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Non-coding RNAs include highly abundant and functionally important RNAs that fulfill various functions in the regulation of cellular processes in both pro- and eukaryotes. They play a central role in regulating gene expression and are subdivided into different classes by function and size. Depending on the aim of the project differently sized libraries can be prepared to e.g. specifically study small non-coding RNAs like miRNAs (micro RNAs), siRNAs (short interfering RNAs) or piRNAs (piwi-interacting RNAs) or other classes of untranslated transcripts.
Chromatin immunoprecipitation (ChIP) is an in vivo method of identifying the bonding sites of proteins to a DNA sequence. The knowledge about such DNA-protein interactions is important for the understanding of many biological processes and various diseases. Whereas the established method of ChIP analysis using microarrays relies on prior knowledge of precise DNA binding sites , the sequencing with Next Generation technologies allows the identification of all genomic regions associated with a specific DNA-protein interaction across entire genomes.