Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Fifty years of genetic and molecular experiments have revealed a wealth of molecular interactions involved in the control of cell division. In light of the complexity of this control system, mathematical modeling has proved useful in analyzing biochemical hypotheses that can be tested experimentally. Stochastic modeling has been especially useful in understanding the intrinsic variability of cell cycle events, but stochastic modeling has been hampered by a lack of reliable data on the absolute numbers of mRNA molecules per cell for cell cycle control genes. To fill this void, we used fluorescence in situ hybridization (FISH) to collect single molecule mRNA data for 16 cell cycle regulators in budding yeast, Saccharomyces cerevisiae. From statistical distributions of single-cell mRNA counts, we are able to extract the periodicity, timing, and magnitude of transcript abundance during the cell cycle. We used these parameters to improve a stochastic model of the cell cycle to better reflect the variability of molecular and phenotypic data on cell cycle progression in budding yeast.

An interplay between transcription, processing, and degradation determines tRNA levels in yeast

tRNA biogenesis in yeast involves the synthesis of the initial transcript by RNA polymerase III followed by processing and controlled degradation in both the nucleus and the cytoplasm. A vast landscape of regulatory elements controlling tRNA stability in yeast has emerged from recent studies. Diverse pathways of tRNA maturation generate multiple stable and unstable intermediates. A significant impact on tRNA stability is exerted by a variety of nucleotide modifications. Pre-tRNAs are targets of exosome-dependent surveillance in the nucleus. Some tRNAs that are hypomodified or bear specific destabilizing mutations are directed to the rapid tRNA decay pathway leading to 5'→3' exonucleolytic degradation by Rat1 and Xrn1. tRNA molecules are selectively marked for degradation by a double CCA at their 3' ends. In addition, under different stress conditions, tRNA half-molecules can be generated by independent endonucleolytic cleavage events. Recent studies reveal unexpected relationships between the subsequent steps of tRNA biosynthesis and the mechanisms controlling its quality and turnover.

Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA

Gene expression studies commonly examine total cellular RNA, which only provides information about its steady-state pool of RNA. It remains unclear whether differences in the steady-state reflects variable rates of transcription or RNA degradation. To specifically monitor RNA synthesis and degradation genome-wide, we developed Bru-Seq and BruChase-Seq. These assays are based on metabolic pulse-chase labeling of RNA using bromouridine (Bru). In Bru-Seq, recently labeled RNAs are sequenced to reveal spans of nascent transcription in the genome. In BruChase-Seq, cells are chased in uridine for different periods of time following Bru-labeling, allowing for the isolation of RNA populations of specific ages. Here we describe these methodologies in detail and highlight their usefulness in assessing RNA synthesis and stability as well as splicing kinetics with examples of specific genes from different human cell lines.

The roles of 3'-exoribonucleases and the exosome in trypanosome mRNA degradation

The degradation of eukaryotic mRNAs can be initiated by deadenylation, decapping, or endonuclease cleavage. This is followed by 5'-3' degradation by homologs of Xrn1, and/or 3'-5' degradation by the exosome. We previously reported that, in African trypanosome Trypanosoma brucei, most mRNAs are deadenylated prior to degradation, and that depletion of the major 5'-3' exoribonuclease XRNA preferentially stabilizes unstable mRNAs. We now show that depletion of either CAF1 or CNOT10, two components of the principal deadenylation complex, strongly inhibits degradation of most mRNAs. RNAi targeting another deadenylase, PAN2, or RRP45, a core component of the exosome, preferentially stabilized mRNAs with intermediate half-lives. RRP45 depletion resulted in a 5' bias of mRNA sequences, suggesting action by a distributive 3'-5' exoribonuclease. Results suggested that the exosome is involved in the processing of trypanosome snoRNAs. There was no correlation between effects on half-lives and on mRNA abundance.

The 5'-3' exoribonuclease Pacman (Xrn1) regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in Drosophila wing imaginal discs

Pacman/Xrn1 is a highly conserved exoribonuclease known to play a critical role in gene regulatory events such as control of mRNA stability, RNA interference and regulation via miRNAs. Although Pacman has been well studied in Drosophila tissue culture cells, the biologically relevant cellular pathways controlled by Pacman in natural tissues are unknown. This study shows that a hypomorphic mutation in pacman (pcm⁵) results in smaller wing imaginal discs. These tissues, found in the larva, are known to grow and differentiate to form wing and thorax structures in the adult fly. Using microarray analysis, followed by quantitative RT-PCR, we show that eight mRNAs were increased in level by > 2-fold in the pcm⁵ mutant wing discs compared with the control. The levels of pre-mRNAs were tested for five of these mRNAs; four did not increase in the pcm⁵ mutant, showing that they are regulated at the post-transcriptional level and, therefore, could be directly affected by Pacman. These transcripts include one that encodes the heat shock protein Hsp67Bc, which is upregulated 11.9-fold at the post-transcriptional level and 2.3-fold at the protein level. One miRNA, miR-277-3p, is 5.6-fold downregulated at the post-transcriptional level in mutant discs, suggesting that Pacman affects its processing in this tissue. Together, these data show that a relatively small number of mRNAs and miRNAs substantially change in abundance in pacman mutant wing imaginal discs. Since Hsp67Bc is known to regulate autophagy and protein synthesis, it is possible that Pacman may control the growth of wing imaginal discs by regulating these processes.

Quantification of mRNA stability of stress-responsive yeast genes following conditional excision of open reading frames

Eukaryotic cells rapidly adjust the levels of mRNAs in response to environmental stress primarily by controlling transcription and mRNA turnover. How different stress conditions influence the fate of stress-responsive mRNAs, however, is relatively poorly understood. This is largely due to the fact that mRNA half-life assays are traditionally based on interventions (e.g., temperature-shifts using temperature-sensitive RNA polymerase II alleles or treatment with general transcription inhibitory drugs), which, rather than blocking, specifically induce transcription of stress-responsive genes. To study the half-lives of the latter suite of mRNAs, we developed and describe here a minimally perturbing alternative method, coined CEO, which is based on discontinuance of transcription following the conditional excision of open reading frames. Using CEO, we confirm that the target of rapamycin complex I (TORC1), a nutrient-activated, central stimulator of eukaryotic cell growth, favors the decay of mRNAs that depend on the stress- and/or nutrient-regulated transcription factors Msn2/4 and Gis1 for their transcription. We further demonstrate that TORC1 controls the stability of these mRNAs via the Rim15-Igo1/2-PP2A^Cdc55 effector branch, which reportedly also controls Gis1 promoter recruitment. These data pinpoint PP2A^Cdc55 as a central node in homo-directional coordination of transcription and post-transcriptional mRNA stabilization of a specific array of nutrient-regulated genes.

The impact of transcription on posttranscriptional processes in yeast

In eukaryotes, three RNA polymerases are responsible for transcription. These complex enzymes show many similarities with one another, such as several common or highly homologue subunits, while some other features, such as transcript length, diversity, processing, and transcription regulation, are unique to each polymerase. The present article reviews recent publications focusing on the impact of transcription of various RNA species in yeast on posttranscriptional steps such as pre-RNA processing, transport and decay. Two major conclusions emerge from a critical analysis of the current knowledge. (1) The kinetics of transcription elongation affects cotranscriptional pre-RNA processing. (2) The efficiency of transcription, by saturating the proteins interacting with RNA, indirectly affects the processing, export and decay of transcripts.

How cells get the message: dynamic assembly and function of mRNA-protein complexes

mRNA is packaged into ribonucleoprotein particles called mRNPs. A multitude of RNA-binding proteins as well as a host of associated proteins participate in the fate of mRNA from transcription and processing in the nucleus to translation and decay in the cytoplasm. Methodological innovations in cell biology and genome-wide high-throughput approaches have revealed an unexpected diversity of mRNA-associated proteins and unforeseen interconnections between mRNA-processing steps. Recent insights into mRNP formation in vivo have also highlighted the importance of mRNP packaging, which can sort RNAs on the basis of their length and determine mRNA fate through alternative mRNP assembly, processing and export pathways.

Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression

mRNA concentration depends on the balance between transcription and degradation rates. On both sides of the equilibrium, synthesis and degradation show, however, interesting differences that have conditioned the evolution of gene regulatory mechanisms. Here, we discuss recent genome-wide methods for determining mRNA half-lives in eukaryotes. We also review pre- and posttranscriptional regulons that coordinate the fate of functionally related mRNAs by using protein- or RNA-based trans factors. Some of these factors can regulate both transcription and decay rates, thereby maintaining proper mRNA homeostasis during eukaryotic cell life.

Temporal and spatial characterization of nonsense-mediated mRNA decay

Nonsense-mediated mRNA decay (NMD) is a quality control mechanism responsible for "surveying" mRNAs during translation and degrading those that harbor a premature termination codon (PTC). Currently the intracellular spatial location of NMD and the kinetics of its decay step in mammalian cells are under debate. To address these issues, we used single-RNA fluorescent in situ hybridization (FISH) and measured the NMD of PTC-containing β-globin mRNA in intact single cells after the induction of β-globin gene transcription. This approach preserves temporal and spatial information of the NMD process, both of which would be lost in an ensemble study. We determined that decay of the majority of PTC-containing β-globin mRNA occurs soon after its export into the cytoplasm, with a half-life of <1 min; the remainder is degraded with a half-life of >12 h, similar to the half-life of normal PTC-free β-globin mRNA, indicating that it had evaded NMD. Importantly, NMD does not occur within the nucleoplasm, thus countering the long-debated idea of nuclear degradation of PTC-containing transcripts. We provide a spatial and temporal model for the biphasic decay of NMD targets.

The fate of the messenger is pre-determined: a new model for regulation of gene expression

Recent years have seen a rise in publications demonstrating coupling between transcription and mRNA decay. This coupling most often accompanies cellular processes that involve transitions in gene expression patterns, for example during mitotic division and cellular differentiation and in response to cellular stress. Transcription can affect the mRNA fate by multiple mechanisms. The most novel finding is the process of co-transcriptional imprinting of mRNAs with proteins, which in turn regulate cytoplasmic mRNA stability. Transcription therefore is not only a catalyst of mRNA synthesis but also provides a platform that enables imprinting, which coordinates between transcription and mRNA decay. Here we present an overview of the literature, which provides the evidence of coupling between transcription and decay, review the mechanisms and regulators by which the two processes are coupled, discuss why such coupling is beneficial and present a new model for regulation of gene expression. This article is part of a Special Issue entitled: RNA Decay mechanisms.

The Not3/5 subunit of the Ccr4-Not complex: a central regulator of gene expression that integrates signals between the cytoplasm and the nucleus in eukaryotic cells

The Ccr4-Not complex is a conserved multi-subunit complex in eukaryotes that carries 2 enzymatic activities: ubiquitination mediated by the Not4 RING E3 ligase and deadenylation mediated by the Ccr4 and Caf1 orthologs. This complex has been implicated in all aspects of the mRNA life cycle, from synthesis of mRNAs in the nucleus to their degradation in the cytoplasm. More recently the complex has also been implicated in many aspects of the life cycle of proteins, from quality control during synthesis of peptides, to assembly of protein complexes and protein degradation. Consistently, the Ccr4-Not complex is found both in the nucleus, where it is connected to transcribing ORFs, and in the cytoplasm, where it was revealed to be both associated with translating ribosomes and in RNA processing bodies. This functional and physical presence of the Ccr4-Not complex at all stages of gene expression raises the question of its fundamental role. This review will summarize recent evidence designing the Not3/5 module of the Ccr4-Not complex as a functional module involved in coordination of the regulation of gene expression between the nucleus and the cytoplasm.

Mediator phosphorylation prevents stress response transcription during non-stress conditions

The multiprotein complex Mediator is a coactivator of RNA polymerase (Pol) II transcription that is required for the regulated expression of protein-coding genes. Mediator serves as an end point of signaling pathways and regulates Pol II transcription, but the mechanisms it uses are not well understood. Here, we used mass spectrometry and dynamic transcriptome analysis to investigate a functional role of Mediator phosphorylation in gene expression. Affinity purification and mass spectrometry revealed that Mediator from the yeast Saccharomyces cerevisiae is phosphorylated at multiple sites of 17 of its 25 subunits. Mediator phosphorylation levels change upon an external stimulus set by exposure of cells to high salt concentrations. Phosphorylated sites in the Mediator tail subunit Med15 are required for suppression of stress-induced changes in gene expression under non-stress conditions. Thus dynamic and differential Mediator phosphorylation contributes to gene regulation in eukaryotic cells.

Widespread promoter-mediated coordination of transcription and mRNA degradation

Background

Previous work showed that mRNA degradation is coordinated with transcription in yeast, and in several genes the control of mRNA degradation was linked to promoter elements through two different mechanisms. Here we show at the genomic scale that the coordination of transcription and mRNA degradation is promoter-dependent in yeast and is also observed in humans.

Results

We first demonstrate that swapping upstream cis-regulatory sequences between two yeast species affects both transcription and mRNA degradation and suggest that while some cis-regulatory elements control either transcription or degradation, multiple other elements enhance both processes. Second, we show that adjacent yeast genes that share a promoter (through divergent orientation) have increased similarity in their patterns of mRNA degradation, providing independent evidence for the promoter-mediated coupling of transcription to mRNA degradation. Finally, analysis of the differences in mRNA degradation rates between mammalian cell types or mammalian species suggests a similar coordination between transcription and mRNA degradation in humans.

Conclusions

Our results extend previous studies and suggest a pervasive promoter-mediated coordination between transcription and mRNA degradation in yeast. The diverse genes and regulatory elements associated with this coordination suggest that it is generated by a global mechanism of gene regulation and modulated by gene-specific mechanisms. The observation of a similar coupling in mammals raises the possibility that coupling of transcription and mRNA degradation may reflect an evolutionarily conserved phenomenon in gene regulation.

C2ORF29/CNOT11 and CNOT10 form a new module of the CCR4-NOT complex

The CCR4-NOT complex was originally identified and its composition and organization characterized in the yeast Saccharomyces cerevisiae. It was first suggested to participate in transcription regulation, but since then it has become clear that it plays a key role in mRNA decay in all eukaryotes, thereby contributing importantly to gene expression regulation. Hence, the mammalian CCR4-NOT complex was recently shown to participate in miRNA-mediated mRNA repression. A better characterization of the composition and organization of this complex in higher eukaryotes is thus warranted. Purifications of the CCR4-NOT complex, performed by others and us, suggest that the protein of unknown function C2ORF29 is associated with this assembly. We demonstrate here that C2ORF29 is indeed a bona fide subunit of the human CCR4-NOT complex and propose to rename it CNOT11. In addition, we show that CNOT11 interacts with the first amino acids of CNOT1 and with CNOT10 and is required for the association of CNOT10 with the CCR4-NOT complex. Thus, the human CCR4-NOT complex possesses in addition to the CCR4-CAF1 deadenylase module and to the NOT module, a module composed of CNOT10 and CNOT11 that interacts with the N-terminal part of CNOT1. Phylogenetic analyses indicate that the CNOT10/CNOT11 module is conserved in all eukaryotes except fungi.

Kinetic analysis of pre-ribosome structure in vivo

Pre-ribosomal particles undergo numerous structural changes during maturation, but their high complexity and short lifetimes make these changes very difficult to follow in vivo. In consequence, pre-ribosome structure and composition have largely been inferred from purified particles and analyzed in vitro. Here we describe techniques for kinetic analyses of the changes in pre-ribosome structure in living cells of Saccharomyces cerevisiae. To allow this, in vivo structure probing by DMS modification was combined with affinity purification of newly synthesized 20S pre-rRNA over a time course of metabolic labeling with 4-thiouracil. To demonstrate that this approach is generally applicable, we initially analyzed the accessibility of the region surrounding cleavage site D site at the 3' end of the mature 18S rRNA region of the pre-rRNA. This revealed a remarkably flexible structure throughout 40S subunit biogenesis, with little stable RNA-protein interaction apparent. Analysis of folding in the region of the 18S central pseudoknot was consistent with previous data showing U3 snoRNA-18S rRNA interactions. Dynamic changes in the structure of the hinge between helix 28 (H28) and H44 of pre-18S rRNA were consistent with recently reported interactions with the 3' guide region of U3 snoRNA. Finally, analysis of the H18 region indicates that the RNA structure matures early, but additional protection appears subsequently, presumably reflecting protein binding. The structural analyses described here were performed on total, affinity-purified, newly synthesized RNA, so many classes of RNA and RNA-protein complex are potentially amenable to this approach.

Maf1, a general negative regulator of RNA polymerase III in yeast

tRNA synthesis by yeast RNA polymerase III (Pol III) is down-regulated under growth-limiting conditions. This control is mediated by Maf1, a global negative regulator of Pol III transcription. Conserved from yeast to man, Maf1 was originally discovered in Saccharomyces cerevisiae by a genetic approach. Details regarding the molecular basis of Pol III repression by Maf1 are now emerging from the recently reported structural and biochemical data on Pol III and Maf1. The phosphorylation status of Maf1 determines its nuclear localization and interaction with the Pol III complex and several Maf1 kinases have been identified to be involved in Pol III control. Moreover, Maf1 indirectly affects tRNA maturation and decay. Here I discuss the current understanding of the mechanisms that oversee the Maf1-mediated regulation of Pol III activity and the role of Maf1 in the control of tRNA biosynthesis in yeast. This article is part of a Special Issue entitled: Transcription by Odd Pols.

Architecture of the nuclease module of the yeast Ccr4-not complex: the Not1-Caf1-Ccr4 interaction

Shortening eukaryotic poly(A) tails represses mRNA translation and induces mRNA turnover. The major cytoplasmic deadenylase, the Ccr4-Not complex, is a conserved multisubunit assembly. Ccr4-Not is organized around Not1, a large scaffold protein that recruits two 3'-5' exoribonucleases, Caf1 and Ccr4. We report structural studies showing that the N-terminal arm of yeast Not1 has a HEAT-repeat structure with domains related to the MIF4G fold. A MIF4G domain positioned centrally within the Not1 protein recognizes Caf1, which in turn binds the LRR domain of Ccr4 and tethers the Ccr4 nuclease domain. The interactions that form the nuclease core of the Ccr4-Not complex are evolutionarily conserved. Their specific disruption affects cell growth and mRNA deadenylation and decay in vivo in yeast. Thus, the N-terminal arm of Not1 forms an extended platform reminiscent of scaffolding proteins like eIF4G and CBP80, and places the two nucleases in a pivotal position within the Ccr4-Not complex.

The eukaryotic transcriptional machinery regulates mRNA translation and decay in the cytoplasm

In eukaryotes, nuclear mRNA synthesis is physically separated from its cytoplasmic translation and degradation. Recent unexpected findings have revealed that, despite this separation, the transcriptional machinery can remotely control the cytoplasmic stages. Key to this coupling is the capacity of the transcriptional machinery to "imprint" the transcript with factors that escort it to the cytoplasm and regulate its localization, translation and decay. Some of these factors are known transcriptional regulators that also function in mRNA decay and are hence named "synthegradases". Imprinting can be carried out and/or regulated by RNA polymerase II or by promoter cis- and trans-acting elements. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.

Coordinating genome expression with cell size

Cell size is highly variable; cells from various tissues differ in volume over orders of magnitudes, from tiny lymphocytes to giant neurons, and cells of a given type change size during the cell cycle. Larger cells need to produce and maintain higher amounts of RNA and protein to sustain biomass and function, although the genome content often remains constant. Available data indicate that the transcriptional and translational outputs scale with cell size at a genome-wide level, but how such remarkably coordinated regulation is achieved remains largely mysterious. With global and systems-level approaches becoming more widespread and quantitative, it is worth revisiting this fascinating problem. Here, we outline current knowledge of the fundamental relations between genome regulation and cell size, and highlight the biological implications and potential mechanisms of the global tuning of gene expression to cellular volume.

MC EMiNEM maps the interaction landscape of the Mediator

The Mediator is a highly conserved, large multiprotein complex that is involved essentially in the regulation of eukaryotic mRNA transcription. It acts as a general transcription factor by integrating regulatory signals from gene-specific activators or repressors to the RNA Polymerase II. The internal network of interactions between Mediator subunits that conveys these signals is largely unknown. Here, we introduce MC EMiNEM, a novel method for the retrieval of functional dependencies between proteins that have pleiotropic effects on mRNA transcription. MC EMiNEM is based on Nested Effects Models (NEMs), a class of probabilistic graphical models that extends the idea of hierarchical clustering. It combines mode-hopping Monte Carlo (MC) sampling with an Expectation-Maximization (EM) algorithm for NEMs to increase sensitivity compared to existing methods. A meta-analysis of four Mediator perturbation studies in Saccharomyces cerevisiae, three of which are unpublished, provides new insight into the Mediator signaling network. In addition to the known modular organization of the Mediator subunits, MC EMiNEM reveals a hierarchical ordering of its internal information flow, which is putatively transmitted through structural changes within the complex. We identify the N-terminus of Med7 as a peripheral entity, entailing only local structural changes upon perturbation, while the C-terminus of Med7 and Med19 appear to play a central role. MC EMiNEM associates Mediator subunits to most directly affected genes, which, in conjunction with gene set enrichment analysis, allows us to construct an interaction map of Mediator subunits and transcription factors.