而沉默子则没有。弗里德曼等人。开发了一种称为信息内容的新指标，该指标捕获顺式调控序列可能具有的不同转录结合位点的多种组合。 Friedman 等人使用这个指标。表明可以根据增强子的信息内容区分增强子和消音子。了解顺式调控区域的 DNA 序列如何决定其活性至关重要，因为基因组这些区域的突变可能导致疾病。然而，由于每个人的顺式调控序列中都有数千个良性突变，因此识别相对罕见的特定致病突变是一个挑战。增强子和沉默子模型（例如 Friedman 等人的信息内容模型）的一个长期目标是了解突变如何影响顺式调控序列，并在某些情况下导致疾病。
Enhancers and silencers often depend on the same transcription factors (TFs) and are conflated in genomic assays of TF binding or chromatin state. To identify sequence features that distinguish enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF cone-rod homeobox (CRX) in mouse retinas. Both enhancers and silencers contain more TF motifs than inactive sequences, but relative to silencers, enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. The ability of information content to distinguish enhancers and silencers targeted by the same TF illustrates how motif context determines the activity of cis-regulatory sequences. Different cell types are established by activating and repressing the activity of specific sets of genes, a process controlled by proteins called transcription factors. Transcription factors work by recognizing and binding short stretches of DNA in parts of the genome called cis-regulatory sequences. A cis-regulatory sequence that increases the activity of a gene when bound by transcription factors is called an enhancer, while a sequence that causes a decrease in gene activity is called a silencer. To establish a cell type, a particular transcription factor will act on both enhancers and silencers that control the activity of different genes. For example, the transcription factor cone-rod homeobox (CRX) is critical for specifying different types of cells in the retina, and it acts on both enhancers and silencers. In rod photoreceptors, CRX activates rod genes by binding their enhancers, while repressing cone photoreceptor genes by binding their silencers. However, CRX always recognizes and binds to the same DNA sequence, known as its binding site, making it unclear why some cis-regulatory sequences bound to CRX act as silencers, while others act as enhancers. Friedman et al. sought to understand how enhancers and silencers, both bound by CRX, can have different effects on the genes they control. Since both enhancers and silencers contain CRX binding sites, the difference between the two must lie in the sequence of the DNA surrounding these binding sites. Using retinas that have been explanted from mice and kept alive in the laboratory, Friedman et al. tested the activity of thousands of CRX-binding sequences from the mouse genome. This showed that both enhancers and silencers have more copies of CRX-binding sites than sequences of the genome that are inactive. Additionally, the results revealed that enhancers have a diverse collection of binding sites for other transcription factors, while silencers do not. Friedman et al. developed a new metric they called information content, which captures the diverse combinations of different transcription binding sites that cis-regulatory sequences can have. Using this metric, Friedman et al. showed that it is possible to distinguish enhancers from silencers based on their information content. It is critical to understand how the DNA sequences of cis-regulatory regions determine their activity, because mutations in these regions of the genome can cause disease. However, since every person has thousands of benign mutations in cis-regulatory sequences, it is a challenge to identify specific disease-causing mutations, which are relatively rare. One long-term goal of models of enhancers and silencers, such as Friedman et al.’s information content model, is to understand how mutations can affect cis-regulatory sequences, and, in some cases, lead to disease.