A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression. Hofbauer et al.

Cell type-specific gene transcription is a profoundly regulated process that enables development and homeostasis in all animals. Two major classes of distal cis-regulatory DNA elements (CREs), enhancers and silencers, activate or repress transcription, respectively. However, while enhancers have been thoroughly characterized, the sequence and chromatin properties of silencers, as well as their mechanisms of distal transcriptional repression, remain largely unknown. We performed an unbiased genome-wide silencer screen in Drosophila melanogaster S2 cells and discover a novel class of silencers, which recruit one of three different zinc finger transcription factors (TFs) through conserved DNA motifs. Surprisingly, these silencers lack detectable DNA accessibility, placing them outside current chromatin-defined catalogs of CREs (e.g. modENCODE). Further we find that the TF CG11247, which we term Saft, binds to one type of silencers via the orphan DLM3 motif and seems to safeguard cell fate decisions by repressing trachea- and cuticle-specific genes in non- trachea/non-cuticle tissues, such as the ovary or brain. Saft contains the previously unknown, highly conserved effector domain ZAC and functions via the corepressor G9a, yet independently of G9a’s H3K9 methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanism of action has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes.

细胞类型特异性基因转录是一种受到深刻调控的过程，它促使所有动物的生长发育与稳态维持。远端顺式调控DNA元件（CREs）分为两大类，即增强子和沉默子，分别负责激活或抑制转录。尽管增强子已被详尽地描述，但沉默子的序列、染色质属性及其远端转录抑制机制仍鲜为人知。本研究在黑腹果蝇S2细胞中进行了无偏见的基因组-wide沉默子筛选，并发现了一类新型的沉默子，这些沉默子通过保守的DNA基序招募三种不同的锌指转录因子（TFs）。令人惊讶的是，这些沉默子缺乏可检测的DNA可及性，将它们置于了当前基于染色质定义的CREs目录之外（例如modENCODE）。进一步研究发现，TF CG11247，我们称之为Saft，通过孤儿DLM3基序与一种沉默子结合，似乎通过抑制气管和表皮特异性基因在非气管/非表皮组织中（如卵巢或大脑）的转录来保护细胞命运决定。Saft含有之前未知的、高度保守的效应域ZAC，并通过共抑制因子G9a发挥作用，但独立于G9a的H3K9甲基转移酶活性。总体而言，我们识别出具有意外属性和作用机制的沉默子，这对理解抑制性CREs以及动物基因组的功能注释具有重要意义。