AUTHOR=Bezzecchi Eugenia , Pagani Giulia , Forte Barbara , Percio Stefano , Zaffaroni Nadia , Dolfini Diletta , Gandellini Paolo 

TITLE=MIR205HG/LEADR Long Noncoding RNA Binds to Primed Proximal Regulatory Regions in Prostate Basal Cells Through a Triplex- and Alu-Mediated Mechanism

JOURNAL=Frontiers in Cell and Developmental Biology

VOLUME=10

YEAR=2022

URL=https://www.frontiersin.org/journals/cell-and-developmental-biology/articles/10.3389/fcell.2022.909097

DOI=10.3389/fcell.2022.909097

ISSN=2296-634X

ABSTRACT=<p>Aside serving as host gene for <italic>miR-205</italic>, <italic>MIR205HG</italic> transcribes for a chromatin-associated long noncoding RNA (lncRNA) able to restrain the differentiation of prostate basal cells, thus being reannotated as <italic>LEADR</italic> (Long Epithelial <italic>Alu</italic>-interacting Differentiation-related RNA). We previously showed the presence of <italic>Alu</italic> sequences in the promoters of genes modulated upon <italic>MIR205HG</italic>/<italic>LEADR</italic> manipulation. Notably, an <italic>Alu</italic> element also spans the first and second exons of <italic>MIR205HG</italic>/<italic>LEADR</italic>, suggesting its possible involvement in target selection/binding. Here, we performed ChIRP-seq to map <italic>MIR205HG</italic>/<italic>LEADR</italic> 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 <italic>MIR205HG</italic>/<italic>LEADR</italic>-bound genes, peaking at −1,500/−500 bp from TSS. Triplexes formed with one or two putative DNA binding sites within <italic>MIR205HG</italic>/<italic>LEADR</italic> sequence, located just upstream of the <italic>Alu</italic> element. Notably, triplex-forming regions of bound genes were themselves enriched in <italic>Alu</italic> elements. These data suggest, from one side, that triplex formation may be the prevalent mechanism by which <italic>MIR205HG</italic>/<italic>LEADR</italic> selects and physically interacts with target DNA, from the other that direct or protein-mediated <italic>Alu</italic> (RNA)/<italic>Alu</italic> (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 <italic>MIR205HG</italic>/<italic>LEADR</italic> may preferentially bind to primed proximal regulatory elements. This may underscore the need for basal cells to keep <italic>MIR205HG</italic>/<italic>LEADR</italic> target genes repressed but, at the same time, responsive to differentiation cues.</p>