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GOV ESRA, ARGA KAZIMYALCIN. GENETIC MUTATIONS ARE CHARACTERIZED BY INCREASE IN ENTROPY AT THE TRANSCRIPTIONAL LEVEL. J BIOL SYST 2014. [DOI: 10.1142/s0218339014500132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Predicting the genomic and phenotypic re-programming in organisms undergoing genetic perturbations is a challenging task in modern biology. It is hypothesized that genomic alterations perturb the dynamics of biological information flow. In the present study, a statistical data analysis framework was designed and the network entropy concept was employed to quantify the level of disorder at the transcriptional level as a result of the genomic re-programming of S. cerevisiae cells under genetic perturbations. The customized re-programming in transcription levels to different genetic modifications was observed and genetic mutations were characterized by enhanced network entropies, which revealed higher degree of randomness in mRNA expression levels. To our knowledge, this study constitutes the first numerical demonstration on the conservative energetic state of the microorganisms against genetic perturbations.
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Affiliation(s)
- ESRA GOV
- Department of Bioengineering, Faculty of Engineering, Marmara University, 34722 Göztepe, Istanbul, Turkey
| | - KAZIM YALCIN ARGA
- Department of Bioengineering, Faculty of Engineering, Marmara University, 34722 Göztepe, Istanbul, Turkey
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Samaranayake D, Atencio D, Morse R, Wade JT, Chaturvedi V, Hanes SD. Role of Ess1 in growth, morphogenetic switching, and RNA polymerase II transcription in Candida albicans. PLoS One 2013; 8:e59094. [PMID: 23516603 PMCID: PMC3597612 DOI: 10.1371/journal.pone.0059094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 02/12/2013] [Indexed: 11/18/2022] Open
Abstract
Candida albicans is a fungal pathogen that causes potentially fatal infections among immune-compromised individuals. The emergence of drug resistant C. albicans strains makes it important to identify new antifungal drug targets. Among potential targets are enzymes known as peptidyl-prolyl cis/trans isomerases (PPIases) that catalyze isomerization of peptide bonds preceding proline. We are investigating a PPIase called Ess1, which is conserved in all major human pathogenic fungi. Previously, we reported that C. albicans Ess1 is essential for growth and morphogenetic switching. In the present study, we re-evaluated these findings using more rigorous genetic analyses, including the use of additional CaESS1 mutant alleles, distinct marker genes, and the engineering of suitably-matched isogenic control strains. The results confirm that CaEss1 is essential for growth in C. albicans, but show that reduction of CaESS1 gene dosage by half (δ/+) does not interfere with morphogenetic switching. However, further reduction of CaEss1 levels using a conditional allele does reduce morphogenetic switching. We also examine the role of the linker α-helix that distinguishes C. albicans Ess1 from the human Pin1 enzyme, and present results of a genome-wide transcriptome analysis. The latter analysis indicates that CaEss1 has a conserved role in regulation of RNA polymerase II function, and is required for efficient termination of small nucleolar RNAs and repression of cryptic transcription in C. albicans.
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Affiliation(s)
- Dhanushki Samaranayake
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
| | - David Atencio
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York, United States of America
| | - Randall Morse
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
| | - Vishnu Chaturvedi
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Mycology Laboratory, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
| | - Steven D. Hanes
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Division of Infectious Disease, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York, United States of America
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Multiple roles for the Ess1 prolyl isomerase in the RNA polymerase II transcription cycle. Mol Cell Biol 2012; 32:3594-607. [PMID: 22778132 DOI: 10.1128/mcb.00672-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Ess1 prolyl isomerase in Saccharomyces cerevisiae regulates RNA polymerase II (pol II) by isomerizing peptide bonds within the pol II carboxy-terminal domain (CTD) heptapeptide repeat (YSPTSPS). Ess1 preferentially targets the Ser5-Pro6 bond when Ser5 is phosphorylated. Conformational changes in the CTD induced by Ess1 control the recruitment of essential cofactors to the pol II complex and may facilitate the ordered transition between initiation, elongation, termination, and RNA processing. Here, we show that Ess1 associates with the phospho-Ser5 form of polymerase in vivo, is present along the entire length of coding genes, and is critical for regulating the phosphorylation of Ser7 within the CTD. In addition, Ess1 represses the initiation of cryptic unstable transcripts (CUTs) and is required for efficient termination of mRNA transcription. Analysis using strains lacking nonsense-mediated decay suggests that as many as half of all yeast genes depend on Ess1 for efficient termination. Finally, we show that Ess1 is required for trimethylation of histone H3 lysine 4 (H3K4). Thus, Ess1 has direct effects on RNA polymerase transcription by controlling cofactor binding via conformationally induced changes in the CTD and indirect effects by influencing chromatin modification.
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Radman-Livaja M, Verzijlbergen KF, Weiner A, van Welsem T, Friedman N, Rando OJ, van Leeuwen F. Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biol 2011; 9:e1001075. [PMID: 21666805 PMCID: PMC3110181 DOI: 10.1371/journal.pbio.1001075] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 04/22/2011] [Indexed: 11/18/2022] Open
Abstract
Tracking of ancestral histone proteins over multiple generations of genome
replication in yeast reveals that old histones move along genes from 3′
toward 5′ over time, and that maternal histones move up to around 400 bp
during genomic replication. Replicating chromatin involves disruption of histone-DNA contacts and subsequent
reassembly of maternal histones on the new daughter genomes. In bulk, maternal
histones are randomly segregated to the two daughters, but little is known about
the fine details of this process: do maternal histones re-assemble at preferred
locations or close to their original loci? Here, we use a recently developed
method for swapping epitope tags to measure the disposition of ancestral histone
H3 across the yeast genome over six generations. We find that ancestral H3 is
preferentially retained at the 5′ ends of most genes, with strongest
retention at long, poorly transcribed genes. We recapitulate these observations
with a quantitative model in which the majority of maternal histones are
reincorporated within 400 bp of their pre-replication locus during replication,
with replication-independent replacement and transcription-related retrograde
nucleosome movement shaping the resulting distributions of ancestral histones.
We find a key role for Topoisomerase I in retrograde histone movement during
transcription, and we find that loss of Chromatin Assembly Factor-1 affects
replication-independent turnover. Together, these results show that specific
loci are enriched for histone proteins first synthesized several generations
beforehand, and that maternal histones re-associate close to their original
locations on daughter genomes after replication. Our findings further suggest
that accumulation of ancestral histones could play a role in shaping histone
modification patterns. It is widely believed that chromatin, the nucleoprotein packaged state of
eukaryotic genomes, can carry epigenetic information and thus transmit gene
expression patterns to replicating cells. However, the inheritance of genomic
packaging status is subject to mechanistic challenges that do not confront the
inheritance of genomic DNA sequence. Most notably, histone proteins must at
least transiently dissociate from the maternal genome during replication, and it
is unknown whether or not maternal proteins re-associate with daughter genomes
near the sequence they originally occupied on the maternal genome. Here, we use
a novel method for tracking old proteins to determine where histone proteins
accumulate after 1, 3, or 6 generations of growth in yeast. To our surprise,
ancestral histones accumulate near the 5′ end of long, relatively inactive
genes. Using a mathematical model, we show that our results can be explained by
the combined effects of histone replacement, histone movement along genes from
3′ towards 5′ ends, and histone spreading during replication. Our
results show that old histones do move but stay relatively close to their
original location (within around 400 base-pairs), which places important
constraints on how chromatin could potentially carry epigenetic information. Our
findings also suggest that accumulation of the ancestral histones that are
inherited can influence histone modification patterns.
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Affiliation(s)
- Marta Radman-Livaja
- Department of Biochemistry and Molecular
Pharmacology, University of Massachusetts Medical School, Worcester,
Massachusetts, United States of America
| | - Kitty F. Verzijlbergen
- Division of Gene Regulation, Netherlands
Cancer Institute, and Netherlands Proteomics Center, Amsterdam, The
Netherlands
| | - Assaf Weiner
- School of Computer Science and Engineering,
The Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life
Sciences, The Hebrew University, Jerusalem, Israel
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands
Cancer Institute, and Netherlands Proteomics Center, Amsterdam, The
Netherlands
| | - Nir Friedman
- School of Computer Science and Engineering,
The Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life
Sciences, The Hebrew University, Jerusalem, Israel
- * E-mail: (NF); (OJR); (FVL)
| | - Oliver J. Rando
- Department of Biochemistry and Molecular
Pharmacology, University of Massachusetts Medical School, Worcester,
Massachusetts, United States of America
- * E-mail: (NF); (OJR); (FVL)
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands
Cancer Institute, and Netherlands Proteomics Center, Amsterdam, The
Netherlands
- * E-mail: (NF); (OJR); (FVL)
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Abstract
Transcriptional silencing in Saccharomyces cerevisiae is mediated by heterochromatin. There is a plethora of information regarding the roles of histone residues in transcriptional silencing, but exactly how histone residues contribute to heterochromatin structure is not resolved. We address this question by testing the effects of a series of histone H3 and H4 mutations involving residues in their aminoterminal tails, on the solvent-accessible and lateral surfaces of the nucleosome, and at the interface of the H3/H4 tetramer and H2A/H2B dimer on heterochromatin structure and transcriptional silencing. The general state, stability, and conformational heterogeneity of chromatin are examined with a DNA topology-based assay, and the primary chromatin structure is probed by micrococcal nuclease. We demonstrate that the histone mutations differentially affect heterochromatin. Mutations of lysine 16 of histone H4 (H4-K16) and residues in the LRS (loss of rDNA silencing) domain of nucleosome surface markedly alter heterochromatin structure, supporting the notion that H4-K16 and LRS play key roles in heterochromatin formation. Deletion of the aminoterminal tail of H3 moderately alters heterochromatin structure. Interestingly, a group of mutations in the globular domains of H3 and H4 that abrogate or greatly reduce transcriptional silencing increase the conformational heterogeneity and/or reduce the stability of heterochromatin without affecting its overall structure. Surprisingly, yet another series of mutations abolish or reduce silencing without significantly affecting the structure, stability, or conformational heterogeneity of heterochromatin. Therefore, histone residues may contribute to the structure, stability, conformational heterogeneity, or other yet-to-be-characterized features of heterochromatin important for transcriptional silencing.
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Mediator complex association with constitutively transcribed genes in yeast. Proc Natl Acad Sci U S A 2009; 106:16734-9. [PMID: 19805365 DOI: 10.1073/pnas.0905103106] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mediator is a large, multisubunit complex that is essential for transcription of mRNA by RNA Pol II in eukaryotes and is believed to bridge transcriptional activators and the general transcription machinery. However, several recent studies suggest that the requirement for Mediator during transcriptional activation is not universal, but rather activator dependent, and may be indirect for some genes. Here we have investigated Mediator association with several constitutively transcribed genes in yeast by comparing a yeast strain that harbors a temperature-sensitive mutation in an essential Mediator subunit, Srb4, with its wild-type (WT) counterpart. We find modest association of Mediator with constitutively active genes and show that this association is strongly decreased in srb4 ts yeast, whereas association with a nontranscribed region or repressed gene promoters is lower and unaffected in the mutant yeast. The tail module of Mediator remains associated with ribosomal protein (RP) gene promoters in srb4 ts yeast, while subunits from the head and middle modules are lost. Tail module association at Rap1-dependent gene promoters is lost in rap1 ts yeast, indicating that Rap1 is required for Mediator recruitment at these gene promoters and that its recruitment occurs via the tail module. Pol II association is also rapidly and severely affected in srb4 ts yeast, indicating that Mediator is directly required for pol II association at constitutively transcribed genes. Our results are consistent with Mediator functioning as a general transcription factor in yeast.
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Notebaart RA, Kensche PR, Huynen MA, Dutilh BE. Asymmetric relationships between proteins shape genome evolution. Genome Biol 2009; 10:R19. [PMID: 19216750 PMCID: PMC2688278 DOI: 10.1186/gb-2009-10-2-r19] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 01/28/2009] [Accepted: 02/12/2009] [Indexed: 12/18/2022] Open
Abstract
An investigation of metabolic networks in E. coli and S. cerevisiae reveals that asymmetric protein interactions affect gene expression, the relative effect of gene-knockouts and genome evolution. Background The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the converging pathways depend on the enzymes in the central pathway, but the enzymes in the latter do not depend on any specific enzyme in the converging pathways. Asymmetric relations are analogous to the “if->then” logical relation where A implies B, but B does not imply A (A->B). Results We show that the majority of relationships between enzymes in metabolic flux models of metabolism in Escherichia coli and Saccharomyces cerevisiae are asymmetric. We show furthermore that these asymmetric relationships are reflected in the expression of the genes encoding those enzymes, the effect of gene knockouts and the evolution of genomes. From the asymmetric relative dependency, one would expect that the gene that is relatively independent (B) can occur without the other dependent gene (A), but not the reverse. Indeed, when only one gene of an A->B pair is expressed, is essential, is present in a genome after an evolutionary gain or loss, it tends to be the independent gene (B). This bias is strongest for genes encoding proteins whose asymmetric relationship is evolutionarily conserved. Conclusions The asymmetric relations between proteins that arise from the system properties of metabolic networks affect gene expression, the relative effect of gene knockouts and genome evolution in a predictable manner.
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Affiliation(s)
- Richard A Notebaart
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
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Dai J, Hyland EM, Yuan DS, Huang H, Bader JS, Boeke JD. Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants. Cell 2008; 134:1066-78. [PMID: 18805098 DOI: 10.1016/j.cell.2008.07.019] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 06/03/2008] [Accepted: 07/14/2008] [Indexed: 01/27/2023]
Abstract
Nucleosome structural integrity underlies the regulation of DNA metabolism and transcription. Using a synthetic approach, a versatile library of 486 systematic histone H3 and H4 substitution and deletion mutants that probes the contribution of each residue to nucleosome function was generated in Saccharomyces cerevisiae. We probed fitness contributions of each residue to perturbations of chromosome integrity and transcription, mapping global patterns of chemical sensitivities and requirements for transcriptional silencing onto the nucleosome surface. Each histone mutant was tagged with unique molecular barcodes, facilitating identification of histone mutant pools through barcode amplification, labeling, and TAG microarray hybridization. Barcodes were used to score complex phenotypes such as competitive fitness in a chemostat, DNA repair proficiency, and synthetic genetic interactions, revealing new functions for distinct histone residues and new interdependencies among nucleosome components and their modifiers.
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Affiliation(s)
- Junbiao Dai
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Dispersed mutations in histone H3 that affect transcriptional repression and chromatin structure of the CHA1 promoter in Saccharomyces cerevisiae. EUKARYOTIC CELL 2008; 7:1649-60. [PMID: 18658255 DOI: 10.1128/ec.00233-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The histone H3 amino terminus, but not that of H4, is required to prevent the constitutively bound activator Cha4 from remodeling chromatin and activating transcription at the CHA1 gene in Saccharomyces cerevisiae. Here we show that neither the modifiable lysine residues nor any specific region of the H3 tail is required for repression of CHA1. We then screened for histone H3 mutations that cause derepression of the uninduced CHA1 promoter and identified six mutants, three of which are also temperature-sensitive mutants and four of which exhibit a sin(-) phenotype. Histone mutant levels were similar to that of wild-type H3, and the mutations did not cause gross alterations in nucleosome structure. One specific and strongly derepressing mutation, H3 A111G, was examined in depth and found to cause a constitutively active chromatin configuration at the uninduced CHA1 promoter as well as at the ADH2 promoter. Transcriptional derepression and altered chromatin structure of the CHA1 promoter depend on the activator Cha4. These results indicate that modest perturbations in distinct regions of the nucleosome can substantially affect the repressive function of chromatin, allowing activation in the absence of a normal inducing signal (at CHA1) or of Swi/Snf (resulting in a sin(-) phenotype).
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Oti M, van Reeuwijk J, Huynen MA, Brunner HG. Conserved co-expression for candidate disease gene prioritization. BMC Bioinformatics 2008; 9:208. [PMID: 18433471 PMCID: PMC2383918 DOI: 10.1186/1471-2105-9-208] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 04/23/2008] [Indexed: 11/16/2022] Open
Abstract
Background Genes that are co-expressed tend to be involved in the same biological process. However, co-expression is not a very reliable predictor of functional links between genes. The evolutionary conservation of co-expression between species can be used to predict protein function more reliably than co-expression in a single species. Here we examine whether co-expression across multiple species is also a better prioritizer of disease genes than is co-expression between human genes alone. Results We use co-expression data from yeast (S. cerevisiae), nematode worm (C. elegans), fruit fly (D. melanogaster), mouse and human and find that the use of evolutionary conservation can indeed improve the predictive value of co-expression. The effect that genes causing the same disease have higher co-expression than do other genes from their associated disease loci, is significantly enhanced when co-expression data are combined across evolutionarily distant species. We also find that performance can vary significantly depending on the co-expression datasets used, and just using more data does not necessarily lead to better prioritization. Instead, we find that dataset quality is more important than quantity, and using a consistent microarray platform per species leads to better performance than using more inclusive datasets pooled from various platforms. Conclusion We find that evolutionarily conserved gene co-expression prioritizes disease candidate genes better than human gene co-expression alone, and provide the integrated data as a new resource for disease gene prioritization tools.
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Affiliation(s)
- Martin Oti
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands.
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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