Bezzecchi Eugenia, Pagani Giulia, Forte Barbara, Percio Stefano, Zaffaroni Nadia, Dolfini Diletta, Gandellini Paolo
Department of Biosciences, University of Milan, Milan, Italy.
Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy.
Front Cell Dev Biol. 2022 Jun 17;10:909097. doi: 10.3389/fcell.2022.909097. eCollection 2022.
Aside serving as host gene for , transcribes for a chromatin-associated long noncoding RNA (lncRNA) able to restrain the differentiation of prostate basal cells, thus being reannotated as (Long Epithelial -interacting Differentiation-related RNA). We previously showed the presence of sequences in the promoters of genes modulated upon / manipulation. Notably, an element also spans the first and second exons of /, suggesting its possible involvement in target selection/binding. Here, we performed ChIRP-seq to map / chromatin occupancy at genome-wide level in prostate basal cells. Our results confirmed preferential binding to regions proximal to gene transcription start site (TSS). Moreover, enrichment of triplex-forming sequences was found upstream of /-bound genes, peaking at -1,500/-500 bp from TSS. Triplexes formed with one or two putative DNA binding sites within / sequence, located just upstream of the element. Notably, triplex-forming regions of bound genes were themselves enriched in elements. These data suggest, from one side, that triplex formation may be the prevalent mechanism by which / selects and physically interacts with target DNA, from the other that direct or protein-mediated (RNA)/ (DNA) interaction may represent a further functional requirement. We also found that triplex-forming regions were enriched in specific histone modifications, including H3K4me1 in the absence of H3K27ac, H3K4me3 and H3K27me3, indicating that in prostate basal cells / may preferentially bind to primed proximal regulatory elements. This may underscore the need for basal cells to keep / target genes repressed but, at the same time, responsive to differentiation cues.
除了作为……的宿主基因外，……转录生成一种与染色质相关的长链非编码RNA（lncRNA），它能够抑制前列腺基底细胞的分化，因此被重新注释为……（长上皮相互作用分化相关RNA）。我们之前发现，在……/……操作后被调控的基因启动子中存在……序列。值得注意的是，一个……元件也跨越了……/……的第一和第二外显子，表明其可能参与了靶标选择/结合。在这里，我们进行了ChIRP-seq实验，以在全基因组水平上绘制前列腺基底细胞中……/……的染色质占据情况。我们的结果证实了其优先结合在基因转录起始位点（TSS）近端的区域。此外，在……结合基因的上游发现了三链体形成序列的富集，在距离TSS -1500/-500 bp处达到峰值。三链体由……序列内一个或两个假定的DNA结合位点形成，位于……元件的上游。值得注意的是，结合基因的三链体形成区域本身富含……元件。这些数据一方面表明，三链体形成可能是……选择并与靶标DNA进行物理相互作用的主要机制，另一方面表明直接的或蛋白质介导的……（RNA）/……（DNA）相互作用可能代表了进一步的功能需求。我们还发现，三链体形成区域富含特定的组蛋白修饰包括在没有H3K27ac的情况下的H3K4me1、H3K4me3和H3K27me3，这表明在前列腺基底细胞中……可能优先结合到起始的近端调控元件上。这可能强调了基底细胞需要使……靶标基因保持抑制状态，但同时又能对分化信号作出反应。
