Liu Chenli, Danilowicz Claudia, Kleckner Nancy, Prentiss Mara
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
Center for Synthetic Biology Engineering Research, Shenzhen Institute Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
Nucleic Acids Res. 2017 Jan 25;45(2):894-901. doi: 10.1093/nar/gkw758. Epub 2016 Aug 31.
Long non-coding RNAs (lncRNAs) are prominently associated with chromosomes in an ever-increasing diversity of roles. To provide further insight into the potential nature of these associations, we have explored, for the first time, the interaction of long single-stranded (ss) RNAs with cognate homologous double-stranded (ds) DNA in vitro Using magnetic tweezers, we measured the effects of ssRNA on force extension curves for dsDNA. We observe that the presence of ssRNA impedes the extension of dsDNA, specifically at low forces, dependent on homology between the RNA and DNA species, and dependent on ssRNA lengths (≥1 kb). The observed effect also depends on the concentration of ssRNA and is abolished by overstretching of the dsDNA. These findings show that significant homologous contacts can occur between long ssRNA and dsDNA in the absence of protein and that these contacts alter the mechanical properties of the dsDNA. We propose that long ssRNA interacts paranemically with long dsDNA via periodic short homologous interactions, e.g. mediated by RNA/DNA triplex-formation, and that dsDNA extension is impeded by formation of RNA secondary structure in the intervening unbound regions. Analogous interactions in vivo would permit lncRNAs to mediate the juxtaposition of two or more DNA regions on the same or different chromosomes.
长链非编码RNA（lncRNAs）在越来越多样化的作用中与染色体显著相关。为了进一步深入了解这些关联的潜在本质，我们首次在体外探索了长单链（ss）RNA与同源双链（ds）DNA的相互作用。使用磁镊，我们测量了ssRNA对dsDNA力-伸长曲线的影响。我们观察到，ssRNA的存在会阻碍dsDNA的伸长，特别是在低力作用下，这取决于RNA和DNA物种之间的同源性，以及ssRNA的长度（≥1 kb）。观察到的效应还取决于ssRNA的浓度，并且dsDNA过度拉伸会消除这种效应。这些发现表明，在没有蛋白质的情况下，长ssRNA和dsDNA之间可以发生显著的同源接触，并且这些接触会改变dsDNA的力学性质。我们提出，长ssRNA通过周期性的短同源相互作用与长dsDNA旁向相互作用，例如由RNA/DNA三链体形成介导，并且dsDNA的伸长受到中间未结合区域中RNA二级结构形成的阻碍。体内类似的相互作用将使lncRNAs能够介导同一或不同染色体上两个或更多DNA区域的并列。
