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Regulation of ncRNA Transcription by Chromatin

Transcription and ncRNA

The development of genomics approaches has led to the discovery of many new classes of noncoding RNA. In budding yeast, a class of short noncoding transcripts termed cryptic unstable transcripts (CUTs) has been shown to emanate bi-directionally from nucleosome depleted regions at the 5’ ends of genes. Importantly, CUTs are degraded by the exosome, which is why much of this transcription has previously been overlooked. The pathway that triggers degradation generally involves 3’ polyadenylation by noncanonical poly(A) polymerases. Polyadenylation stimulates RNA degradation by the nuclear exonuclease Rrp6. Transcription of some cryptic transcripts is subject to control by chromatin structure. Using genome-wide chromatin and RNA mapping approaches, we have previously shown that the chromatin remodeling complex Isw2 can repress transcription of a number of cryptic RNA molecules (Whitehouse et al., 2007).

A significant obstacle to our understanding of CUTs is their complexity — they are short (100-400nt), they often overlap open reading frames, and they contain multiple start and termination sites. To accurately define CUTs and mRNA transcripts, we are using deep sequencing approaches to map cryptic transcripts at single-nucleotide resolution.

In this project we address three important, unresolved questions:

  1. How does the cell distinguish mRNA from CUTs?

  2. How is the synthesis of CUTs regulated?

  3. Does cryptic RNA have a function?