Sequence determinants of human gene regulatory elements, ChIP-seq experiments. Sequence determinants of human gene regulatory elements, ChIP-seq experiments

DNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. Here, we measured transcriptional activity of DNA sequences that represent ~100 times larger sequence space than the human genome using massively parallel reporter assays. Machine learning models revealed that transcription factors (TFs) act generally in an additive manner with weak grammar, and that enhancers increase expression from a promoter by a mechanism that does not involve specific TF-TF interactions. The enhancers themselves can be classified into three distinct types: classical, closed chromatin and chromatin-dependent enhancers. We also show that few TFs are strongly active in a cell, with most activities similar between cell types. Individual TFs can have multiple gene regulatory activities, including chromatin opening, enhancing, promoting and TSS determining activity – consistent with the view that the TF binding motif is the only atomic unit of gene expression. Overall design: Transcription factor (TF) binding and enrichment of histone modifications were analyzed by chromatin immunoprecipitation followed by deep sequencing (ChIP-seq)

DNA可决定基因表达的时空位置与时机，但目前尚未明确调控基因表达的全套序列决定因子。本研究采用大规模平行报告基因检测（massively parallel reporter assays），对远超人类基因组序列空间约100倍的DNA序列的转录活性进行了检测。机器学习模型分析显示，转录因子（transcription factors, TFs）通常以加法模式发挥作用，且仅受较弱的序列语法约束；增强子通过不依赖特定转录因子间相互作用的机制，提升启动子驱动的基因表达水平。增强子本身可分为三类截然不同的亚型：经典型增强子、封闭染色质型增强子以及染色质依赖型增强子。研究同时发现，细胞内仅少量转录因子具有强活性，且多数转录因子的活性在不同细胞类型间保持相似。单个转录因子可兼具多种基因调控活性，包括染色质开放、增强表达、启动调控以及转录起始位点（transcription start site, TSS）确定活性——这与"转录因子结合基序是基因表达调控的唯一原子级功能单元"的观点相一致。实验整体设计：本研究通过染色质免疫共沉淀联合深度测序（chromatin immunoprecipitation followed by deep sequencing, ChIP-seq），对转录因子结合情况以及组蛋白修饰的富集水平进行了分析。