Deciphering the Regulatory Logic of an Ancient, Ultraconserved Nuclear Receptor Enhancer Module

作者：Bagama**ad Pia D; Bonett Ronald M; Sachs Laurent; Buisine Nicolas; Raj Samhitha; Knoedler Joseph R; Kyono Yasuhiro; Ruan Yijun; Ruan Xiaoan; Denver Robert J^*

来源：Molecular Endocrinology, 2015, 29(6): 856-872.

DOI：10.1210/me.2014-1349

Cooperative, synergistic gene regulation by nuclear hormone receptors can increase sensitivity and amplify cellular responses to hormones. We investigated thyroid hormone (TH) and glucocorticoid (GC) synergy on the Kruppel-like factor (Klf9) gene, which codes for a zinc finger transcription factor involved in development and homeostasis of diverse tissues. Weidentified regions of the Xenopus and mouse Klf9 genes 5-6 kb upstream of the transcription start sites that supported synergistic transactivation by THplus GC. Within these regions, we found an orthologous sequence of approximately 180 bp that is highly conserved among tetrapods, but absent in other chordates, and possesses chromatin marks characteristic of an enhancer element. The Xenopus and mouse approximately 180-bp DNA element conferred synergistic transactivation by hormones in transient transfection assays, so we designate this the Klf9 synergy module (KSM). Weidentified binding sites within the mouse KSM for TH receptor, GC receptor, and nuclear factor kappa B. TH strongly increased recruitment of liganded GC receptor and serine 5 phosphorylated (initiating) RNA polymerase II to chromatin at the KSM, suggesting a mechanism for transcriptional synergy. The KSM is transcribed to generate long noncoding RNAs, which are also synergistically induced by combined hormone treatment, and the KSM interacts with the Klf9 promoter and a far upstream region through chromosomal looping. Our findings support that the KSM plays a central role in hormone regulation of vertebrate Klf9 genes, it evolved in the tetrapod lineage, and has been maintained by strong stabilizing selection.

• 出版日期2015-6