Abstract
Recent studies on yeast transcriptome have revealed the presence of a large set of RNA polymerase II transcripts mapping to intergenic and antisense regions or overlapping canonical genes. Most of these ncRNAs (ncRNAs) are subject to termination by the Nrd1-dependent pathway and rapid degradation by the nuclear exosome and have been dubbed cryptic unstable transcripts (CUTs). CUTs are often considered as by-products of transcriptional noise, but in an increasing number of cases they play a central role in the control of gene expression. Regulatory mechanisms involving expression of a CUT are diverse and include attenuation, transcriptional interference, and alternative transcription start site choice. This review focuses on the impact of cryptic transcription on gene expression, describes the role of the Nrd1-complex as the main actor in preventing nonfunctional and potentially harmful transcription, and details a few systems where expression of a CUT has an essential regulatory function. We also summarize the most recent studies concerning other types of ncRNAs and their possible role in regulation.
Highlights
The development of new technologies in the field of transcriptome analysis has revealed an unexpected level of complexity in the eukaryotic transcription landscape
This review focuses on the impact of cryptic transcription on gene expression, describes the role of the Nrd1-complex as the main actor in preventing nonfunctional and potentially harmful transcription, and details a few systems where expression of a cryptic unstable transcripts (CUTs) has an essential regulatory function
Because CUTs are by far the best-characterized class of ncRNAs in terms of origin, metabolism, and implication in regulation of gene expression, in this review we focus on the Nrd1-dependent termination pathway and its key role in limiting pervasive transcription and we describe the mechanisms of regulation that involve expression of a CUT
Summary
The development of new technologies in the field of transcriptome analysis has revealed an unexpected level of complexity in the eukaryotic transcription landscape. Recent deep sequencing of nascent transcripts [3] has allowed a more direct analysis of RNA polymerase distribution in wild-type yeast cells obviating the need for working in mutants of the degradation pathway These experiments have nicely confirmed the existence of hidden transcription. CUTs can be by-products of divergent transcription, and functional units with an important role in the control of gene expression Another abundant class of non-coding RNAs has been named SUTs for Stable Unannotated Transcripts [8]. Their origin is the same as for the CUTs (5 and 3 end NFRs), but it has been proposed that they differ in their transcription termination mode since they are stable, and detectable in wild-type conditions, and often longer than CUTs [1]. The impact of cryptic transcription on global gene expression as well as the possible biological significance of this special way of regulation will be discussed
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