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Han X, Wang Z, Shi L, Zhu J, Shi L, Ren A, Zhao M. Phospholipase D and phosphatidic acid mediate regulation in the biosynthesis of spermidine and ganoderic acids by activating
GlMyb
in
Ganoderma lucidum
under heat stress. Environ Microbiol 2022; 24:5345-5361. [DOI: 10.1111/1462-2920.16211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaofei Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences Nanjing Agricultural University Nanjing Jiangsu China
| | - Zi Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences Nanjing Agricultural University Nanjing Jiangsu China
| | - Lingyan Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences Nanjing Agricultural University Nanjing Jiangsu China
| | - Jing Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences Nanjing Agricultural University Nanjing Jiangsu China
| | - Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences Nanjing Agricultural University Nanjing Jiangsu China
| | - Ang Ren
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences Nanjing Agricultural University Nanjing Jiangsu China
| | - Mingwen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences Nanjing Agricultural University Nanjing Jiangsu China
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Roy K, Gabunilas J, Gillespie A, Ngo D, Chanfreau GF. Common genomic elements promote transcriptional and DNA replication roadblocks. Genome Res 2016; 26:1363-1375. [PMID: 27540088 PMCID: PMC5052057 DOI: 10.1101/gr.204776.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 08/18/2016] [Indexed: 11/25/2022]
Abstract
RNA polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p (NNS) pathway is critical for the production of stable noncoding RNAs and the control of pervasive transcription in Saccharomyces cerevisiae. To uncover determinants of NNS termination, we mapped the 3′-ends of NNS-terminated transcripts genome-wide. We found that nucleosomes and specific DNA-binding proteins, including the general regulatory factors (GRFs) Reb1p, Rap1p, and Abf1p, and Pol III transcription factors enhance the efficiency of NNS termination by physically blocking Pol II progression. The same DNA-bound factors that promote NNS termination were shown previously to define the 3′-ends of Okazaki fragments synthesized by Pol δ during DNA replication. Reduced binding of these factors results in defective NNS termination and Pol II readthrough. Furthermore, inactivating NNS enables Pol II elongation through these roadblocks, demonstrating that effective Pol II termination depends on a synergy between the NNS machinery and obstacles in chromatin. Consistent with this finding, loci exhibiting Pol II readthrough at GRF binding sites are depleted for upstream NNS signals. Overall, these results underscore how RNA termination signals influence the behavior of Pol II at chromatin obstacles, and establish that common genomic elements define boundaries for both DNA and RNA synthesis machineries.
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Affiliation(s)
- Kevin Roy
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095-1570, USA
| | - Jason Gabunilas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA
| | - Abigail Gillespie
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA
| | - Duy Ngo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095-1570, USA
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3
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Qiu Y, Fakas S, Han GS, Barbosa AD, Siniossoglou S, Carman GM. Transcription factor Reb1p regulates DGK1-encoded diacylglycerol kinase and lipid metabolism in Saccharomyces cerevisiae. J Biol Chem 2013; 288:29124-33. [PMID: 23970552 PMCID: PMC3790011 DOI: 10.1074/jbc.m113.507392] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, the DGK1-encoded diacylglycerol kinase catalyzes the CTP-dependent phosphorylation of diacylglycerol to form phosphatidate. This enzyme, in conjunction with PAH1-encoded phosphatidate phosphatase, controls the levels of phosphatidate and diacylglycerol for phospholipid synthesis, membrane growth, and lipid droplet formation. In this work, we showed that a functional level of diacylglycerol kinase is regulated by the Reb1p transcription factor. In the electrophoretic mobility shift assay, purified recombinant Reb1p was shown to specifically bind its consensus recognition sequence (CGGGTAA, -166 to -160) in the DGK1 promoter. Analysis of cells expressing the PDGK1-lacZ reporter gene showed that mutations (GT→TG) in the Reb1p-binding sequence caused an 8.6-fold reduction in β-galactosidase activity. The expression of DGK1(reb1), a DGK1 allele containing the Reb1p-binding site mutation, was greatly lower than that of the wild type allele, as indicated by analyses of DGK1 mRNA, Dgk1p, and diacylglycerol kinase activity. In the presence of cerulenin, an inhibitor of de novo fatty acid synthesis, the dgk1Δ mutant expressing DGK1(reb1) exhibited a significant defect in growth as well as in the synthesis of phospholipids from triacylglycerol mobilization. Unlike DGK1, the DGK1(reb1) expressed in the dgk1Δ pah1Δ mutant did not result in the nuclear/endoplasmic reticulum membrane expansion, which occurs in cells lacking phosphatidate phosphatase activity. Taken together, these results indicate that the Reb1p-mediated regulation of diacylglycerol kinase plays a major role in its in vivo functions in lipid metabolism.
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Affiliation(s)
- Yixuan Qiu
- From the Department of Food Science, Rutgers Center for Lipid Research, and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901 and
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Németh A, Perez-Fernandez J, Merkl P, Hamperl S, Gerber J, Griesenbeck J, Tschochner H. RNA polymerase I termination: Where is the end? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:306-17. [PMID: 23092677 DOI: 10.1016/j.bbagrm.2012.10.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/10/2012] [Accepted: 10/17/2012] [Indexed: 01/01/2023]
Abstract
The synthesis of ribosomal RNA (rRNA) precursor molecules by RNA polymerase I (Pol I) terminates with the dissociation of the protein-DNA-RNA ternary complex. Based on in vitro results the mechanism of Pol I termination appeared initially to be rather conserved and simple until this process was more thoroughly re-investigated in vivo. A picture emerged that Pol I termination seems to be connected to co-transcriptional processing, re-initiation of transcription and, possibly, other processes downstream of Pol I transcription units. In this article, our current understanding of the mechanism of Pol I termination and how this process might be implicated in other biological processes in yeast and mammals is summarized and discussed. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Attila Németh
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, 93053 Regensburg, Germany.
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5
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Gjuvsland AB, Vik JO, Woolliams JA, Omholt SW. Order-preserving principles underlying genotype-phenotype maps ensure high additive proportions of genetic variance. J Evol Biol 2011; 24:2269-79. [PMID: 21831198 DOI: 10.1111/j.1420-9101.2011.02358.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In quantitative genetics, the degree of resemblance between parents and offspring is described in terms of the additive variance (V(A)) relative to genetic (V(G)) and phenotypic (V(P)) variance. For populations with extreme allele frequencies, high V(A)/V(G) can be explained without considering properties of the genotype-phenotype (GP) map. We show that randomly generated GP maps in populations with intermediate allele frequencies generate far lower V(A)/V(G) values than empirically observed. The main reason is that order-breaking behaviour is ubiquitous in random GP maps. Rearrangement of genotypic values to introduce order-preservation for one or more loci causes a dramatic increase in V(A)/V(G). This suggests the existence of order-preserving design principles in the regulatory machinery underlying GP maps. We illustrate this feature by showing how the ubiquitously observed monotonicity of dose-response relationships gives much higher V(A)/V(G) values than a unimodal dose-response relationship in simple gene network models.
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Affiliation(s)
- A B Gjuvsland
- Department of Mathematical Sciences and Technology, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway.
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6
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Tøndel K, Indahl UG, Gjuvsland AB, Vik JO, Hunter P, Omholt SW, Martens H. Hierarchical cluster-based partial least squares regression (HC-PLSR) is an efficient tool for metamodelling of nonlinear dynamic models. BMC SYSTEMS BIOLOGY 2011; 5:90. [PMID: 21627852 PMCID: PMC3127793 DOI: 10.1186/1752-0509-5-90] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 06/01/2011] [Indexed: 11/22/2022]
Abstract
Background Deterministic dynamic models of complex biological systems contain a large number of parameters and state variables, related through nonlinear differential equations with various types of feedback. A metamodel of such a dynamic model is a statistical approximation model that maps variation in parameters and initial conditions (inputs) to variation in features of the trajectories of the state variables (outputs) throughout the entire biologically relevant input space. A sufficiently accurate mapping can be exploited both instrumentally and epistemically. Multivariate regression methodology is a commonly used approach for emulating dynamic models. However, when the input-output relations are highly nonlinear or non-monotone, a standard linear regression approach is prone to give suboptimal results. We therefore hypothesised that a more accurate mapping can be obtained by locally linear or locally polynomial regression. We present here a new method for local regression modelling, Hierarchical Cluster-based PLS regression (HC-PLSR), where fuzzy C-means clustering is used to separate the data set into parts according to the structure of the response surface. We compare the metamodelling performance of HC-PLSR with polynomial partial least squares regression (PLSR) and ordinary least squares (OLS) regression on various systems: six different gene regulatory network models with various types of feedback, a deterministic mathematical model of the mammalian circadian clock and a model of the mouse ventricular myocyte function. Results Our results indicate that multivariate regression is well suited for emulating dynamic models in systems biology. The hierarchical approach turned out to be superior to both polynomial PLSR and OLS regression in all three test cases. The advantage, in terms of explained variance and prediction accuracy, was largest in systems with highly nonlinear functional relationships and in systems with positive feedback loops. Conclusions HC-PLSR is a promising approach for metamodelling in systems biology, especially for highly nonlinear or non-monotone parameter to phenotype maps. The algorithm can be flexibly adjusted to suit the complexity of the dynamic model behaviour, inviting automation in the metamodelling of complex systems.
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Affiliation(s)
- Kristin Tøndel
- Centre for Integrative Genetics, Dept. of Mathematical Sciences and Technology, Norwegian University of Life Sciences, N-1432 Ås, Norway.
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7
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Gjuvsland AB, Plahte E, Ådnøy T, Omholt SW. Allele interaction--single locus genetics meets regulatory biology. PLoS One 2010; 5:e9379. [PMID: 20186347 PMCID: PMC2826424 DOI: 10.1371/journal.pone.0009379] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2009] [Accepted: 01/07/2010] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Since the dawn of genetics, additive and dominant gene action in diploids have been defined by comparison of heterozygote and homozygote phenotypes. However, these definitions provide little insight into the underlying intralocus allelic functional dependency and thus cannot serve directly as a mediator between genetics theory and regulatory biology, a link that is sorely needed. METHODOLOGY/PRINCIPAL FINDINGS We provide such a link by distinguishing between positive, negative and zero allele interaction at the genotype level. First, these distinctions disclose that a biallelic locus can display 18 qualitatively different allele interaction sign motifs (triplets of +, - and 0). Second, we show that for a single locus, Mendelian dominance is not related to heterozygote allele interaction alone, but is actually a function of the degrees of allele interaction in all the three genotypes. Third, we demonstrate how the allele interaction in each genotype is directly quantifiable in gene regulatory models, and that there is a unique, one-to-one correspondence between the sign of autoregulatory feedback loops and the sign of the allele interactions. CONCLUSION/SIGNIFICANCE The concept of allele interaction refines single locus genetics substantially, and it provides a direct link between classical models of gene action and gene regulatory biology. Together with available empirical data, our results indicate that allele interaction can be exploited experimentally to identify and explain intricate intra- and inter-locus feedback relationships in eukaryotes.
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Affiliation(s)
- Arne B. Gjuvsland
- Centre for Integrative Genetics (CIGENE), Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Erik Plahte
- Centre for Integrative Genetics (CIGENE), Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Tormod Ådnøy
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Stig W. Omholt
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
- * E-mail:
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Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 2009; 6:283-9. [PMID: 19305407 PMCID: PMC2668528 DOI: 10.1038/nmeth.1313] [Citation(s) in RCA: 441] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 02/19/2009] [Indexed: 11/26/2022]
Abstract
The orchestrated binding of transcriptional activators and repressors to specific DNA sequences in the context of chromatin defines the regulatory program of eukaryotic genomes. We developed a digital approach to assay regulatory protein occupancy on genomic DNA in vivo by dense mapping of individual DNase I cleavages from intact nuclei using massively parallel DNA sequencing. Analysis of > 23 million cleavages across the Saccharomyces cerevisiae genome revealed thousands of protected regulatory protein footprints, enabling de novo derivation of factor binding motifs as well as the identification of hundreds of novel binding sites for major regulators. We observed striking correspondence between nucleotide-level DNase I cleavage patterns and protein-DNA interactions determined by crystallography. The data also yielded a detailed view of larger chromatin features including positioned nucleosomes flanking factor binding regions. Digital genomic footprinting provides a powerful approach to delineate the cis-regulatory framework of any organism with an available genome sequence.
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9
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Dalgaard JZ, Eydmann T, Koulintchenko M, Sayrac S, Vengrova S, Yamada-Inagawa T. Random and site-specific replication termination. Methods Mol Biol 2009; 521:35-53. [PMID: 19563100 DOI: 10.1007/978-1-60327-815-7_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Bi-directionality is a common feature observed for genomic replication for all three phylogenetic kingdoms: Eubacteria, Archaea, and Eukaryotes. A consequence of bi-directional replication, where the two replication forks initiated at an origin move away from each other, is that the replication termination will occur at positions away from the origin sequence(s). The replication termination processes are therefore physically and mechanistically dissociated from the replication initiation. The replication machinery is a highly processive complex that in short time copies huge numbers of bases while competing for the DNA substrate with histones, transcription factors, and other DNA-binding proteins. Importantly, the replication machinery generally wins out; meanwhile, when converging forks meet termination occurs, thus preventing over-replication and genetic instability. Very different scenarios for the replication termination processes have been described for the three phylogenetic kingdoms. In eubacterial genomes replication termination is site specific, while in archaea and eukaryotes termination is thought to occur randomly within zones where converging replication forks meet. However, a few site-specific replication barrier elements that mediate replication termination have been described in eukaryotes. This review gives an overview about what is known about replication termination, with a focus on these natural site-specific replication termination sites.
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10
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Eydmann T, Sommariva E, Inagawa T, Mian S, Klar AJS, Dalgaard JZ. Rtf1-mediated eukaryotic site-specific replication termination. Genetics 2008; 180:27-39. [PMID: 18723894 PMCID: PMC2535681 DOI: 10.1534/genetics.108.089243] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 06/30/2008] [Indexed: 11/18/2022] Open
Abstract
The molecular mechanisms mediating eukaryotic replication termination and pausing remain largely unknown. Here we present the molecular characterization of Rtf1 that mediates site-specific replication termination at the polar Schizosaccharomyces pombe barrier RTS1. We show that Rtf1 possesses two chimeric myb/SANT domains: one is able to interact with the repeated motifs encoded by the RTS1 element as well as the elements enhancer region, while the other shows only a weak DNA binding activity. In addition we show that the C-terminal tail of Rtf1 mediates self-interaction, and deletion of this tail has a dominant phenotype. Finally, we identify a point mutation in Rtf1 domain I that converts the RTS1 element into a replication barrier of the opposite polarity. Together our data establish that multiple protein DNA and protein-protein interactions between Rtf1 molecules and both the repeated motifs and the enhancer region of RTS1 are required for site-specific termination at the RTS1 element.
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Affiliation(s)
- T Eydmann
- Marie Curie Research Institute, The Chart, Oxted RH8 0TL, United Kingdom
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11
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Raijman D, Shamir R, Tanay A. Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites. PLoS Comput Biol 2008; 4:e7. [PMID: 18193940 PMCID: PMC2186363 DOI: 10.1371/journal.pcbi.0040007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 11/28/2007] [Indexed: 11/18/2022] Open
Abstract
In comparative genomics one analyzes jointly evolutionarily related species in order to identify conserved and diverged sequences and to infer their function. While such studies enabled the detection of conserved sequences in large genomes, the evolutionary dynamics of regulatory regions as a whole remain poorly understood. Here we present a probabilistic model for the evolution of promoter regions in yeast, combining the effects of regulatory interactions of many different transcription factors. The model expresses explicitly the selection forces acting on transcription factor binding sites in the context of a dynamic evolutionary process. We develop algorithms to compute likelihood and to learn de novo collections of transcription factor binding motifs and their selection parameters from alignments. Using the new techniques, we examine the evolutionary dynamics in Saccharomyces species promoters. Analyses of an evolutionary model constructed using all known transcription factor binding motifs and of a model learned from the data automatically reveal relatively weak selection on most binding sites. Moreover, according to our estimates, strong binding sites are constraining only a fraction of the yeast promoter sequence that is under selection. Our study demonstrates how complex evolutionary dynamics in noncoding regions emerges from formalization of the evolutionary consequences of known regulatory mechanisms. Cells use sophisticated regulation to transform static genomic information into flexible function. We are still far from understanding how such regulation evolves. Short DNA sequences that physically bind transcription factors in promoter areas near target genes play an important role in gene regulation and are directly subject to mutation and selection. In this work, we develop a methodology for studying the evolution of promoter sequences under the effect of multiple regulatory interactions. We present a model that describes the evolutionary process at each genomic locus, taking into account a random flux of mutations that occur in it and the effects of transcription factor binding sites gain or loss. Our model accounts for dependencies (or epistasis) between adjacent loci that contribute to the same regulatory interactions: mutation in one such locus immediately changes the effect of mutations in the other. Using our model, we characterize the evolution of promoters in yeast, showing that many regulatory interactions that were discovered experimentally or computationally are evolutionarily unstable. The dynamic nature of transcriptional interactions may be explained if the regulatory phenotype is achieved through multiple interactions at different levels of specificity, and if only relatively few of these interactions are essential for themselves.
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Affiliation(s)
- Daniela Raijman
- School of Computer Science, Tel Aviv University, Ramat Aviv, Israel
| | - Ron Shamir
- School of Computer Science, Tel Aviv University, Ramat Aviv, Israel
- * To whom correspondence should be addressed. E-mail: (RS); (AT)
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, The Weizmann Institute, Rehovot, Israel
- * To whom correspondence should be addressed. E-mail: (RS); (AT)
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12
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Wu WS, Li WH, Chen BS. Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 2006; 7:421. [PMID: 17010188 PMCID: PMC1637117 DOI: 10.1186/1471-2105-7-421] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 09/29/2006] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND A transcriptional regulatory module (TRM) is a set of genes that is regulated by a common set of transcription factors (TFs). By organizing the genome into TRMs, a living cell can coordinate the activities of many genes and carry out complex functions. Therefore, identifying TRMs is helpful for understanding gene regulation. RESULTS Integrating gene expression and ChIP-chip data, we develop a method, called MOdule Finding Algorithm (MOFA), for reconstructing TRMs of the yeast cell cycle. MOFA identified 87 TRMs, which together contain 336 distinct genes regulated by 40 TFs. Using various kinds of data, we validated the biological relevance of the identified TRMs. Our analysis shows that different combinations of a fairly small number of TFs are responsible for regulating a large number of genes involved in different cell cycle phases and that there may exist crosstalk between the cell cycle and other cellular processes. MOFA is capable of finding many novel TF-target gene relationships and can determine whether a TF is an activator or/and a repressor. Finally, MOFA refines some clusters proposed by previous studies and provides a better understanding of how the complex expression program of the cell cycle is regulated. CONCLUSION MOFA was developed to reconstruct TRMs of the yeast cell cycle. Many of these TRMs are in agreement with previous studies. Further, MOFA inferred many interesting modules and novel TF combinations. We believe that computational analysis of multiple types of data will be a powerful approach to studying complex biological systems when more and more genomic resources such as genome-wide protein activity data and protein-protein interaction data become available.
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Affiliation(s)
- Wei-Sheng Wu
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wen-Hsiung Li
- Department of Evolution and Ecology, University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Bor-Sen Chen
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
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Hediger F, Berthiau AS, van Houwe G, Gilson E, Gasser SM. Subtelomeric factors antagonize telomere anchoring and Tel1-independent telomere length regulation. EMBO J 2006; 25:857-67. [PMID: 16467853 PMCID: PMC1383557 DOI: 10.1038/sj.emboj.7600976] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Accepted: 01/09/2006] [Indexed: 11/09/2022] Open
Abstract
Yeast telomeres are anchored at the nuclear envelope (NE) through redundant pathways that require the telomere-binding factors yKu and Sir4. Significant variation is observed in the efficiency with which different telomeres are anchored, however, suggesting that other forces influence this interaction. Here, we show that subtelomeric elements and the insulator factors that bind them antagonize the association of telomeres with the NE. This is detectable when the redundancy in anchoring pathways is compromised. Remarkably, these same conditions lead to a reduction in steady-state telomere length in the absence of the ATM-kinase homologue Tel1. Both the delocalization of telomeres and reduction in telomere length can be induced by targeting of Tbf1 or Reb1, or the viral transactivator VP16, to a site 23 kb away from the TG repeat. This correlation suggests that telomere anchoring and a Tel1-independent pathway of telomere length regulation are linked, lending a functional significance to the association of yeast telomeres with the NE.
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Affiliation(s)
- Florence Hediger
- Department of Molecular Biology and NCCR Frontiers in Genetics, University of Geneva, Geneva, Switzerland
| | - Anne-Sophie Berthiau
- Laboratoire de Biologie Moléculaire de la Cellule de l'Ecole Normale Supérieure de Lyon, CNRS UMR5161, Lyon, France
| | - Griet van Houwe
- Department of Molecular Biology and NCCR Frontiers in Genetics, University of Geneva, Geneva, Switzerland
| | - Eric Gilson
- Laboratoire de Biologie Moléculaire de la Cellule de l'Ecole Normale Supérieure de Lyon, CNRS UMR5161, Lyon, France
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel CH-4058, Switzerland. Tel.: +41 61 697 7255; Fax: +41 61 697 3976; E-mail:
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Tanay A, Gat-Viks I, Shamir R. A global view of the selection forces in the evolution of yeast cis-regulation. Genome Res 2004; 14:829-34. [PMID: 15123582 PMCID: PMC479109 DOI: 10.1101/gr.2064404] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Accepted: 01/28/2004] [Indexed: 11/24/2022]
Abstract
The interaction between transcription factors and their DNA binding sites is key to understanding gene regulation. By performing a genome-wide study of the evolutionary dynamics in yeast promoters, we provide a first global view of the network of selection forces in the evolution of transcription factor binding sites. This analysis gives rise to new models for binding site activity, identifies families of related binding sites, and characterizes the functional similarities among them. We discovered rich and highly optimized selective pressures operating inside and around these families. In several cases, this organization reveals that a single transcription factor has multiple functional modes. We demonstrate how such functional heterogeneity is related to the binding site's affinity and how it is exploited in transcription programs.
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Affiliation(s)
- Amos Tanay
- School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel.
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15
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Sánchez-Gorostiaga A, López-Estraño C, Krimer DB, Schvartzman JB, Hernández P. Transcription termination factor reb1p causes two replication fork barriers at its cognate sites in fission yeast ribosomal DNA in vivo. Mol Cell Biol 2004; 24:398-406. [PMID: 14673172 PMCID: PMC303360 DOI: 10.1128/mcb.24.1.398-406.2004] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polar replication fork barriers (RFBs) near the 3' end of the rRNA transcriptional unit are a conserved feature of ribosomal DNA (rDNA) replication in eukaryotes. In the mouse, in vivo studies indicate that the cis-acting Sal boxes required for rRNA transcription termination are also involved in replication fork blockage. On the contrary, in the budding yeast Saccharomyces cerevisiae, the rRNA transcription termination factors are not required for RFBs. Here we characterized the rDNA RFBs in the fission yeast Schizosaccharomyces pombe. S. pombe rDNA contains three closely spaced polar replication barriers named RFB1, RFB2, and RFB3 in the 3' to 5' order. The transcription termination protein reb1 and its two binding sites, present at the 3' end of the coding region, were required for fork arrest at RFB2 and RFB3 in vivo. On the other hand, fork arrest at the strongest RFB1 barrier was independent of the above transcription termination factors. Therefore, RFB2 and RFB3 resemble the barriers present in the mouse rDNA, whereas RFB1 is similar to the budding yeast RFBs. These results suggest that during evolution, cis- and trans-acting factors required for rRNA transcription termination became involved in replication fork blockage also. S. pombe is suggested to be a transitional species in which both mechanisms coexist.
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Affiliation(s)
- Alicia Sánchez-Gorostiaga
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
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Van Slyke C, Grayhack EJ. The essential transcription factor Reb1p interacts with the CLB2 UAS outside of the G2/M control region. Nucleic Acids Res 2003; 31:4597-607. [PMID: 12888520 PMCID: PMC169905 DOI: 10.1093/nar/gkg638] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Regulation of CLB2 is important both for completion of the normal vegetative cell cycle in Saccharomyces cerevisiae and for departure from the vegetative cell cycle upon nitrogen deprivation. Cell cycle-regulated transcription of CLB2 in the G2/M phase is known to be brought about by a set of proteins including Mcm1p, Fkh2/1p and Ndd1p that associate with a 35 bp G2/M-specific sequence common to a set of co-regulated genes. CLB2 transcription is regulated by additional signals, including by nitrogen levels, by positive feedback from the Clb2-Cdc28 kinase, and by osmotic stress, but the corresponding regulatory sequences and proteins have not been identified. We have found that the essential Reb1 transcription factor binds with high affinity to a sequence upstream of CLB2, within a region implicated previously by others in regulated expression, but upstream of the known G2/M-specific site. CLB2 sequence from the region around the Reb1p site blocks activation by the Gal4 protein when positioned downstream of the Gal4-binding site. Since a mutation in the Reb1p site abrogates this effect, we suggest that Reb1p is likely to occupy this site in vivo.
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Affiliation(s)
- Ceri Van Slyke
- Department of Biochemistry and Biophysics, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
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Colombo MV, Gutiérrez D, Palacios JM, Imperial J, Ruiz-Argüeso T. A novel autoregulation mechanism of fnrN expression in Rhizobium leguminosarum bv viciae. Mol Microbiol 2000; 36:477-86. [PMID: 10792733 DOI: 10.1046/j.1365-2958.2000.01867.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The fnrN gene from Rhizobium leguminosarum UPM791 controls microaerobic expression of both nitrogen fixation and hydrogenase activities in symbiotic cells. Two copies of fnrN are present in this strain, one chromosomal (fnrN1) and the other located in the symbiotic plasmid (fnrN2). Their expression was studied by cloning the regulatory regions in lacZ promoter-probe vectors. The fnrN genes were found to be autoregulated: they are expressed only at basal levels under aerobic conditions; they are highly expressed under microaerobic conditions; and they are expressed at basal levels in the double mutant DG2 (fnrN1 fnrN2) under any condition. The promoters of both genes contain two FnrN-binding sequences (anaeroboxes), centred at positions -12.5 (proximal anaerobox) and -44.5 (distal anaerobox). Expression analysis and gel retardation experiments with fnrN1-derivative promoter mutants altered in key bases of the anaerobox sequences demonstrated that binding of FnrN1 to the distal anaerobox is necessary for microaerobic activation of transcription, and that binding of FnrN1 to the proximal anaerobox results in transcriptional repression. The apparent affinity of FnrN1 for the proximal anaerobox was fivefold lower than for the distal anaerobox, resulting in repression of transcription of fnrN1 only at high-FnrN1 concentrations. This positive and negative autoregulation mechanism ensures an equilibrated expression of fnrN in response to microaerobic conditions.
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Affiliation(s)
- M V Colombo
- Laboratorio de Microbiología, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, s/n, 28040 Madrid, Spain
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