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Yun Chen, Albin Sandelin, Torben Heick Jensen and colleagues describe general rules governing the expression of reverse-oriented promoter upstream transcripts (PROMPTs) based on the orientation and proximity of promoter pairs. They characterize how the distance between promoters affects the expression of PROMPTs and the usage of alternate mRNA transcription start sites.

Nonsense-mediated mRNA decay (NMD) degrades mRNAs with abnormally positioned translation termination codons. It is now becoming apparent that NMD targets mRNAs to enable mammalian cells to adjust their transcriptomes and their proteomes to changing physiological conditions and during diverse cellular processes.

Dubiez and colleagues present a cryo-EM structure of the complex responsible for nuclear export of pre-small nuclear RNAs, comprising CBC–PHAX–CRM1–RanGTP. The structure provides insights into the complex architecture, assembly and target RNA recognition.

Using the FANTOM5 CAGE expression atlas, the authors show that bidirectional capped RNAs are a signature feature of active enhancers and identify over 40,000 enhancer candidates from over 800 human cell and tissue samples across the whole human body.

Pervasive transcription generates numerous unadenylated RNAs, usually degraded by the NEXT/nuclear exosome pathway. Here, the authors show that, upon NEXT inactivation, these RNAs are removed by compensatory RNA decay pathways relying on RNA 3′end A- or U-tailing.

RNA polyadenosine tails are important for the export, translation and stability of mRNAs and play a role in non-coding RNA biogenesis. Here the authors measure yeast poly(A) tail lengths by direct RNA sequencing, revealing its dynamics in yeast exonuclease, deadenylase and poly(A) polymerase mutants.

In eukaryotes, newly manufactured mRNA is subject to strict quality control. If certain standards are not met, offending messages are retained in the nucleus and degraded by the exosome complex. New data suggest that exosome-mediated processes are intimately coupled to the transcription machinery, which makes the mRNA in the first place.

The human RNA exosome contains a nuclear co-factor MTR4, which unwinds structural RNAs and recruits adaptors for different RNA processing and decay pathways. Here the authors uncover new variations of the arch-interacting motif (AIM) in NVL and ZCCHC8 and characterise their interaction with MTR4.

RBM7 and ZCCHC8 are two core subunits of the Nuclear Exosome Targeting complex, which regulates the degradation of selected non-coding RNAs in human cells. Here, the authors use structural and biochemical methods to show how ZCCHC8 recruits RBM7 in the complex, leaving the RNA binding site accessible and revealing possible implications for splicing.

Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II derived transcripts. Here the authors use temporal-iCLIP which combines transcriptional synchronisation with UV cross-linking of RNA-protein complexes to reveal dynamic RNA-protein interactions during the early phases of transcription and beyond.

Extraction conditions can have a substantial effect on protein complexes isolated from within cells. A platform for rapid, systematic screening of these conditions is described, which should enable the identification of biologically relevant complexes.

Nonsense-mediated decay (NMD) is an mRNA surveillance process that targets transcripts containing a premature stop codon for degradation. Evidence now suggests that mammalian NMD involves an endonucleolytic cleavage that is mediated by human SMG6.

Despite our growing understanding of their complexity, different types of RNA are still classified using technical rather than functional criteria. Andersson et al.show that categorization of RNAs based on stability and direction of transcription is an effective means of functional classification.

Most mammalian promoters are inherently bidirectional, but transcription only elongates productively in one direction. Data presented in this paper demonstrate that at least part of the answer lies in the asymmetric distribution of polyadenylation-site sequences around human gene promoters causing termination of upstream antisense transcription.

Eukaryotic transcriptomes are considerably larger than estimated from simple gene counts. However, much of this 'excess' RNA is immediately cleared from cells. Two recent studies reveal that so-called cryptic unstable transcripts constitutively transcribed from the yeast genome are rapidly eliminated in a process that couples transcription termination to RNA degradation.

The nuclear cap–binding complex (CBC) stimulates RNA maturation, but the mechanistic basis is not well understood. In vitro reconstitution experiments combined with functional analyses have revealed a new CBC complex containing ARS2, a major effector of CBC. ARS2 links the cap to 3'-end maturation for several RNA families, thus favoring the production of short RNAs.

How the nuclear exosome is targeted to nuclear RNA substrates is poorly understood. An affinity-capture MS approach and functional analyses now demonstrate a physical and functional connection between the human exosome and the cap-binding complex (CBC). A CBC-containing complex was found to promote transcription termination of several RNA types, thus suggesting a direct link to exosomal RNA degradation.

The nature of small RNA species derived from gene termini and intron-exon junctions is now further examined. By sequencing transcripts between 12 and 100 nucleotides derived from cells depleted for RNA decay factors as well as those associated with Argonaute proteins, insights into how these RNAs are produced is provided. Moreover, new small RNAs are identified.

RNA is controlled at various stages of transcription and processing to achieve appropriate gene regulation. Whereas much research has focused on the cytoplasmic control of RNA levels, this Review discusses our emerging appreciation of the importance of nuclear RNA regulation, including the molecular machinery involved in nuclear RNA decay, how functional RNAs bypass degradation and roles for nuclear RNA decay in physiology and disease.