PuSH - Publikationsserver des Helmholtz Zentrums München: The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance.

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Rinck, A. ; Preusse, M. ; Laggerbauer, B.* ; Lickert, H. ; Engelhardt, S.* ; Theis, F.J.

The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance.

RNA Biol. 10, 1125-1135 (2013)

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Heat denaturation of native phages SD suspensions, phage "shadows", and isolated phage DNA solutions were studied by scanning microcalorimetry and viscosimetry. Energetic parameters of cooperative transitions of protein fraction and DNA were measured. DNA melting was shown to be preceded by the destruction of capsid and protein denaturation. The melting curve of isolated DNA and DNA in the presence of protein component is characterized by a fine structure which is completely restored at repeated denaturation only in the presence of the protein component. "Creeping" of DNA out of the capsid in heated suspensions at 50-52 degrees C was shown to proceed with "zero" enthalpy without significant endo- and exo-thermal effects. No change of specific heat capacity of the suspension was also observed. It is emphasized that the mechanism of DNA going out of the capsid can be understood by studying DNA hydration inside the phage and its change in the course of liberation of the phage genome from the protein capsid.MiRNAs are short, non-coding RNAs that regulate gene expression post-transcriptionally through specific binding to mRNA. Deregulation of miRNAs is associated with various diseases and interference with miRNA function has proven therapeutic potential. Most mRNAs are thought to be regulated by multiple miRNAs and there is some evidence that such joint activity is enhanced if a short distance between sites allows for cooperative binding. Until now, however, the concept of cooperativity among miRNAs has not been addressed in a transcriptome-wide approach. Here, we computationally screened human mRNAs for distances between miRNA binding sites that are expected to promote cooperativity. We find that sites with a maximal spacing of 26 nucleotides are enriched for naturally occurring miRNAs compared with control sequences. Furthermore, miRNAs with similar characteristics as indicated by either co-expression within a specific tissue or co-regulation in a disease context are predicted to target a higher number of mRNAs cooperatively than unrelated miRNAs. These bioinformatic data were compared with genome-wide sets of biochemically validated miRNA targets derived by Argonaute crosslinking and immunoprecipitation (HITS-CLIP and PAR-CLIP). To ease further research into combined and cooperative miRNA function, we developed miRco, a database connecting miRNAs and respective targets involved in distance-defined cooperative regulation (mips.helmholtz-muenchen.de/mirco). In conclusion, our findings suggest that cooperativity of miRNA-target interaction is a widespread phenomenon that may play an important role in miRNA-mediated gene regulation.

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