Gene loops juxtapose promoters and terminators in yeast

O’Sullivan, Justin M.; Tan-Wong, Sue Mei; Morillon, Antonin; Lee, Barbara; Coles, Joel; Mellor, Jane; Proudfoot, Nick J.

doi:10.1038/ng1411

Cited by 325 publications

(297 citation statements)

References 27 publications

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“…Subsequent transfer of CPSF to the CTD may promote 39-end processing (Dantonel et al 1997). Communication between the promoter and terminator through gene loop formation (O'Sullivan et al 2004;Perkins et al 2008) may also afford efficient transfer of cleavage/poly(A) factors from the 39 end of the gene back to new Pol II initiation complexes (Glover-Cutter et al 2008;Mapendano et al 2010). Also, very recently, specific transcription activators have been shown to enhance 39-end processing through recruitment of a specific elongation factor complex (PAF1c) that, in turn, enhances PAS recognition (Nagaike et al 2011).…”

Section: Alternative Pas (Apa) Define Different Mrna 39 Utrsmentioning

confidence: 99%

Ending the message: poly(A) signals then and now

Proudfoot¹

2011

Genes Dev.

523

486

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Polyadenylation [poly(A)] signals (PAS) are a defining feature of eukaryotic protein-coding genes. The central sequence motif AAUAAA was identified in the mid1970s and subsequently shown to require flanking, auxiliary elements for both 39-end cleavage and polyadenylation of premessenger RNA (pre-mRNA) as well as to promote downstream transcriptional termination. More recent genomic analysis has established the generality of the PAS for eukaryotic mRNA. Evidence for the mechanism of mRNA 39-end formation is outlined, as is the way this RNA processing reaction communicates with RNA polymerase II to terminate transcription. The widespread phenomenon of alternative poly(A) site usage and how this interrelates with pre-mRNA splicing is then reviewed. This shows that gene expression can be drastically affected by how the message is ended. A central theme of this review is that while genomic analysis provides generality for the importance of PAS selection, detailed mechanistic understanding still requires the direct analysis of specific genes by genetic and biochemical approaches.

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Section: Alternative Pas (Apa) Define Different Mrna 39 Utrsmentioning

confidence: 99%

Ending the message: poly(A) signals then and now

Proudfoot¹

2011

Genes Dev.

523

486

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“…One scenario is that this facilitates recruitment of polyadenylation factors to active genes, and that these factors travel with the EC during transcription (e.g., Dantonel et al 1997). Alternatively, studies in yeast suggest that gene looping brings promoter and terminator regions together during early stages of transcription, facilitating RNAPII reinitiation (O'Sullivan et al 2004;Ansari and Hampsey 2005;Singh and Hampsey 2007). Moreover, these studies showed that gene looping is dependent on components of the cleavage/polyadenylation machinery and the general transcription factor TFIIB.…”

Section: Trans-acting Factor Dynamics At the Poly(a) Site Affect Tranmentioning

confidence: 99%

Transcription termination by nuclear RNA polymerases

Richard

Manley²

2009

Genes Dev.

291

326

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Gene transcription in the cell nucleus is a complex and highly regulated process. Transcription in eukaryotes requires three distinct RNA polymerases, each of which employs its own mechanisms for initiation, elongation, and termination. Termination mechanisms vary considerably, ranging from relatively simple to exceptionally complex. In this review, we describe the present state of knowledge on how each of the three RNA polymerases terminates and how mechanisms are conserved, or vary, from yeast to human.

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“…Similarly, in yeast the promoters and terminators of genes are in close proximity to one another (3,48) and tethered to the nuclear pore (10,52). The consequence of this spatial organization is that the DNA between these regulatory elements is looped out.…”

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confidence: 99%

Long-Range Communication between the Silencers of HMR

Valenzuela

Dhillon

Dubey

et al. 2008

Molecular and Cellular Biology

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Gene regulation involves long-range communication between silencers, enhancers, and promoters. In Saccharomyces cerevisiae, silencers flank transcriptionally repressed genes to mediate regional silencing. Silencers recruit the Sir proteins, which then spread along chromatin to encompass the entire silenced domain. In this report we have employed a boundary trap assay, an enhancer activity assay, chromatin immunoprecipitations, and chromosome conformation capture analyses to demonstrate that the two HMR silencer elements are in close proximity and functionally communicate with one another in vivo. We further show that silencing is necessary for these long-range interactions, and we present models for Sir-mediated silencing based upon these results.Gene activation and gene repression are central to the proper development and differentiation of organisms. DNA elements such as promoters, enhancers, and silencers play a central role in eukaryotic gene regulation. These elements are separated from each other by several kilobase pairs of DNA but are able to communicate with one another to regulate the activation or repression of genes. The exact mechanism by which distally located elements communicate with one another is not clear and is one of the key questions in gene regulation. Long-range communication between distantly located elements in chromosomes is thought to occur by one of two principal mechanisms (8). One class of models postulate that a signal emanating from a distal regulatory element spreads along the DNA fiber until it encounters a proximal regulatory element. A second class of models postulate that distal and proximal regulatory elements interact with one another directly, with the intervening DNA forming a loop. Both mechanisms must function within the context of the global chromosome structure, which appears to be composed of large chromosome loops that attach to a proteinaceous superstructure (11). The nucleus appears to be divided further into distinct chromatin compartments, with heterochromatic domains being present in regions near the nuclear periphery while euchromatic domains are found mainly in the interior of the nucleus, although a significant portion of euchromatin is located near nuclear pores.It has been suggested that the functionally and structurally defined chromatin domains may be coincident (36). Enhancers and locus control regions (LCRs) are long-range regulatory elements that activate promoters in a distance-and orientation-independent manner, and recent studies indicate that enhancers and LCRs often cluster together in three-dimensional space to form an "active chromatin hub" (23,49,58,59).Similarly, in yeast the promoters and terminators of genes are in close proximity to one another (3, 48) and tethered to the nuclear pore (10, 52). The consequence of this spatial organization is that the DNA between these regulatory elements is looped out. It is thought that the formation of these nuclear substructures aids in transcription activation.Silencers are negative regulatory element...

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Gene loops juxtapose promoters and terminators in yeast

Cited by 325 publications

References 27 publications

Ending the message: poly(A) signals then and now

Ending the message: poly(A) signals then and now

Transcription termination by nuclear RNA polymerases

Long-Range Communication between the Silencers of HMR

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