The extent of RNA degradation in the nucleus has traditionally been underestimated. However, all major RNA species are synthesized, processed and can be degraded in this compartment and consequently an enormous amount of nucleosides are turned over and recycled. The RNA exosome, a multisubunit complex of 3’-5’ exoribonucleases, is a key player in these processive/degradative pathways. The exosome is highly conserved between yeast and man, and exists in a cytoplasmic and a nuclear form; the 3’-5’ exoribonuclease Rrp6 (human homologue PM/Scl100) is a specific component of the nuclear exosome.Studies in yeast using exosome-mutant strains has revealed specific functions of the nuclear exosome: (i) processing or degradation of small nuclear/nucleolar RNAs (snRNAs, snoRNAs), (ii) surveillance and degradation of malformed mRNAs and (iii) processing or degradation of ribosomal precursor RNA to mature rRNAs. There is also evidence that Rrp6 is involved in the degradation of small RNA transcripts synthesised by RNA polymerase II from intergenic regions in the genome. These transcripts belong to a hitherto uncharacterised eukaryotic RNA class, that recently has been shown to be highly abundant in transcriptome mapping studies and might provide regulatory functions.The aim of our work is to identify functional pathways and new targets of the nuclear exosome in human cells. Therefore, we analyse the consequences of depletion of two exosomal components (Rrp6 and the core component Rrp46) by specific RNAi-mediated knock down. We have initiated a transcriptome analysis to investigate the global influence of the nuclear exosome on the abundance of various RNAs (e.g. normal mRNAs, intergenic transcripts, miRNAs, endogenous retroviral RNAs and small non-coding RNAs). We use an ENCODE (ENCyclopedia of DNA Elements) tiling array that covers discrete regions from different chromosomes to represent a range of gene content and exonic/nonexonic conservation grades of the human genome.