The p53 family of transcription factors (p53, p63 and p73) regulate diverse organismal processes including tumor suppression, maintenance of genome integrity and the development of skin and limbs. Crosstalk between transcription factors with highly similar DNA binding profiles, like those in the p53 family, can dramatically alter gene regulation. While p53 is primarily associated with transcriptional activation, p63 mediates both activation and repression. The specific mechanisms controlling p63-dependent gene regulatory activity are not well understood. Here, we use massively parallel reporter assays (MPRA) to investigate how local DNA sequence context influences p63-dependent transcriptional activity. Most regulatory elements with a p63 response element motif (p63RE) activate transcription, although binding of the p63 paralog, p53, drives a substantial proportion of that activity. p63RE sequence content and co-enrichment with other known activating and repressing transcription factors, including lineage-specific factors, correlates with differential p63RE-mediated activities. p63 isoforms dramatically alter transcriptional behavior, primarily shifting inactive regulatory elements towards high p63-dependent activity. Our analysis provides novel insight into how local sequence and cellular context influences p63-dependent behaviors and highlights the key, yet still understudied, role of transcription factor paralogs and isoforms in controlling gene regulatory element activity.

中文翻译：

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旁系同源物和亚型之间的串扰影响 p63 依赖性调节元件活性


转录因子 p53 家族 （p53、p63 和 p73） 调节多种生物过程，包括肿瘤抑制、基因组完整性的维持以及皮肤和四肢的发育。具有高度相似 DNA 结合谱的转录因子（如 p53 家族中的转录因子）之间的串扰可以显著改变基因调控。虽然 p53 主要与转录激活有关，但 p63 介导激活和抑制。控制 p63 依赖性基因调控活性的具体机制尚不清楚。在这里，我们使用大规模平行报告基因分析 （MPRA） 来研究局部 DNA 序列环境如何影响 p63 依赖性转录活性。大多数具有 p63 反应元件基序 （p63RE） 的调节元件会激活转录，尽管 p63 旁系同源物 p53 的结合驱动了很大一部分活性。p63RE 序列内容和与其他已知激活和抑制转录因子（包括谱系特异性因子）的共富集与 p63RE 介导的差异活性相关。p63 亚型显著改变转录行为，主要将失活调节元件转向高 p63 依赖性活性。我们的分析为局部序列和细胞环境如何影响 p63 依赖性行为提供了新的见解，并强调了转录因子旁系同源物和亚型在控制基因调控元件活性中的关键但仍未得到充分研究的作用。