Sequence determinants of human gene regulatory elements, ATI experiment

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: One ATI experiment, cycles 4 and 0 (input control) compared.

DNA决定基因的表达时空模式，但目前尚不明确控制基因表达的全部序列决定因子。本研究利用大规模平行报告基因测定（massively parallel reporter assays），对序列空间规模约为人类基因组100倍的DNA序列的转录活性开展了检测。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调控作用，且其调控规则较为松散；增强子可通过不依赖特异性转录因子间相互作用的机制，提升启动子介导的基因表达水平。增强子自身可分为三类截然不同的亚型：经典型、封闭染色质型与染色质依赖型增强子。本研究还发现，细胞中仅少数转录因子具备强调控活性，且多数转录因子的活性在不同细胞类型间高度相似。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、促进及转录起始位点（Transcription Start Site, TSS）确定活性，这与“转录因子结合基序是基因表达的唯一基本单元”的观点相一致。实验整体设计：开展1次ATI实验，对第4轮与第0轮（输入对照）样本进行对比分析。