Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function

Abstract

The genome is pervasively transcribed across various species, yielding numerous non-coding RNAs. As a counterbalance for pervasive transcription, various organisms have a nuclear RNA exosome complex, whose structure is well conserved between yeast and mammalian cells. The RNA exosome not only regulates the processing of stable RNA species, such as rRNAs, tRNAs, small nucleolar RNAs, and small nuclear RNAs, but also plays a central role in RNA surveillance by degrading many unstable RNAs and misprocessed pre-mRNAs. In addition, associated cofactors of RNA exosome direct the exosome to distinct classes of RNA substrates, suggesting divergent and/or multi-layer control of RNA quality in the cell. While the RNA exosome is essential for cell viability and influences various cellular processes, mutations and alterations in the RNA exosome components are linked to the collection of rare diseases and various diseases including cancer, respectively. The present review summarizes the relationships between pervasive transcription and RNA exosome, including evolutionary crosstalk, mechanisms of RNA exosome-mediated RNA surveillance, and physiopathological effects of perturbation of RNA exosome.

ZCCHC3 is a stress granule zinc knuckle protein that strongly suppresses LINE-1 retrotransposition

“…Partial overlap of EXOSC3 with both exogenous and endogenous ZCCHC3 proteins was observed (mainly in fractions 7 to 9) although the majority of EXOSC3 protein remained concentrated in LMW fractions ( Fig 8F and 8G ). EXOSC3 is reportedly less stably associated with the core exosome, and so perhaps dissociates easily in a gradient [ 87 ].…”

Genome-Wide Characterization of the RNA Exosome Complex in Relation to Growth, Development, and Pathogenicity of Fusarium graminearum

“…The RNA exosome complex not only regulates the processing of rRNAs, tRNAs, snRNAs, and snoRNAs but also degrades mRNA and misprocessed RNA, playing an important role in RNA surveillance ( 63 ). The RNA exosome has been shown to be the primary regulatory element after transcription, which controls cell differentiation by regulating the transcriptome and proteome ( 64 ).…”

Viral RNA capping: Mechanisms and antiviral therapy

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