多种逻辑和语法编码脊索增强子。

Diverse logics and grammar encode notochord enhancers.

机构信息

Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.

Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.

出版信息

Cell Rep. 2023 Feb 28;42(2):112052. doi: 10.1016/j.celrep.2023.112052. Epub 2023 Jan 31.

DOI:10.1016/j.celrep.2023.112052

PMID:36729834

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10387507/

Abstract

The notochord is a defining feature of all chordates. The transcription factors Zic and ETS regulate enhancer activity within the notochord. We conduct high-throughput screens of genomic elements within developing Ciona embryos to understand how Zic and ETS sites encode notochord activity. Our screen discovers an enhancer located near Lama, a gene critical for notochord development. Reversing the orientation of an ETS site within this enhancer abolishes expression, indicating that enhancer grammar is critical for notochord activity. Similarly organized clusters of Zic and ETS sites occur within mouse and human Lama1 introns. Within a Brachyury (Bra) enhancer, FoxA and Bra, in combination with Zic and ETS binding sites, are necessary and sufficient for notochord expression. This binding site logic also occurs within other Ciona and vertebrate Bra enhancers. Collectively, this study uncovers the importance of grammar within notochord enhancers and discovers signatures of enhancer logic and grammar conserved across chordates.

摘要

脊索是所有脊索动物的特征。转录因子 Zic 和 ETS 调节脊索内增强子的活性。我们对正在发育的海鞘胚胎中的基因组元件进行高通量筛选，以了解 Zic 和 ETS 位点如何编码脊索活性。我们的筛选发现了一个位于 Lama 附近的增强子，Lama 是脊索发育的关键基因。在这个增强子内反转 ETS 位点的方向会使表达失活，表明增强子语法对脊索活性至关重要。在小鼠和人类的 Lama1 内含子中，也存在类似组织的 Zic 和 ETS 位点簇。在 Brachyury（Bra）增强子中，FoxA 和 Bra 与 Zic 和 ETS 结合位点一起，是脊索表达所必需且充分的。这种结合位点逻辑也存在于其他海鞘和脊椎动物的 Bra 增强子中。总的来说，这项研究揭示了脊索增强子中语法的重要性，并发现了跨脊索动物保守的增强子逻辑和语法特征。