Post-transcriptional gene regulation: From genome-wide studies to principles

Halbeisen, Regula E.; Galgano, Alessia; Scherrer, Tanja; Gerber, André P.

doi:10.1007/s00018-007-7447-6

Cited by 163 publications

(164 citation statements)

References 120 publications

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“…These studies also added strong support for the presence of RNA regulons, as most RBPs in eukaryotes appear to coordinate/regulate groups of mRNAs coding for functionally related proteins. Furthermore, this characteristic can be seen in diverse species, suggesting that RNA regulons constitute a universally conserved feature of post-transcriptional gene regulation in eukaryotes (28,66) . For instance, impressive RNA regulons are found among fi ve yeast Puf-family RBPs, for which mRNA targets share striking common functional and cytotopic features (67) .…”

Section: Coordination -Organization Of Functionally Related Messagesmentioning

confidence: 99%

“…Application of RIP or CLIP techniques combined with a systematic analysis of associated/bound RNA molecules via DNA microarrays or sequencing has provided valuable insights into the organization and conservation of post-transcriptional gene regulation (9,28,66) . These studies also added strong support for the presence of RNA regulons, as most RBPs in eukaryotes appear to coordinate/regulate groups of mRNAs coding for functionally related proteins.…”

Section: Coordination -Organization Of Functionally Related Messagesmentioning

confidence: 99%

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RNA regulons and the RNA-protein interaction network

Imig¹,

Kanitz²,

Gerber

2012

BioMolecular Concepts

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The development of genome-wide analysis tools has prompted global investigation of the gene expression program, revealing highly coordinated control mechanisms that ensure proper spatiotemporal activity of a cell ' s macromolecular components. With respect to the regulation of RNA transcripts, the concept of RNA regulons, which -by analogy with DNA regulons in bacteria -refers to the coordinated control of functionally related RNA molecules, has emerged as a unifying theory that describes the logic of regulatory RNA-protein interactions in eukaryotes. Hundreds of RNA-binding proteins and small non-coding RNAs, such as microRNAs, bind to distinct elements in target RNAs, thereby exerting specifi c and concerted control over posttranscriptional events. In this review, we discuss recent reports committed to systematically explore the RNA-protein interaction network and outline some of the principles and recurring features of RNA regulons: the coordination of functionally related mRNAs through RNAbinding proteins or non-coding RNAs, the modular structure of its components, and the dynamic rewiring of RNA-protein interactions upon exposure to internal or external stimuli. We also summarize evidence for robust combinatorial control of mRNAs, which could determine the ultimate fate of each mRNA molecule in a cell. Finally, the compilation and integration of global protein-RNA interaction data has yielded fi rst insights into network structures and provided the hypothesis that RNA regulons may, in part, constitute noise ' buffers ' to handle stochasticity in cellular transcription.

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Section: Coordination -Organization Of Functionally Related Messagesmentioning

confidence: 99%

Section: Coordination -Organization Of Functionally Related Messagesmentioning

confidence: 99%

RNA regulons and the RNA-protein interaction network

Imig¹,

Kanitz²,

Gerber

2012

BioMolecular Concepts

View full text Add to dashboard Cite

show abstract

“…The sets of bound RNAs were often related containing mRNAs coding for functionally or cytotopically related proteins (e.g. [4][5][6]; reviewed in [7][8][9]). These findings lead to a model that proposes important coordinative roles for RBPs in the expression of functionally related groups of messages, referred to as 'RNA regulons' or 'post-transcriptional operons' [7].…”

Section: Introductionmentioning

confidence: 99%

Environmental Regulation of Prions in Yeast

2014

Investigations in Yeast Functional Genomics and Molecular Biology

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Hundreds of RNA-binding proteins (RBPs) control diverse aspects of post-transcriptional gene regulation. To identify novel and unconventional RBPs, we probed high-density protein microarrays with fluorescently labeled RNA and selected 200 proteins that reproducibly interacted with different types of RNA from budding yeast Saccharomyces cerevisiae. Surprisingly, more than half of these proteins represent previously known enzymes, many of them acting in metabolism, providing opportunities to directly connect intermediary metabolism with posttranscriptional gene regulation. We mapped the RNA targets for 13 proteins identified in this screen and found that they were associated with distinct groups of mRNAs, some of them coding for functionally related proteins. We also found that overexpression of the enzyme Map1 negatively affects the expression of experimentally defined mRNA targets. Our results suggest that many proteins may associate with mRNAs and possibly control their fates, providing dense connections between different layers of cellular regulation.

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“…In our current model we simply assume that the rate of protein production is proportional to mRNA concentration and that the rate of protein decay is fixed. This excludes several known biologically important processes including posttranscriptional regulation (Halbeisen et al 2008), diminishing returns in translation due to ribosome saturation, and targeted degradation of protein. This leads to a modified system…”

Section: Two-stage Model Of Mrna and Protein Concentrationmentioning

confidence: 99%

Gene expression dynamics in randomly varying environments

Smiley

Proulx

2009

J. Math. Biol.

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A simple model of gene regulation in response to stochastically changing environmental conditions is developed and analyzed. The model consists of a differential equation driven by a continuous time 2-state Markov process. The density function of the resulting process converges to a beta distribution. We show that the moments converge to their stationary values exponentially in time. Simulations of a two-stage process where protein production depends on mRNA concentrations are also presented demonstrating that protein concentration tracks the environment whenever the rate of protein turnover is larger than the rate of environmental change. Single-celled organisms are therefore expected to have relatively high mRNA and protein turnover rates for genes that respond to environmental fluctuations.

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Post-transcriptional gene regulation: From genome-wide studies to principles

Cited by 163 publications

References 120 publications

RNA regulons and the RNA-protein interaction network

RNA regulons and the RNA-protein interaction network

Environmental Regulation of Prions in Yeast

Gene expression dynamics in randomly varying environments

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