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Movilla Miangolarra A, Saxton DS, Yan Z, Rine J, Howard M. Two-way feedback between chromatin compaction and histone modification state explains Saccharomyces cerevisiae heterochromatin bistability. Proc Natl Acad Sci U S A 2024; 121:e2403316121. [PMID: 38593082 PMCID: PMC11032488 DOI: 10.1073/pnas.2403316121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/02/2024] [Indexed: 04/11/2024] Open
Abstract
Compact chromatin is closely linked with gene silencing in part by sterically masking access to promoters, inhibiting transcription factor binding and preventing polymerase from efficiently transcribing a gene. However, a broader hypothesis suggests that chromatin compaction can be both a cause and a consequence of the locus histone modification state, with a tight bidirectional interaction underpinning bistable transcriptional states. To rigorously test this hypothesis, we developed a mathematical model for the dynamics of the HMR locus in Saccharomyces cerevisiae, that incorporates activating histone modifications, silencing proteins, and a dynamic, acetylation-dependent, three-dimensional locus size. Chromatin compaction enhances silencer protein binding, which in turn feeds back to remove activating histone modifications, leading to further compaction. The bistable output of the model was in good agreement with prior quantitative data, including switching rates from expressed to silent states (and vice versa), and protein binding/histone modification levels within the locus. We then tested the model by predicting changes in switching rates as the genetic length of the locus was increased, which were then experimentally verified. Such bidirectional feedback between chromatin compaction and the histone modification state may be a widespread and important regulatory mechanism given the hallmarks of many heterochromatic regions: physical chromatin compaction and dimerizing (or multivalent) silencing proteins.
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Affiliation(s)
| | - Daniel S. Saxton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Zhi Yan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
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Bondra ER, Rine J. Context-dependent function of the transcriptional regulator Rap1 in gene silencing and activation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2023; 120:e2304343120. [PMID: 37769255 PMCID: PMC10556627 DOI: 10.1073/pnas.2304343120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/04/2023] [Indexed: 09/30/2023] Open
Abstract
In Saccharomyces cerevisiae, heterochromatin is formed through interactions between site-specific DNA-binding factors, including the transcriptional activator Repressor Activator Protein (Rap1), and Sir proteins. Despite an understanding of the establishment and maintenance of Sir-silenced chromatin, the mechanism of gene silencing by Sir proteins has remained a mystery. Utilizing high-resolution chromatin immunoprecipitation, we found that Rap1, the native activator of the bidirectional HMLα promoter, bound its recognition sequence in silenced chromatin, and its binding was enhanced by the presence of Sir proteins. In contrast to prior results, various components of transcription machinery were not able to access HMLα in the silenced state. These findings disproved the long-standing model of indiscriminate steric occlusion by Sir proteins and led to investigation of the role of the transcriptional activator Rap1 in Sir-silenced chromatin. Using a highly sensitive assay that monitors loss-of-silencing events, we identified a role for promoter-bound Rap1 in the maintenance of silent chromatin through interactions with the Sir complex. We also found that promoter-bound Rap1 activated HMLα when in an expressed state, and aided in the transition from transcription initiation to elongation. Highlighting the importance of epigenetic context in transcription factor function, these results point toward a model in which the duality of Rap1 function was mediated by local chromatin environment rather than binding-site availability.
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Affiliation(s)
- Eliana R. Bondra
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
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Miangolarra AM, Saxton DS, Yan Z, Rine J, Howard M. Two-way feedback between chromatin compaction and histone modification state explains S. cerevisiae heterochromatin bistability. bioRxiv 2023:2023.08.12.552948. [PMID: 37645983 PMCID: PMC10461966 DOI: 10.1101/2023.08.12.552948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Compact chromatin is closely linked with gene silencing in part by sterically masking access to promoters, inhibiting transcription factor binding and preventing polymerase from efficiently transcribing a gene. Here, we propose a broader view: chromatin compaction can be both a cause and a consequence of the histone modification state, and this tight bidirectional interaction can underpin bistable transcriptional states. To test this theory, we developed a mathematical model for the dynamics of the HMR locus in S. cerevisiae, that incorporates activating histone modifications, silencing proteins and a dynamic, acetylation-dependent, three-dimensional locus size. Chromatin compaction enhances silencer protein binding, which in turn feeds back to remove activating histone modifications, leading to further compaction. The bistable output of the model was in good agreement with prior quantitative data, including switching rates from expressed to silent states, and vice versa, and protein binding levels within the locus. We then tested the model by predicting changes in switching rates as the genetic length of the locus was increased, which were then experimentally verified. This bidirectional feedback between chromatin compaction and the histone modification state may be an important regulatory mechanism at many loci.
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Affiliation(s)
- Ander Movilla Miangolarra
- Dept. of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Daniel S Saxton
- Dept. of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Zhi Yan
- Dept. of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jasper Rine
- Dept. of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Martin Howard
- Dept. of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Bondra ER, Rine J. Context dependent function of the transcriptional regulator Rap1 in gene silencing and activation in Saccharomyces cerevisiae. bioRxiv 2023:2023.05.08.539937. [PMID: 37214837 PMCID: PMC10197613 DOI: 10.1101/2023.05.08.539937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In Saccharomyces cerevisiae, heterochromatin is formed through interactions between site-specific DNA-binding factors, including the transcriptional activator Rap1, and Sir proteins. Despite a vast understanding of the establishment and maintenance of Sir-silenced chromatin, the mechanism of gene silencing by Sir proteins has remained a mystery. Utilizing high resolution chromatin immunoprecipitation, we found that Rap1, the native activator of the bi-directional HML α promoter, bound its recognition sequence in silenced chromatin and its binding was enhanced by the presence of Sir proteins. In contrast to prior results, various components of transcription machinery were not able to access HML α in the silenced state. These findings disproved the long-standing model of indiscriminate steric occlusion by Sir proteins and led to investigation of the transcriptional activator Rap1 in Sir-silenced chromatin. Using a highly sensitive assay that monitors loss-of-silencing events, we identified a novel role for promoter-bound Rap1 in the maintenance of silent chromatin through interactions with the Sir complex. We also found that promoter-bound Rap1 activated HML α when in an expressed state, and aided in the transition from transcription initiation to elongation. Highlighting the importance of epigenetic context in transcription factor function, these results point toward a model in which the duality of Rap1 function was mediated by local chromatin environment rather than binding-site availability. Significance Statement The coarse partitioning of the genome into regions of active euchromatin and repressed heterochromatin is an important, and conserved, level gene expression regulation in eukaryotes. Repressor Activator Protein (Rap1) is a transcription factor that promotes the activation of genes when recruited to promoters, and aids in the establishment of heterochromatin through interactions with silencer elements. Here, we investigate the role of Rap1 when bound to a promoter in silent chromatin and dissect the context-specific epigenetic cues that regulate the dual properties of this transcription factor. Together, our data highlight the importance of protein-protein interactions and local chromatin state on transcription factor function.
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Affiliation(s)
- Eliana R Bondra
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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Fouet M, Rine J. Limits to transcriptional silencing in Saccharomyces cerevisiae. Genetics 2022; 223:6887216. [PMID: 36495285 PMCID: PMC9910407 DOI: 10.1093/genetics/iyac180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/12/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Mating-type switching in the budding yeast Saccharomyces cerevisiae relies on the Sir protein complex to silence HML and HMR, the two loci containing copies of the alleles of the mating type locus, MAT. Sir-based transcriptional silencing has been considered locus-specific, but the recent discovery of rare and transient escapes from silencing at HMLα2 with a sensitive assay called to question if these events extend to the whole locus. Adapting the same assay, we measured that transient silencing failures at HML were more frequent for the α2 gene than α1, similarly to their expression level in unsilenced cells. By coupling a mating assay, at HML we found that one of the two genes at that locus can be transiently expressed while the other gene is maintained silent. Thus, transient silencing loss can be a property of the gene rather than the locus. Cells lacking the SIR1 gene experience epigenetic bistability at HML and HMR. Our previous result led us to ask if HML could allow for two independent epigenetic states within the locus in a sir1Δ mutant. A simple construct using a double fluorescent reporter at HMLα1 and HMLα2 ruled out this possibility. Each HML locus displayed a single epigenetic state. We revisited the question of the correlation between the states of two HML loci in diploid cells, and showed they were independent. Finally, we determined the relative strength of gene repression achieved by Sir-based silencing with that achieved by the a1-α2 repressor.
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Affiliation(s)
- Marc Fouet
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jasper Rine
- Corresponding author: Department of Molecular and Cellular Biology, California Institute of Quantitative Biosciences, 406 Barker Hall, U.C. Berkeley, Berkeley, CA 94720-3202, USA.
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Saxton DS, Rine J. Distinct silencer states generate epigenetic states of heterochromatin. Mol Cell 2022; 82:3566-3579.e5. [PMID: 36041432 DOI: 10.1016/j.molcel.2022.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/23/2022] [Accepted: 07/30/2022] [Indexed: 11/26/2022]
Abstract
Heterochromatic loci can exhibit different transcriptional states in genetically identical cells. A popular model posits that the inheritance of modified histones is sufficient for inheritance of the silenced state. However, silencing inheritance requires silencers and therefore cannot be driven by the inheritance of modified histones alone. To address these observations, we determined the chromatin architectures produced by strong and weak silencers in Saccharomyces. Strong silencers recruited Sir proteins and silenced the locus in all cells. Strikingly, weakening these silencers reduced Sir protein recruitment and stably silenced the locus in some cells; however, this silenced state could probabilistically convert to an expressed state that lacked Sir protein recruitment. Additionally, changes in the constellation of silencer-bound proteins or the concentration of a structural Sir protein modulated the probability that a locus exhibited the silenced or expressed state. These findings argued that distinct silencer states generate epigenetic states and regulate their dynamics.
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Affiliation(s)
- Daniel S Saxton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Brothers M, Rine J. Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae. eLife 2022; 11:75653. [PMID: 35073254 PMCID: PMC8830885 DOI: 10.7554/elife.75653] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
The formation of heterochromatin at HML, HMR, and telomeres in Saccharomyces cerevisiae involves two main steps: Recruitment of Sir proteins to silencers and their spread throughout the silenced domain. We developed a method to study these two processes at single base-pair resolution. Using a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII, we mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein and by ChIP-seq to map the distribution of Sir3-M.EcoGII. A silencing-deficient mutant of Sir3 lacking its Bromo-Adjacent Homology (BAH) domain, sir3-bah∆, was still recruited to HML, HMR, and telomeres. However, in the absence of the BAH domain, it was unable to spread away from those recruitment sites. Overexpression of Sir3 did not lead to further spreading at HML, HMR, and most telomeres. A few exceptional telomeres, like 6R, exhibited a small amount of Sir3 spreading, suggesting that boundaries at telomeres responded variably to Sir3 overexpression. Finally, by using a temperature-sensitive allele of SIR3 fused to M.ECOGII, we tracked the positions first methylated after induction and found that repression of genes at HML and HMR began before Sir3 occupied the entire locus.
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Affiliation(s)
- Molly Brothers
- Department of Molecular and Cell Biology, University of California, Berkeley
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley
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Farris D, Saxton DS, Rine J. A novel allele of SIR2 reveals a heritable intermediate state of gene silencing. Genetics 2021; 218:6169529. [PMID: 33713126 DOI: 10.1093/genetics/iyab041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/08/2021] [Indexed: 12/22/2022] Open
Abstract
Genetic information acquires additional meaning through epigenetic regulation, the process by which genetically identical cells can exhibit heritable differences in gene expression and phenotype. Inheritance of epigenetic information is a critical step in maintaining cellular identity and organismal health. In Saccharomyces cerevisiae, one form of epigenetic regulation is the transcriptional silencing of two mating-type loci, HML and HMR, by the SIR-protein complex. To focus on the epigenetic dimension of this gene regulation, we conducted a forward mutagenesis screen to identify mutants exhibiting an epigenetic or metastable silencing defect. We utilized fluorescent reporters at HML and HMR, and screened yeast colonies for epigenetic silencing defects. We uncovered numerous independent sir1 alleles, a gene known to be required for stable epigenetic inheritance. More interestingly, we recovered a missense mutation within SIR2, which encodes a highly conserved histone deacetylase. In contrast to sir1Δ, which exhibits states that are either fully silenced or fully expressed, this sir2 allele exhibited heritable states that were either fully silenced or expressed at an intermediate level. The heritable nature of this unique silencing defect was influenced by, but not completely dependent on, changes in rDNA copy number. Therefore, this study revealed a heritable state of intermediate silencing and linked this state to a central silencing factor, Sir2.
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Affiliation(s)
- Delaney Farris
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Daniel S Saxton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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9
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Abstract
The establishment of silent chromatin, a heterochromatin-like structure at HML and HMR in Saccharomyces cerevisiae, depends on progression through S phase of the cell cycle, but the molecular nature of this requirement has remained elusive despite intensive study. Using high-resolution chromatin immunoprecipitation and single-molecule RNA analysis, we found that silencing establishment proceeded via gradual repression of transcription in individual cells over several cell cycles, and that the cell-cycle-regulated step was downstream of Sir protein recruitment. In contrast to prior results, HML and HMR had identical cell-cycle requirements for silencing establishment, with no apparent contribution from a tRNA gene adjacent to HMR. We identified the cause of the S-phase requirement for silencing establishment: removal of transcription-favoring histone modifications deposited by Dot1, Sas2, and Rtt109. These results revealed that silencing establishment was absolutely dependent on the cell-cycle-regulated interplay between euchromatic and heterochromatic histone modifications.
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Affiliation(s)
- Davis Goodnight
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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Sun S, Weile J, Verby M, Wu Y, Wang Y, Cote AG, Fotiadou I, Kitaygorodsky J, Vidal M, Rine J, Ješina P, Kožich V, Roth FP. A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase. Genome Med 2020; 12:13. [PMID: 32000841 PMCID: PMC6993387 DOI: 10.1186/s13073-020-0711-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 01/10/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND For the majority of rare clinical missense variants, pathogenicity status cannot currently be classified. Classical homocystinuria, characterized by elevated homocysteine in plasma and urine, is caused by variants in the cystathionine beta-synthase (CBS) gene, most of which are rare. With early detection, existing therapies are highly effective. METHODS Damaging CBS variants can be detected based on their failure to restore growth in yeast cells lacking the yeast ortholog CYS4. This assay has only been applied reactively, after first observing a variant in patients. Using saturation codon-mutagenesis, en masse growth selection, and sequencing, we generated a comprehensive, proactive map of CBS missense variant function. RESULTS Our CBS variant effect map far exceeds the performance of computational predictors of disease variants. Map scores correlated strongly with both disease severity (Spearman's ϱ = 0.9) and human clinical response to vitamin B6 (ϱ = 0.93). CONCLUSIONS We demonstrate that highly multiplexed cell-based assays can yield proactive maps of variant function and patient response to therapy, even for rare variants not previously seen in the clinic.
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Affiliation(s)
- Song Sun
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE 75123, Uppsala, Sweden
| | - Jochen Weile
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.
| | - Marta Verby
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Yingzhou Wu
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Yang Wang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Atina G Cote
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Iosifina Fotiadou
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Julia Kitaygorodsky
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Jasper Rine
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Pavel Ješina
- Department of Pediatrics and Adolescent Medicine, Charles University, First Faculty of Medicine and General University Hospital in Prague, 128 08, Praha 2, Czech Republic
| | - Viktor Kožich
- Department of Pediatrics and Adolescent Medicine, Charles University, First Faculty of Medicine and General University Hospital in Prague, 128 08, Praha 2, Czech Republic.
| | - Frederick P Roth
- The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.
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Abstract
Heterochromatic gene silencing is an important form of gene regulation that usually requires specific histone modifications. A popular model posits that inheritance of modified histones, especially in the form of H3-H4 tetramers, underlies inheritance of heterochromatin. Because H3-H4 tetramers are randomly distributed between daughter chromatids during DNA replication, rare occurrences of asymmetric tetramer inheritance within a heterochromatic domain would have the potential to destabilize heterochromatin. This model makes a prediction that shorter heterochromatic domains would experience unbalanced tetramer inheritance more frequently, and thereby be less stable. In contrast to this prediction, we found that shortening a heterochromatic domain in Saccharomyces had no impact on the strength of silencing nor its heritability. Additionally, we found that replisome mutations that disrupt inheritance of H3-H4 tetramers had only minor effects on heterochromatin stability. These findings suggest that histones carry little or no memory of the heterochromatin state through DNA replication. A crucial process in life is the ability of cells to pass on useful information to their descendants. Some of this information is encoded within molecules of DNA, including genes that contain specific coded instructions. Another layer of information helps to specify whether individual genes are switched on or off, which means cells with the same genes can perform different tasks. However, it remains unclear exactly how cells pass on this additional layer of “epigenetic” information. Inside human, yeast and other eukaryotic cells, DNA is wrapped around scaffold proteins known as histones. Cells modify histones by adding chemical tags to them, and histones within the same gene often have specific patterns of chemical tags. One popular hypothesis is that these marked histones constitute epigenetic information that may be passed on when DNA replicates before a cell divides to make two daughter cells. This model predicts that the marked histones need to be divided equally between the two sets of DNA to allow the epigenetic information to be faithfully passed on to both daughter cells. To test this prediction, Saxton and Rine studied a gene called HMR that is involved in mating in yeast. This gene is constantly silenced (in other words, not actively providing instructions to the cell) and contains histones with very specific patterns of chemical tags. For the experiments, Saxton and Rine made a series of mutations in the yeast that increased how often these marked histones were divided unequally when the yeast cells replicated their DNA. Unexpectedly, these mutations had little impact on the ability of the cells to pass on the silenced state of HMR to their offspring. These findings argue against the classic model that marked histones carry epigenetic information.
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Affiliation(s)
- Daniel S Saxton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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12
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Brothers M, Rine J. Mutations in the PCNA DNA Polymerase Clamp of Saccharomyces cerevisiae Reveal Complexities of the Cell Cycle and Ploidy on Heterochromatin Assembly. Genetics 2019; 213:449-463. [PMID: 31451562 PMCID: PMC6781887 DOI: 10.1534/genetics.119.302452] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 08/23/2019] [Indexed: 01/19/2023] Open
Abstract
In Saccharomyces cerevisiae, transcriptional silencing at HML and HMR maintains mating-type identity. The repressive chromatin structure at these loci is replicated every cell cycle and must be re-established quickly to prevent transcription of the genes at these loci. Mutations in a component of the replisome, the proliferating cell nuclear antigen (PCNA), encoded by POL30, cause a loss of transcriptional silencing at HMR We used an assay that captures transient losses of silencing at HML and HMR to perform extended genetic analyses of the pol30-6, pol30-8, and pol30-79 alleles. All three alleles destabilized silencing only transiently and only in cycling cells. Whereas pol30-8 caused loss of silencing by disrupting the function of Chromatin Assembly Factor 1, pol30-6 and pol30-79 acted through a separate genetic pathway, but one still dependent on histone chaperones. Surprisingly, the silencing-loss phenotypes of pol30-6 and pol30-79 depended on ploidy, but not on POL30 dosage or mating-type identity. Separately from silencing loss, the pol30-6 and pol30-79 alleles also displayed high levels of mitotic recombination in diploids. These results established that histone trafficking involving PCNA at replication forks is crucial to the maintenance of chromatin state and genome stability during DNA replication. They also raised the possibility that increased ploidy may protect chromatin states when the replisome is perturbed.
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Affiliation(s)
- Molly Brothers
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
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13
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Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, Baets GD, Bromberg Y, Cao C, Capriotti E, Casadio R, Durme JV, Giollo M, Karchin R, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Pal LR, Radivojac P, Rousseau F, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SC, Vihinen M, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I. Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Hum Mutat 2019; 40:1530-1545. [PMID: 31301157 PMCID: PMC7325732 DOI: 10.1002/humu.23868] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/22/2019] [Accepted: 07/09/2019] [Indexed: 12/28/2022]
Abstract
Accurate prediction of the impact of genomic variation on phenotype is a major goal of computational biology and an important contributor to personalized medicine. Computational predictions can lead to a better understanding of the mechanisms underlying genetic diseases, including cancer, but their adoption requires thorough and unbiased assessment. Cystathionine-beta-synthase (CBS) is an enzyme that catalyzes the first step of the transsulfuration pathway, from homocysteine to cystathionine, and in which variations are associated with human hyperhomocysteinemia and homocystinuria. We have created a computational challenge under the CAGI framework to evaluate how well different methods can predict the phenotypic effect(s) of CBS single amino acid substitutions using a blinded experimental data set. CAGI participants were asked to predict yeast growth based on the identity of the mutations. The performance of the methods was evaluated using several metrics. The CBS challenge highlighted the difficulty of predicting the phenotype of an ex vivo system in a model organism when classification models were trained on human disease data. We also discuss the variations in difficulty of prediction for known benign and deleterious variants, as well as identify methodological and experimental constraints with lessons to be learned for future challenges.
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Affiliation(s)
- Laura Kasak
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Constantina Bakolitsa
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Changhua Yu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jasper Rine
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Dago F. Dimster-Denk
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Gaurav Pandey
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Greet De Baets
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Chen Cao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD, USA
| | - Emidio Capriotti
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Joost Van Durme
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Vrije Universiteit Brussel, Brussels, Belgium
| | - Manuel Giollo
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Rachel Karchin
- Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - David Masica
- Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Ayodeji Olatubosun
- Institute of Medical Technology, University of Tampere, Tampere, Finland
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA
| | - Predrag Radivojac
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | | | - Mauno Vihinen
- Institute of Medical Technology, University of Tampere, Tampere, Finland
| | - Jouni Väliaho
- Institute of Medical Technology, University of Tampere, Tampere, Finland
| | - Susanna Repo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - John Moult
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Iddo Friedberg
- Department of Microbiology, Miami University, Oxford, OH, USA
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA USA
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14
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Marini NJ, Asrani K, Yang W, Rine J, Shaw GM. Accumulation of rare coding variants in genes implicated in risk of human cleft lip with or without cleft palate. Am J Med Genet A 2019; 179:1260-1269. [PMID: 31063268 PMCID: PMC6557678 DOI: 10.1002/ajmg.a.61183] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/11/2019] [Accepted: 04/19/2019] [Indexed: 01/15/2023]
Abstract
Cleft lip with/without cleft palate (CLP) is a common craniofacial malformation with complex etiologies, reflecting both genetic and environmental factors. Most of the suspected genetic risk for CLP has yet to be identified. To further classify risk loci and estimate the contribution of rare variants, we sequenced the exons in 49 candidate genes in 323 CLP cases and 211 nonmalformed controls. Our findings indicated that rare, protein-altering variants displayed markedly higher burdens in CLP cases at relevant loci. First, putative loss-of-function mutations (nonsense, frameshift) were significantly enriched among cases: 13 of 323 cases (~4%) harbored such alleles within these 49 genes, versus one such change in controls (p = 0.01). Second, in gene-level analyses, the burden of rare alleles showed greater case-association for several genes previously implicated in cleft risk. For example, BHMT displayed a 10-fold increase in protein-altering variants in CLP cases (p = .03), including multiple case occurrences of a rare frameshift mutation (K400 fs). Other loci with greater rare, coding allele burdens in cases were in signaling pathways relevant to craniofacial development (WNT9B, BMP4, BMPR1B) as well as the methionine cycle (MTRR). We conclude that rare coding variants may confer risk for isolated CLP.
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Affiliation(s)
- Nicholas J Marini
- California Institute for Quantitative Biosciences, Department of Molecular and Cellular Biology, University of California, Berkeley, California
| | - Kripa Asrani
- California Institute for Quantitative Biosciences, Department of Molecular and Cellular Biology, University of California, Berkeley, California
| | - Wei Yang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Jasper Rine
- California Institute for Quantitative Biosciences, Department of Molecular and Cellular Biology, University of California, Berkeley, California
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
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15
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Gonseth S, Shaw GM, Roy R, Segal MR, Asrani K, Rine J, Wiemels J, Marini NJ. Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk. Epigenetics 2019; 14:198-213. [PMID: 30870065 PMCID: PMC6557558 DOI: 10.1080/15592294.2019.1581591] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common human birth defect whose etiologies remain largely unknown. Several studies have demonstrated that periconceptional supplementation of folic acid can reduce risk of CL/P in offspring. In this study, we tested the hypothesis that the preventive effect of folic acid is manifested through epigenetic modifications by determining whether DNA methylation changes are associated with CL/P. To more readily observe the potential effects of maternal folate on the offspring epigenome, we focused on births prior to mandatory dietary folate fortification in the United States (i.e. birth year 1997 or earlier). Genomic DNA methylation levels were assessed from archived newborn bloodspots in a 182-member case-control study using the Illumina® Human Beadchip 450K array. CL/P cases displayed striking epigenome-wide hypomethylation relative to controls: 63% of CpGs interrogated had lower methylation levels in case newborns, a trend which held up in racially stratified sub-groups. 28 CpG sites reached epigenome-wide significance and all were case-hypomethylated. The most significant CL/P-associated differentially methylated region encompassed the VTRNA2-1 gene, which was also hypomethylated in cases (FWER p = 0.014). This region has been previously characterized as a nutritionally-responsive, metastable epiallele and CL/P-associated methylation changes, in general, were greater at or near putative metastable epiallelic regions. Gene Set Enrichment Analysis of CL/P-associated DMRs showed an over-representation of genes involved in palate development such as WNT9B, MIR140 and LHX8. CL/P-associated DNA methylation changes may partly explain the mechanism by which orofacial clefts are responsive to maternal folate levels.
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Affiliation(s)
- Semira Gonseth
- a School of Public Health , University of California , Berkeley , CA , USA.,b Institute of Social and Preventive Medicine , Lausanne University Hospital , Lausanne , Switzerland
| | - Gary M Shaw
- c Department of Pediatrics , Stanford University School of Medicine , Stanford , CA , USA
| | - Ritu Roy
- d Cancer Research Institute , University of California , San Francisco , CA , USA
| | - Mark R Segal
- e Department of Epidemiology and Biostatistics , University of California , San Francisco , CA , USA
| | - Kripa Asrani
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
| | - Jasper Rine
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
| | - Joseph Wiemels
- g Center for Genetic Epidemiology , University of Southern California School of Medicine , Los Angeles , CA , USA
| | - Nicholas J Marini
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
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16
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Sieverman KJ, Rine J. Impact of Homologous Recombination on Silent Chromatin in Saccharomyces cerevisiae. Genetics 2018; 208:1099-1113. [PMID: 29339409 PMCID: PMC5844325 DOI: 10.1534/genetics.118.300704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/08/2018] [Indexed: 11/18/2022] Open
Abstract
Specialized chromatin domains repress transcription of genes within them and present a barrier to many DNA-protein interactions. Silent chromatin in the budding yeast Saccharomyces cerevisiae, akin to heterochromatin of metazoans and plants, inhibits transcription of PolII- and PolIII-transcribed genes, yet somehow grants access to proteins necessary for DNA transactions like replication and homologous recombination. In this study, we adapted a novel assay to detect even transient changes in the dynamics of transcriptional silencing at HML after it served as a template for homologous recombination. Homologous recombination specifically targeted to HML via double-strand-break formation at a homologous locus often led to transient loss of transcriptional silencing at HML Interestingly, many cells could template homology-directed repair at HML without an obligate loss of silencing, even in recombination events with extensive gene conversion tracts. In a population of cells that experienced silencing loss following recombination, transcription persisted for 2-3 hr after all double-strand breaks were repaired. mRNA levels from cells that experienced recombination-induced silencing loss did not approach the amount of mRNA seen in cells lacking transcriptional silencing. Thus, silencing loss at HML after homologous recombination was short-lived and limited.
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Affiliation(s)
- Kathryn J Sieverman
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, California 94720
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17
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Asrani K, Shaw GM, Rine J, Marini NJ. DNA Methylome Profiling on the Infinium HumanMethylation450 Array from Limiting Quantities of Genomic DNA from a Single, Small Archived Bloodspot. Genet Test Mol Biomarkers 2017; 21:516-519. [PMID: 28609193 PMCID: PMC5568181 DOI: 10.1089/gtmb.2017.0019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AIMS Archived newborn bloodspots are valuable sample collections for genetic and epigenetic disease research. However, they have often been stored for long periods of time, under less than ideal circumstances, and nucleic acid yields can be low, particularly when samples become limiting. We wished to determine whether the quantity and quality of genomic DNA (gDNA) isolated from a single, surgical bloodspot punch (2 mm dia.) was adequate for accurate and reliable DNA methylome profiling on the Illumina HumanMethylation450 array. METHODS A total of 25-750 ng of archived bloodspot or Jurkat cell gDNA were bisulfite converted and analyzed on the array without any additional DNA amplification steps. Methylation profiles were assessed for call rate, call confidence (detection p-value), and reproducibility. RESULTS Using 25 ng gDNA from either Jurkat cells or dried bloodspots, array-wide call rates (∼99.9%) and detection p-values (99.9% with p < 5 × 10-6) were excellent. There was good agreement between methylation profiles generated from 25 ng gDNA and those generated from 750 ng (ρ > 0.98), although a fraction of CpG sites (2-8% depending on experiment) exhibited quantitative differences. Genome-wide methylation levels were strikingly reproducible from 25 ng DNA in both replicate and interindividual samples (ρ > 0.98). CONCLUSIONS Twenty-five nanograms of gDNA, isolated from a single, surgical punch (2 mm dia.) of an archived newborn bloodspot, generate a genome-wide methylation profile on the Illumina HumanMethylation450 array that is robust, reproducible, and suitable for differential methylation studies.
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Affiliation(s)
- Kripa Asrani
- 1 California Institute for Quantitative Biosciences, University of California , Berkeley, California
| | - Gary M Shaw
- 2 Department of Pediatrics, Stanford University School of Medicine , Stanford, California
| | - Jasper Rine
- 1 California Institute for Quantitative Biosciences, University of California , Berkeley, California
| | - Nicholas J Marini
- 1 California Institute for Quantitative Biosciences, University of California , Berkeley, California
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18
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Janke R, Iavarone AT, Rine J. Oncometabolite D-2-Hydroxyglutarate enhances gene silencing through inhibition of specific H3K36 histone demethylases. eLife 2017; 6. [PMID: 28346139 PMCID: PMC5388528 DOI: 10.7554/elife.22451] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/17/2017] [Indexed: 11/24/2022] Open
Abstract
Certain mutations affecting central metabolism cause accumulation of the oncometabolite D-2-hydroxyglutarate which promotes progression of certain tumors. High levels of D-2-hydroxyglutarate inhibit the TET family of DNA demethylases and Jumonji family of histone demethylases and cause epigenetic changes that lead to altered gene expression. The link between inhibition of DNA demethylation and changes in expression is strong in some cancers, but not in others. To determine whether D-2-hydroxyglutarate can affect gene expression through inhibiting histone demethylases, orthologous mutations to those known to cause accumulation of D-2-hydroxyglutarate in tumors were generated in Saccharomyces cerevisiae, which has histone demethylases but not DNA methylases or demethylases. Accumulation of D-2-hydroxyglutarate caused inhibition of several histone demethylases. Inhibition of two of the demethylases that act specifically on histone H3K36me2,3 led to enhanced gene silencing. These observations pinpointed a new mechanism by which this oncometabolite can alter gene expression, perhaps repressing critical inhibitors of proliferation. DOI:http://dx.doi.org/10.7554/eLife.22451.001
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Affiliation(s)
- Ryan Janke
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
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19
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Schlissel G, Krzyzanowski MK, Caudron F, Barral Y, Rine J. Aggregation of the Whi3 protein, not loss of heterochromatin, causes sterility in old yeast cells. Science 2017; 355:1184-1187. [PMID: 28302853 DOI: 10.1126/science.aaj2103] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/25/2017] [Indexed: 12/21/2022]
Abstract
In yeast, heterochromatin silencing is reported to decline in aging mother cells, causing sterility in old cells. This process is thought to reflect a decrease in the activity of the NAD+ (oxidized nicotinamide adenine dinucleotide)-dependent deacetylase Sir2. We tested whether Sir2 becomes nonfunctional gradually or precipitously during aging. Unexpectedly, silencing of the heterochromatic HML and HMR loci was not lost during aging. Old cells could initiate a mating response; however, they were less sensitive to mating pheromone than were young cells because of age-dependent aggregation of Whi3, an RNA-binding protein controlling S-phase entry. Removing the polyglutamine domain of Whi3 restored the pheromone sensitivity of old cells. We propose that aging phenotypes previously attributed to loss of heterochromatin silencing are instead caused by aggregation of the Whi3 cell cycle regulator.
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Affiliation(s)
- Gavin Schlissel
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | | | - Fabrice Caudron
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,King's College London, London, UK
| | - Yves Barral
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
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20
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McCleary DF, Steakley DL, Rine J. Sir protein-independent repair of dicentric chromosomes in Saccharomyces cerevisiae. Mol Biol Cell 2016; 27:2879-83. [PMID: 27466318 PMCID: PMC5025274 DOI: 10.1091/mbc.e16-02-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/20/2016] [Indexed: 12/02/2022] Open
Abstract
Sir2 has been reported to be recruited to dicentric chromosomes under tension, and these chromosomes are especially vulnerable to breakage in sir2Δ mutants. Loss of viability in such mutants is an indirect effect of repression of nonhomologous end joining in Sir− mutants. Enrichment of Sir2 at chromosomes under tension is not observed. Sir2 protein has been reported to be recruited to dicentric chromosomes under tension, and such chromosomes are reported to be especially vulnerable to breakage in sir2Δ mutants. We found that the loss of viability in such mutants was an indirect effect of the repression of nonhomologous end joining in Sir− mutants and that the apparent recruitment of Sir2 protein to chromosomes under tension was likely due to methodological weakness in early chromatin immunoprecipitation studies.
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Affiliation(s)
- David F McCleary
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - David Lee Steakley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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21
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Marini NJ, Yang W, Asrani K, Witte JS, Rine J, Lammer EJ, Shaw GM. Sequence variation in folate pathway genes and risks of human cleft lip with or without cleft palate. Am J Med Genet A 2016; 170:2777-2787. [PMID: 27604992 DOI: 10.1002/ajmg.a.37874] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/14/2016] [Indexed: 12/27/2022]
Abstract
In an effort to comprehensively interrogate genetic variation in the folate pathway for risk of cleft lip with or without cleft palate (CLP), we evaluated 504 common and rare variants in 35 folate-related genes in a panel of 330 infants with CLP and 367 non-malformed controls. Odds ratios (OR) with 95% confidence intervals were computed for common genotypes. A Case-Control Difference metric was calculated for rare variants to highlight differentially occurring alleles. Interactions between variants and a maternal folate intake variable were also evaluated. In gene-only results, significant odds ratios were observed for multiple variants in the BHMT/BHMT2/DMGDH gene cluster, particularly in Hispanic infants. Also in this cluster, rare variant analysis highlighted a substantial case-control difference in BHMT rs60340837 (synonymous Y284Y). In Hispanics, the ALDH1L1 I812V variant (rs4646750) was the most significant risk allele: OR = 3.8 (95%CI = 1.6-9.2) when heterozygous. In non-Hispanic white infants, we observed significant risk for AHCYL2 rs1095423 (homozygous OR = 3.0, 95%CI 1.1-7.8) and the 68 bp CBS insertion (c.844ins68; heterozygous OR = 2.4, 95%CI = 1.1-5.3). Rare variant analysis in this group revealed case-control differences in MTRR and several other methionine cycle genes, a process implicated previously in clefting risk. In women with low folate intake specifically, increased risks were observed for CBS rs2851391 (OR = 3.6, 95%CI = 1.3-9.6) and the R259P nonsynonymous variant of TCN2 (rs1801198; OR = 2.8, 95%CI = 1.2-6.3). This comprehensive study provides further direction on candidate loci to help disentangle the folate-related developmental phenomena in human clefting risk. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicholas J Marini
- Department of Molecular and Cellular Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California.
| | - Wei Yang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Kripa Asrani
- Department of Molecular and Cellular Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California
| | - John S Witte
- Department of Epidemiology and Biostatistics and Institute of Human Genetics, University of California, San Francisco, California
| | - Jasper Rine
- Department of Molecular and Cellular Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California
| | - Edward J Lammer
- UCSF Benioff Children's Hospital Oakland, Oakland, California
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
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22
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Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. GENOME ENGINEERING. The Genome Project-Write. Science 2016; 353:126-7. [PMID: 27256881 DOI: 10.1126/science.aaf6850] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We need technology and an ethical framework for genome-scale engineering
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Affiliation(s)
- Jef D Boeke
- The list of author affiliations is available in the supplementary materials.
| | - George Church
- The list of author affiliations is available in the supplementary materials.
| | - Andrew Hessel
- The list of author affiliations is available in the supplementary materials.
| | - Nancy J Kelley
- The list of author affiliations is available in the supplementary materials.
| | - Adam Arkin
- The list of author affiliations is available in the supplementary materials
| | - Yizhi Cai
- The list of author affiliations is available in the supplementary materials
| | - Rob Carlson
- The list of author affiliations is available in the supplementary materials
| | | | - Virginia W Cornish
- The list of author affiliations is available in the supplementary materials
| | - Liam Holt
- The list of author affiliations is available in the supplementary materials
| | - Farren J Isaacs
- The list of author affiliations is available in the supplementary materials
| | - Todd Kuiken
- The list of author affiliations is available in the supplementary materials
| | - Marc Lajoie
- The list of author affiliations is available in the supplementary materials
| | - Tracy Lessor
- The list of author affiliations is available in the supplementary materials
| | - Jeantine Lunshof
- The list of author affiliations is available in the supplementary materials
| | - Matthew T Maurano
- The list of author affiliations is available in the supplementary materials
| | - Leslie A Mitchell
- The list of author affiliations is available in the supplementary materials
| | - Jasper Rine
- The list of author affiliations is available in the supplementary materials
| | - Susan Rosser
- The list of author affiliations is available in the supplementary materials
| | - Neville E Sanjana
- The list of author affiliations is available in the supplementary materials
| | - Pamela A Silver
- The list of author affiliations is available in the supplementary materials
| | - David Valle
- The list of author affiliations is available in the supplementary materials
| | - Harris Wang
- The list of author affiliations is available in the supplementary materials
| | - Jeffrey C Way
- The list of author affiliations is available in the supplementary materials
| | - Luhan Yang
- The list of author affiliations is available in the supplementary materials
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23
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Ellahi A, Rine J. Evolution and Functional Trajectory of Sir1 in Gene Silencing. Mol Cell Biol 2016; 36:1164-79. [PMID: 26811328 PMCID: PMC4800792 DOI: 10.1128/mcb.01013-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/08/2015] [Accepted: 01/21/2016] [Indexed: 01/28/2023] Open
Abstract
We used the budding yeasts Saccharomyces cerevisiae and Torulaspora delbrueckii to examine the evolution of Sir-based silencing, focusing on Sir1, silencers, the molecular topography of silenced chromatin, and the roles of SIR and RNA interference (RNAi) genes in T. delbrueckii. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) analysis of Sir proteins in T. delbrueckii revealed a different topography of chromatin at the HML and HMR loci than was observed in S. cerevisiae. S. cerevisiae Sir1, enriched at the silencers of HMLα and HMR A: , was absent from telomeres and did not repress subtelomeric genes. In contrast to S. cerevisiae SIR1's partially dispensable role in silencing, the T. delbrueckii SIR1 paralog KOS3 was essential for silencing. KOS3 was also found at telomeres with T. delbrueckii Sir2 (Td-Sir2) and Td-Sir4 and repressed subtelomeric genes. Silencer mapping in T. delbrueckii revealed single silencers at HML and HMR, bound by Td-Kos3, Td-Sir2, and Td-Sir4. The KOS3 gene mapped near HMR, and its expression was regulated by Sir-based silencing, providing feedback regulation of a silencing protein by silencing. In contrast to the prominent role of Sir proteins in silencing, T. delbrueckii RNAi genes AGO1 and DCR1 did not function in heterochromatin formation. These results highlighted the shifting role of silencing genes and the diverse chromatin architectures underlying heterochromatin.
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Affiliation(s)
- Aisha Ellahi
- Department of Molecular and Cell Biology and California Institute of Quantitative Biology, University of California Berkeley, Berkeley, California, USA
| | - Jasper Rine
- Department of Molecular and Cell Biology and California Institute of Quantitative Biology, University of California Berkeley, Berkeley, California, USA
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24
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Abstract
Epigenetic mechanisms by which cells inherit information are, to a large extent, enabled by DNA methylation and posttranslational modifications of histone proteins. These modifications operate both to influence the structure of chromatin per se and to serve as recognition elements for proteins with motifs dedicated to binding particular modifications. Each of these modifications results from an enzyme that consumes one of several important metabolites during catalysis. Likewise, the removal of these marks often results in the consumption of a different metabolite. Therefore, these so-called epigenetic marks have the capacity to integrate the expression state of chromatin with the metabolic state of the cell. This review focuses on the central roles played by acetyl-CoA, S-adenosyl methionine, NAD(+), and a growing list of other acyl-CoA derivatives in epigenetic processes. We also review how metabolites that accumulate as a result of oncogenic mutations are thought to subvert the epigenetic program.
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Affiliation(s)
- Ryan Janke
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Anne E Dodson
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
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25
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Abstract
Multiple mechanisms have been proposed for gene silencing in Saccharomyces cerevisiae, ranging from steric occlusion of DNA binding proteins from their recognition sequences in silenced chromatin to a specific block in the formation of the preinitiation complex to a block in transcriptional elongation. This study provided strong support for the steric occlusion mechanism by the discovery that RNA polymerase of bacteriophage T7 could be substantially blocked from transcribing from its cognate promoter when embedded in silenced chromatin. Moreover, unlike previous suggestions, we found no evidence for stalled RNA polymerase II within silenced chromatin. The effectiveness of the Sir protein-based silencing mechanism to block transcription activated by Gal4 at promoters in the domain of silenced chromatin was marginal, yet it improved when tested against mutant forms of the Gal4 protein, highlighting a role for specific activators in their sensitivity to gene silencing.
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Affiliation(s)
- David Lee Steakley
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, Stanley Hall, University of California Berkeley, Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, Stanley Hall, University of California Berkeley, Berkeley, California 94720
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Ellahi A, Thurtle DM, Rine J. The Chromatin and Transcriptional Landscape of Native Saccharomyces cerevisiae Telomeres and Subtelomeric Domains. Genetics 2015; 200:505-21. [PMID: 25823445 PMCID: PMC4492376 DOI: 10.1534/genetics.115.175711] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 03/22/2015] [Indexed: 12/18/2022] Open
Abstract
Saccharomyces cerevisiae telomeres have been a paradigm for studying telomere position effects on gene expression. Telomere position effect was first described in yeast by its effect on the expression of reporter genes inserted adjacent to truncated telomeres. The reporter genes showed variable silencing that depended on the Sir2/3/4 complex. Later studies examining subtelomeric reporter genes inserted at natural telomeres hinted that telomere position effects were less pervasive than previously thought. Additionally, more recent data using the sensitive technology of chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) revealed a discrete and noncontinuous pattern of coenrichment for all three Sir proteins at a few telomeres, calling the generality of these conclusions into question. Here we combined the ChIP-Seq of the Sir proteins with RNA sequencing (RNA-Seq) of messenger RNAs (mRNAs) in wild-type and in SIR2, SIR3, and SIR4 deletion mutants to characterize the chromatin and transcriptional landscape of all native S. cerevisiae telomeres at the highest achievable resolution. Most S. cerevisiae chromosomes had subtelomeric genes that were expressed, with only ∼6% of subtelomeric genes silenced in a SIR-dependent manner. In addition, we uncovered 29 genes with previously unknown cell-type-specific patterns of expression. These detailed data provided a comprehensive assessment of the chromatin and transcriptional landscape of the subtelomeric domains of a eukaryotic genome.
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Affiliation(s)
- Aisha Ellahi
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720
| | - Deborah M Thurtle
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720
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Abstract
Heterochromatin exerts a heritable form of eukaryotic gene repression and contributes to chromosome segregation fidelity and genome stability. However, to date there has been no quantitative evaluation of the stability of heterochromatic gene repression. We designed a genetic strategy to capture transient losses of gene silencing in Saccharomyces as permanent, heritable changes in genotype and phenotype. This approach revealed rare transcription within heterochromatin that occurred in approximately 1/1000 cell divisions. In concordance with multiple lines of evidence suggesting these events were rare and transient, single-molecule RNA FISH showed that transcription was limited. The ability to monitor fluctuations in heterochromatic repression uncovered previously unappreciated roles for Sir1, a silencing establishment factor, in the maintenance and/or inheritance of silencing. In addition, we identified the sirtuin Hst3 and its histone target as contributors to the stability of the silenced state. These approaches revealed dynamics of a heterochromatin function that have been heretofore inaccessible.
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Affiliation(s)
- Anne E Dodson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
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28
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Abstract
Changes in technology are fundamentally reframing our concept of what constitutes a model organism. Nevertheless, research advances in the more traditional model organisms have enabled fresh and exciting opportunities for young scientists to establish new careers and offer the hope of comprehensive understanding of fundamental processes in life. New advances in translational research can be expected to heighten the importance of basic research in model organisms and expand opportunities. However, researchers must take special care and implement new resources to enable the newest members of the community to engage fully with the remarkable legacy of information in these fields.
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Affiliation(s)
- Jasper Rine
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3220
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Abstract
Heterochromatin imparts regional, promoter-independent repression of genes and is epigenetically heritable. Understanding how silencing achieves this regional repression is a fundamental problem in genetics and development. Current models of yeast silencing posit that Sir proteins, recruited by transcription factors bound to the silencers, spread throughout the silenced region. To test this model directly at high resolution, we probed the silenced chromatin architecture by chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-seq) of Sir proteins, histones, and a key histone modification, H4K16-acetyl. These analyses revealed that Sir proteins are strikingly concentrated at and immediately adjacent to the silencers, with lower levels of enrichment over the promoters at HML and HMR, the critical targets for transcriptional repression. The telomeres also showed discrete peaks of Sir enrichment yet a continuous domain of hypoacetylated histone H4K16. Surprisingly, ChIP-seq of cross-linked chromatin revealed a distribution of nucleosomes at silenced loci that was similar to Sir proteins, whereas native nucleosome maps showed a regular distribution throughout silenced loci, indicating that cross-linking captured a specialized chromatin organization imposed by Sir proteins. This specialized chromatin architecture observed in yeast informs the importance of a steric contribution to regional repression in other organisms.
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Affiliation(s)
- Deborah M Thurtle
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
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Abstract
Genes in Saccharomyces cerevisiae involved in sulfur-containing amino acid synthesis are transcriptionally induced by either cysteine or S-adenosyl-methionine deficiency, as well as defects in phosphatidylcholine synthesis. Met30p, a regulator of these genes, changes physically in inducing conditions, which may mediate its regulatory activity. In Saccharomyces cerevisiae, transcription of the MET regulon, which encodes the proteins involved in the synthesis of the sulfur-containing amino acids methionine and cysteine, is repressed by the presence of either methionine or cysteine in the environment. This repression is accomplished by ubiquitination of the transcription factor Met4, which is carried out by the SCF(Met30) E3 ubiquitin ligase. Mutants defective in MET regulon repression reveal that loss of Cho2, which is required for the methylation of phosphatidylethanolamine to produce phosphatidylcholine, leads to induction of the MET regulon. This induction is due to reduced cysteine synthesis caused by the Cho2 defects, uncovering an important link between phospholipid synthesis and cysteine synthesis. Antimorphic mutants in S-adenosyl-methionine (SAM) synthetase genes also induce the MET regulon. This effect is due, at least in part, to SAM deficiency controlling the MET regulon independently of SAM's contribution to cysteine synthesis. Finally, the Met30 protein is found in two distinct forms whose relative abundance is controlled by the availability of sulfur-containing amino acids. This modification could be involved in the nutritional control of SCF(Met30) activity toward Met4.
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Affiliation(s)
- Meru J Sadhu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - Anjali D Zimmer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
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Sadhu MJ, Guan Q, Li F, Sales-Lee J, Iavarone AT, Hammond MC, Cande WZ, Rine J. Nutritional control of epigenetic processes in yeast and human cells. Genetics 2013; 195:831-44. [PMID: 23979574 PMCID: PMC3813867 DOI: 10.1534/genetics.113.153981] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 08/12/2013] [Indexed: 02/02/2023] Open
Abstract
The vitamin folate is required for methionine homeostasis in all organisms. In addition to its role in protein synthesis, methionine is the precursor to S-adenosyl-methionine (SAM), which is used in myriad cellular methylation reactions, including all histone methylation reactions. Here, we demonstrate that folate and methionine deficiency led to reduced methylation of lysine 4 of histone H3 (H3K4) in Saccharomyces cerevisiae. The effect of nutritional deficiency on H3K79 methylation was less pronounced, but was exacerbated in S. cerevisiae carrying a hypomorphic allele of Dot1, the enzyme responsible for H3K79 methylation. This result suggested a hierarchy of epigenetic modifications in terms of their susceptibility to nutritional limitations. Folate deficiency caused changes in gene transcription that mirrored the effect of complete loss of H3K4 methylation. Histone methylation was also found to respond to nutritional deficiency in the fission yeast Schizosaccharomyces pombe and in human cells in culture.
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Affiliation(s)
- Meru J. Sadhu
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
| | - Qiaoning Guan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
| | - Fei Li
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
| | - Jade Sales-Lee
- Department of Chemistry, University of California, Berkeley, California 94720-3220
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
| | - Ming C. Hammond
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
- Department of Chemistry, University of California, Berkeley, California 94720-3220
| | - W. Zacheus Cande
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
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Zunder RM, Antczak AJ, Berger JM, Rine J. Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing. Proc Natl Acad Sci U S A 2012; 109:E144-53. [PMID: 22198837 PMCID: PMC3271894 DOI: 10.1073/pnas.1119095109] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The histone chaperone Rtt106 binds histone H3 acetylated at lysine 56 (H3K56ac) and facilitates nucleosome assembly during several molecular processes. Both the structural basis of this modification-specific recognition and how this recognition informs Rtt106 function are presently unclear. Guided by our crystal structure of Rtt106, we identified two regions on its double-pleckstrin homology domain architecture that mediated histone binding. When histone binding was compromised, Rtt106 localized properly to chromatin but failed to deliver H3K56ac, leading to replication and silencing defects. By mutating analogous regions in the structurally homologous chromatin-reorganizer Pob3, we revealed a conserved histone-binding function for a basic patch found on both proteins. In contrast, a loop connecting two β-strands was required for histone binding by Rtt106 but was dispensable for Pob3 function. Unlike Rtt106, Pob3 histone binding was modification-independent, implicating the loop of Rtt106 in H3K56ac-specific recognition in vivo. Our studies described the structural origins of Rtt106 function, identified a conserved histone-binding surface, and defined a critical role for Rtt106:H3K56ac-binding specificity in silencing and replication-coupled nucleosome turnover.
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Affiliation(s)
- Rachel M. Zunder
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Andrew J. Antczak
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - James M. Berger
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
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Marini NJ, Hoffmann TJ, Lammer EJ, Hardin J, Lazaruk K, Stein JB, Gilbert DA, Wright C, Lipzen A, Pennacchio LA, Carmichael SL, Witte JS, Shaw GM, Rine J. A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis. PLoS One 2011; 6:e28408. [PMID: 22140583 PMCID: PMC3227667 DOI: 10.1371/journal.pone.0028408] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 11/07/2011] [Indexed: 12/16/2022] Open
Abstract
Despite compelling epidemiological evidence that folic acid supplements reduce the frequency of neural tube defects (NTDs) in newborns, common variant association studies with folate metabolism genes have failed to explain the majority of NTD risk. The contribution of rare alleles as well as genetic interactions within the folate pathway have not been extensively studied in the context of NTDs. Thus, we sequenced the exons in 31 folate-related genes in a 480-member NTD case-control population to identify the full spectrum of allelic variation and determine whether rare alleles or obvious genetic interactions within this pathway affect NTD risk. We constructed a pathway model, predetermined independent of the data, which grouped genes into coherent sets reflecting the distinct metabolic compartments in the folate/one-carbon pathway (purine synthesis, pyrimidine synthesis, and homocysteine recycling to methionine). By integrating multiple variants based on these groupings, we uncovered two provocative, complex genetic risk signatures. Interestingly, these signatures differed by race/ethnicity: a Hispanic risk profile pointed to alterations in purine biosynthesis, whereas that in non-Hispanic whites implicated homocysteine metabolism. In contrast, parallel analyses that focused on individual alleles, or individual genes, as the units by which to assign risk revealed no compelling associations. These results suggest that the ability to layer pathway relationships onto clinical variant data can be uniquely informative for identifying genetic risk as well as for generating mechanistic hypotheses. Furthermore, the identification of ethnic-specific risk signatures for spina bifida resonated with epidemiological data suggesting that the underlying pathogenesis may differ between Hispanic and non-Hispanic groups.
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Affiliation(s)
- Nicholas J. Marini
- Department of Molecular and Cellular Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- * E-mail: (NJM); (JR)
| | - Thomas J. Hoffmann
- Department of Epidemiology and Biostatistics and Institute of Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Edward J. Lammer
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Jill Hardin
- VitaPath Genetics, Inc., Foster City, California, United States of America
| | - Katherine Lazaruk
- VitaPath Genetics, Inc., Foster City, California, United States of America
| | - Jason B. Stein
- VitaPath Genetics, Inc., Foster City, California, United States of America
| | - Dennis A. Gilbert
- VitaPath Genetics, Inc., Foster City, California, United States of America
| | - Crystal Wright
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Len A. Pennacchio
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Suzan L. Carmichael
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - John S. Witte
- Department of Epidemiology and Biostatistics and Institute of Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jasper Rine
- Department of Molecular and Cellular Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- * E-mail: (NJM); (JR)
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Anderson WA, Amasino RM, Ares M, Banerjee U, Bartel B, Corces VG, Drennan CL, Elgin SCR, Epstein IR, Fanning E, Guillette LJ, Handelsman J, Hatfull GF, Hoy RR, Kelley D, Leinwand LA, Losick R, Lu Y, Lynn DG, Neuhauser C, O'Dowd DK, Olivera T, Pevzner P, Richards-Kortum RR, Rine J, Sah RL, Strobel SA, Walker GC, Walt DR, Warner IM, Wessler S, Willard HF, Zare RN. Competencies: a cure for pre-med curriculum. Science 2011; 334:760-1. [PMID: 22076362 DOI: 10.1126/science.334.6057.760-b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Osborne EA, Hiraoka Y, Rine J. Symmetry, asymmetry, and kinetics of silencing establishment in Saccharomyces cerevisiae revealed by single-cell optical assays. Proc Natl Acad Sci U S A 2011; 108:1209-16. [PMID: 21262833 PMCID: PMC3029714 DOI: 10.1073/pnas.1018742108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Saccharomyces cerevisiae, silent chromatin inhibits the expression of genes at the HML, HMR, and telomeric loci. When silent chromatin forms de novo, the rate of its establishment is influenced by different chromatin states. In particular, loss of the enzyme Dot1, an H3 K79 methyltransferase, leads to rapid silencing establishment. We tested whether silencing establishment was antagonized by H3 K79 methylation or by the Dot1 protein itself competing with Sir3 for binding sites on nucleosomes. To do so, we monitored fluorescence activity in cells containing a GFP gene within the HML locus during silencing establishment in a series of dot1 and histone mutant backgrounds. Silencing establishment rate was correlated with Dot1's enzymatic function rather than with the Dot1 protein itself. In addition, histone mutants that mimicked the conformation of unmethylated H3 K79 increased the rate of silencing establishment, indicating that the H3 K79 residue affected silencing independently of Dot1 abundance. Using fluorophore-based reporters, we confirmed that mother and daughter cells often silence in concert, but in instances where asymmetric silencing occurs, daughter cells established silencing earlier than their mothers. This noninvasive technique enabled us to demonstrate an asymmetry in silencing establishment of a key regulatory locus controlling cell fate.
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Affiliation(s)
- Erin A. Osborne
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
- Kobe Advanced Information and Communication Technology Research Center, National Institute of Information and Communications Technology, Kobe, Japan; and
| | - Jasper Rine
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720-3220
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Zill OA, Scannell D, Teytelman L, Rine J. Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol 2010; 8:e1000550. [PMID: 21151344 PMCID: PMC2994660 DOI: 10.1371/journal.pbio.1000550] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 10/18/2010] [Indexed: 01/18/2023] Open
Abstract
Co-evolution of transcriptional regulatory proteins and their sites of action has been often hypothesized but rarely demonstrated. Here we provide experimental evidence of such co-evolution in yeast silent chromatin, a finding that emerged from studies of hybrids formed between two closely related Saccharomyces species. A unidirectional silencing incompatibility between S. cerevisiae and S. bayanus led to a key discovery: asymmetrical complementation of divergent orthologs of the silent chromatin component Sir4. In S. cerevisiae/S. bayanus interspecies hybrids, ChIP-Seq analysis revealed a restriction against S. cerevisiae Sir4 associating with most S. bayanus silenced regions; in contrast, S. bayanus Sir4 associated with S. cerevisiae silenced loci to an even greater degree than did S. cerevisiae's own Sir4. Functional changes in silencer sequences paralleled changes in Sir4 sequence and a reduction in Sir1 family members in S. cerevisiae. Critically, species-specific silencing of the S. bayanus HMR locus could be reconstituted in S. cerevisiae by co-transfer of the S. bayanus Sir4 and Kos3 (the ancestral relative of Sir1) proteins. As Sir1/Kos3 and Sir4 bind conserved silencer-binding proteins, but not specific DNA sequences, these rapidly evolving proteins served to interpret differences in the two species' silencers presumably involving emergent features created by the regulatory proteins that bind sequences within silencers. The results presented here, and in particular the high resolution ChIP-Seq localization of the Sir4 protein, provided unanticipated insights into the mechanism of silent chromatin assembly in yeast.
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Affiliation(s)
- Oliver A. Zill
- Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California–Berkeley, Berkeley, California, United States of America
- * E-mail: (JR); (OAZ)
| | - Devin Scannell
- Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California–Berkeley, Berkeley, California, United States of America
| | - Leonid Teytelman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Jasper Rine
- Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California–Berkeley, Berkeley, California, United States of America
- * E-mail: (JR); (OAZ)
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Halley JE, Kaplan T, Wang AY, Kobor MS, Rine J. Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory. PLoS Biol 2010; 8:e1000401. [PMID: 20582323 PMCID: PMC2889906 DOI: 10.1371/journal.pbio.1000401] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 05/13/2010] [Indexed: 12/23/2022] Open
Abstract
H2A.Z does not appear to have a role in GAL1 transcriptional memory, but it does have both acetylation-dependent and acetylation-independent roles in GAL1 induction and expression. H2A.Z is a histone H2A variant conserved from yeast to humans, and is found at 63% of promoters in Saccharomyces cerevisiae. This pattern of localization suggests that H2A.Z is somehow important for gene expression or regulation. H2A.Z can be acetylated at up to four lysine residues on its amino-terminal tail, and acetylated-H2A.Z is enriched in chromatin containing promoters of active genes. We investigated whether H2A.Z's role in GAL1 gene regulation and gene expression depends on H2A.Z acetylation. Our findings suggested that H2A.Z functioned both in gene regulation and in gene expression and that only its role in gene regulation depended upon its acetylation. Our findings provided an alternate explanation for results that were previously interpreted as evidence that H2A.Z plays a role in GAL1 transcriptional memory. Additionally, our findings provided new insights into the phenotypes of htz1Δ mutants: in the absence of H2A.Z, the SWR1 complex, which deposits H2A.Z into chromatin, was deleterious to the cell, and many of the phenotypes of cells lacking H2A.Z were due to the SWR1 complex's activity rather than to the absence of H2A.Z per se. These results highlight the need to reevaluate all studies on the phenotypes of cells lacking H2A.Z. Transcriptional memory is the well-documented phenomenon by which cells can “remember” prior transcriptional states. A paradigmatic example of transcriptional memory is found in the yeast Saccharomyces. S. cerevisiae remembers prior transcription of the galactose metabolism gene GAL1. When a gene is transcribed, the DNA must first be at least partially relieved of its packaging into chromatin by histone proteins. Previous research had suggested that S. cerevisiae used a chromatin modification, the incorporation of the histone variant H2A.Z into the region surrounding the GAL1 promoter, to remember the previous status of GAL1 transcription. Not all H2A.Z molecules are the same, however. For example, it has recently been discovered that H2A.Z can be acetylated on the four lysine residues in its N-terminal tail region. In an attempt to determine whether H2A.Z acetylation is required for GAL1 transcriptional memory, we unexpectedly discovered that, although both H2A.Z and H2A.Z acetylation are important for strong and rapid GAL1 induction, neither H2A.Z nor H2A.Z acetylation plays an important role in GAL1 transcriptional memory. We propose that the discrepancy between our conclusions and those in prior publications arise from the prior analysis of insufficiently short periods of GAL1 induction or from complications arising from the comparison of the phenotypes of wild-type yeast strains to those of htz1Δ mutants (carrying the null mutation of the gene encoding H2A.Z) mutants. In the current work we show that the htz1Δ mutant's phenotype does not simply reflect the absence of H2A.Z in chromatin but instead also reflects the pleiotropic effects of the Swr1 chromatin remodeling complex that is responsible for H2A.Z deposition into chromatin. In the absence of H2A.Z the Swr1 complex itself causes cell damage. In this paper we show that swr1Δ htz1Δ double mutants have substantially less severe mutant phenotypes than htz1Δ mutants. Thus, studies using the swr1Δ htz1Δ mutant offer more detailed insight into the consequences of the absence of H2A.Z in chromatin than do studies performed on single htz1Δ mutants, and our results help to clarify the role of H2A.Z in the regulation of GAL1 induction and transcriptional memory.
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Affiliation(s)
- Jeffrey E. Halley
- Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States
| | - Tommy Kaplan
- Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States
| | - Alice Y. Wang
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S. Kobor
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jasper Rine
- Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States
- * E-mail:
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38
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Marini NJ, Thomas PD, Rine J. The use of orthologous sequences to predict the impact of amino acid substitutions on protein function. PLoS Genet 2010; 6:e1000968. [PMID: 20523748 PMCID: PMC2877731 DOI: 10.1371/journal.pgen.1000968] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 04/22/2010] [Indexed: 12/01/2022] Open
Abstract
Computational predictions of the functional impact of genetic variation play a critical role in human genetics research. For nonsynonymous coding variants, most prediction algorithms make use of patterns of amino acid substitutions observed among homologous proteins at a given site. In particular, substitutions observed in orthologous proteins from other species are often assumed to be tolerated in the human protein as well. We examined this assumption by evaluating a panel of nonsynonymous mutants of a prototypical human enzyme, methylenetetrahydrofolate reductase (MTHFR), in a yeast cell-based functional assay. As expected, substitutions in human MTHFR at sites that are well-conserved across distant orthologs result in an impaired enzyme, while substitutions present in recently diverged sequences (including a 9-site mutant that “resurrects” the human-macaque ancestor) result in a functional enzyme. We also interrogated 30 sites with varying degrees of conservation by creating substitutions in the human enzyme that are accepted in at least one ortholog of MTHFR. Quite surprisingly, most of these substitutions were deleterious to the human enzyme. The results suggest that selective constraints vary between phylogenetic lineages such that inclusion of distant orthologs to infer selective pressures on the human enzyme may be misleading. We propose that homologous proteins are best used to reconstruct ancestral sequences and infer amino acid conservation among only direct lineal ancestors of a particular protein. We show that such an “ancestral site preservation” measure outperforms other prediction methods, not only in our selected set for MTHFR, but also in an exhaustive set of E. coli LacI mutants. The rapid pace of technological advances in DNA sequencing methods is leading to the discovery of genetic variants at a remarkable rate. Indeed, it is conceivable that entire individual genomes will be sequenced routinely in the near future. While these platforms greatly increase our ability to catalog variation, they are also creating a downstream need to efficiently process and filter this information to ultimately identify genetic causes underlying human disease. Since empirical evaluation of the biological effects of mutation is not practical at such a scale, computational methods that predict such effects are needed. In this paper, we describe a novel methodology to predict whether mutations that lead to amino acid substitutions in proteins will impact protein function and, therefore, may be more likely to have physiological consequences. Specifically, we use orthologous proteins to reconstruct the likely sequences of ancestral proteins in the human lineage. We found that the longer a position has been preserved from direct ancestors in the lineage leading to the human enzyme, the more likely that mutation at that site will have a deleterious effect. We demonstrated that the method should be generally applicable to all proteins.
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Affiliation(s)
- Nicholas J. Marini
- California Institute for Quantitative Biosciences, Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail: (NJM); (PDT)
| | - Paul D. Thomas
- Evolutionary Systems Biology Group, SRI International, Menlo Park, California, United States of America
- * E-mail: (NJM); (PDT)
| | - Jasper Rine
- California Institute for Quantitative Biosciences, Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America
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DeAngelo DJ, Tefferi A, Mesa RA, Paley CS, Wadleigh M, Snyder D, Ondovik MS, Rine J, Bhalla KN. A phase II trial of oral panobinostat (LBH589), a novel deacetylase inhibitor (DACi) in patients with primary myelofibrosis (PMF), post-essential thrombocythemia (ET) myelofibrosis, and post-polycythemia vera (PV) myelofibrosis. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.tps283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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40
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Rusche LN, Rine J. Switching the mechanism of mating type switching: a domesticated transposase supplants a domesticated homing endonuclease. Genes Dev 2010; 24:10-4. [PMID: 20047997 DOI: 10.1101/gad.1886310] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Programmed DNA rearrangements are critical for the development of many organisms and, intriguingly, can be catalyzed by domesticated mobile genetic elements. In this issue of Genes & Development, Barsoum and colleagues (pp. 33-44) demonstrate that, in the budding yeast Kluyveromyces lactis, a DNA rearrangement associated with mating type switching requires a domesticated transposase and occurs through a mechanism distinct from that in the related yeast, Saccharomyces cerevisiae. Thus, mechanisms for mating type switching have evolved multiple times, indicating the relative ease with which mobile genetic elements can be captured.
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Affiliation(s)
- Laura N Rusche
- Institute for Genome Sciences and Policy, and Biochemistry Department, Duke University, Durham, North Carolina 27708, USA
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41
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Teytelman L, Özaydın B, Zill O, Lefrançois P, Snyder M, Rine J, Eisen MB. Impact of chromatin structures on DNA processing for genomic analyses. PLoS One 2009; 4:e6700. [PMID: 19693276 PMCID: PMC2725323 DOI: 10.1371/journal.pone.0006700] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 07/31/2009] [Indexed: 11/25/2022] Open
Abstract
Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP) experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome.
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Affiliation(s)
- Leonid Teytelman
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, United States of America
| | - Bilge Özaydın
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, United States of America
| | - Oliver Zill
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, United States of America
| | - Philippe Lefrançois
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Michael Snyder
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jasper Rine
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, United States of America
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- * E-mail:
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Teytelman L, Eisen MB, Rine J. Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts. PLoS Genet 2008; 4:e1000247. [PMID: 18989454 PMCID: PMC2570616 DOI: 10.1371/journal.pgen.1000247] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 10/01/2008] [Indexed: 01/06/2023] Open
Abstract
Subtelomeric DNA in budding yeasts, like metazoan heterochromatin, is gene poor, repetitive, transiently silenced, and highly dynamic. The rapid evolution of subtelomeric regions is commonly thought to arise from transposon activity and increased recombination between repetitive elements. However, we found evidence of an additional factor in this diversification. We observed a surprising level of nucleotide divergence in transcriptionally silenced regions in inter-species comparisons of Saccharomyces yeasts. Likewise, intra-species analysis of polymorphisms also revealed increased SNP frequencies in both intergenic and synonymous coding positions of silenced DNA. This analysis suggested that silenced DNA in Saccharomyces cerevisiae and closely related species had increased single base-pair substitution that was likely due to the effects of the silencing machinery on DNA replication or repair. Many plants, fungi, pathogens, and animals have chromosome regions that are silenced. Special proteins change the chromosome structure in these domains, turning genes off or lowering their expression levels. We found an increased frequency of DNA mutations in these silenced regions of closely related yeasts. This increase is likely due to silencing proteins interfering with DNA repair or replication. Accurate replication of genetic information with minimal mutations is usually critical for the survival and fitness of an organism; however, there are examples where a high mutation rate is beneficial. The silenced regions of chromosomes are often associated with virus-like transposable elements, and with genes that are important in responding to environmental changes. Hence, it is possible that elevated DNA mutations in silenced regions contribute to genome defense against transposable elements or increased genetic diversity to cope with variation in surrounding conditions.
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Affiliation(s)
- Leonid Teytelman
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Michael B. Eisen
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, Berkeley, California, United States of America
- Center for Integrative Genomics, University of California Berkeley, Berkeley, California, United States of America
| | - Jasper Rine
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, Berkeley, California, United States of America
- * E-mail:
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43
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Chao LY, Rine J, Marletta MA. Spectroscopic and kinetic studies of Nor1, a cytochrome P450 nitric oxide reductase from the fungal pathogen Histoplasma capsulatum. Arch Biochem Biophys 2008; 480:132-7. [PMID: 18804446 DOI: 10.1016/j.abb.2008.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2008] [Revised: 09/05/2008] [Accepted: 09/05/2008] [Indexed: 10/21/2022]
Abstract
The fungal respiratory pathogen Histoplasma capsulatum evades the innate immune response and colonizes macrophages during infection. Although macrophage production of the antimicrobial effector nitric oxide (NO) restricts H. capsulatum growth, the pathogen is able to establish a persistent infection. H. capsulatum contains a P450 nitric oxide reductase homologue (NOR1) that may be important for detoxifying NO during infection. To characterize the activity of this putative P450 enzyme, a 404 amino acid fragment of Nor1p was expressed in Escherichia coli and purified to homogeneity. Spectral characterization of Nor1p indicated that it was similar to other fungal P450 nitric oxide reductases. Nor1p catalyzed the reduction of NO to N2O using NADH as the direct reductant. The K(M) for NO was determined to be 20 microM and the k(cat) to be 5000 min(-1). Together, these results provide evidence for a protective role of a P450 nitric oxide reductase against macrophage-derived NO.
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Affiliation(s)
- Lily Y Chao
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Abstract
The mating-type determination circuit in Saccharomyces yeast serves as a classic paradigm for the genetic control of cell type in all eukaryotes. Using comparative genetics, we discovered a central and conserved, yet previously undetected, component of this genetic circuit: active repression of alpha-specific genes in a cells. Upon inactivation of the SUM1 gene in Saccharomyces bayanus, a close relative of Saccharomyces cerevisiae, a cells acquired mating characteristics of alpha cells and displayed autocrine activation of their mating response pathway. Sum1 protein bound to the promoters of alpha-specific genes, repressing their transcription. In contrast to the standard model, alpha1 was important but not required for alpha-specific gene activation and mating of alpha cells in the absence of Sum1. Neither Sum1 protein expression, nor its association with target promoters was mating-type-regulated. Thus, the alpha1/Mcm1 coactivators did not overcome repression by occluding Sum1 binding to DNA. Surprisingly, the mating-type regulatory function of Sum1 was conserved in S. cerevisiae. We suggest that a comprehensive understanding of some genetic pathways may be best attained through the expanded phenotypic space provided by study of those pathways in multiple related organisms.
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Affiliation(s)
- Oliver A Zill
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
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45
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Chao LY, Marletta MA, Rine J. Sre1, an Iron-Modulated GATA DNA-Binding Protein of Iron-Uptake Genes in the Fungal Pathogen Histoplasma capsulatum. Biochemistry 2008; 47:7274-83. [DOI: 10.1021/bi800066s] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lily Y. Chao
- Department of Molecular and Cell Biology, Department of Chemistry, Department of Plant and Microbial Biology, California Institute for Quantitative Biosciences, and Division of Physical Biosciences, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720-3220
| | - Michael A. Marletta
- Department of Molecular and Cell Biology, Department of Chemistry, Department of Plant and Microbial Biology, California Institute for Quantitative Biosciences, and Division of Physical Biosciences, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720-3220
| | - Jasper Rine
- Department of Molecular and Cell Biology, Department of Chemistry, Department of Plant and Microbial Biology, California Institute for Quantitative Biosciences, and Division of Physical Biosciences, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720-3220
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46
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Hwang LH, Mayfield JA, Rine J, Sil A. Histoplasma requires SID1, a member of an iron-regulated siderophore gene cluster, for host colonization. PLoS Pathog 2008; 4:e1000044. [PMID: 18404210 PMCID: PMC2275787 DOI: 10.1371/journal.ppat.1000044] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 03/13/2008] [Indexed: 11/26/2022] Open
Abstract
The macrophage is the primary host cell for the fungal pathogen Histoplasma capsulatum during mammalian infections, yet little is known about fungal genes required for intracellular replication in the host. Since the ability to scavenge iron from the host is important for the virulence of most pathogens, we investigated the role of iron acquisition in H. capsulatum pathogenesis. H. capsulatum acquires iron through the action of ferric reductases and the production of siderophores, but the genes responsible for these activities and their role in virulence have not been determined. We identified a discrete set of co-regulated genes whose transcription is induced under low iron conditions. These genes all appeared to be involved in the synthesis, secretion, and utilization of siderophores. Surprisingly, the majority of these transcriptionally co-regulated genes were found clustered adjacent to each other in the genome of the three sequenced strains of H. capsulatum, suggesting that their proximity might foster coordinate gene regulation. Additionally, we identified a consensus sequence in the promoters of all of these genes that may contribute to iron-regulated gene expression. The gene set included L-ornithine monooxygenase (SID1), the enzyme that catalyzes the first committed step in siderophore production in other fungi. Disruption of SID1 by allelic replacement resulted in poor growth under low iron conditions, as well as a loss of siderophore production. Strains deficient in SID1 showed a significant growth defect in murine bone-marrow-derived macrophages and attenuation in the mouse model of infection. These data indicated that H. capsulatum utilizes siderophores in addition to other iron acquisition mechanisms for optimal growth during infection. Fungal infections are a growing public health threat, particularly for immunocompromised individuals such as people with AIDS, organ transplant recipients, and cancer patients. Present antifungal therapies are often highly toxic and resistance to these therapies continues to rise. Histoplasma capsulatum is a pathogenic fungus that infects humans, causing pulmonary and systemic disease. It is the most common cause of fungal respiratory infection in the world, and is endemic to the Mississippi and Ohio River valleys of the United States. H. capsulatum produces small molecules, called siderophores, to acquire iron, an essential nutrient. We have identified genes that are involved in the synthesis of siderophores in this fungus and have found that siderophore production in H. capsulatum is important for its virulence. Since siderophore production is confined to microbes and plays no role in human biology, it is an excellent target for rational drug design.
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Affiliation(s)
- Lena H. Hwang
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Jacob A. Mayfield
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, United States of America
| | - Jasper Rine
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, United States of America
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- * E-mail:
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Suter B, Pogoutse O, Guo X, Krogan N, Lewis P, Greenblatt JF, Rine J, Emili A. Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p. BMC Biol 2007; 5:38. [PMID: 17880717 PMCID: PMC2140264 DOI: 10.1186/1741-7007-5-38] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Accepted: 09/19/2007] [Indexed: 12/04/2022] Open
Abstract
Background Histone modifications have been implicated in the regulation of transcription and, more recently, in DNA replication and repair. In yeast, a major conserved histone acetyltransferase, Hat1p, preferentially acetylates lysine residues 5 and 12 on histone H4. Results Here, we report that a nuclear sub-complex consisting of Hat1p and its partner Hat2p interacts physically and functionally with the origin recognition complex (ORC). While mutational inactivation of the histone acetyltransferase (HAT) gene HAT1 alone does not compromise origin firing or initiation of DNA replication, a deletion in HAT1 (or HAT2) exacerbates the growth defects of conditional orc-ts mutants. Thus, the ORC-associated Hat1p-dependent histone acetyltransferase activity suggests a novel linkage between histone modification and DNA replication. Additional genetic and biochemical evidence points to the existence of partly overlapping histone H3 acetyltransferase activities in addition to Hat1p/Hat2p for proper DNA replication efficiency. Furthermore, we demonstrated a dynamic association of Hat1p with chromatin during S-phase that suggests a role of this enzyme at the replication fork. Conclusion We have found an intriguing new association of the Hat1p-dependent histone acetyltransferase in addition to its previously known role in nuclear chromatin assembly (Hat1p/Hat2p-Hif1p). The participation of a distinct Hat1p/Hat2p sub-complex suggests a linkage of histone H4 modification with ORC-dependent DNA replication.
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Affiliation(s)
- Bernhard Suter
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Genetics, Department of Medical and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Oxana Pogoutse
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Genetics, Department of Medical and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Xinghua Guo
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Genetics, Department of Medical and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nevan Krogan
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Genetics, Department of Medical and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Peter Lewis
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jack F Greenblatt
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Genetics, Department of Medical and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jasper Rine
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Andrew Emili
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Genetics, Department of Medical and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Abstract
The pathogenic fungus Histoplasma capsulatum causes disease ranging from mild to fatal in healthy and immunocompromised humans. Infection rates reach 80% in endemic areas, including the Midwestern United States. We used inbred mice to identify a 300-fold difference in fungal burden. A/J mice showed lower fungal burden and morbidity than C57BL/6J mice, a reversal of the trend observed for many bacterial pathogens. We mapped the differences in fungal burden to discrete locations on chromosomes 1, 6, 15 and 17 with high significance. Substitution of a single resistant chromosome 17 onto the susceptible background was sufficient to lower fungal burden. These loci will allow dissection of the fungal-specific immune program.
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Affiliation(s)
- J A Mayfield
- Department of Molecular and Cell Biology, The University of California Berkeley, Berkeley, CA 94720-3202, USA
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49
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Jeong H, Herskowitz I, Kroetz DL, Rine J. Function-altering SNPs in the human multidrug transporter gene ABCB1 identified using a Saccharomyces-based assay. PLoS Genet 2007; 3:e39. [PMID: 17352537 PMCID: PMC1817653 DOI: 10.1371/journal.pgen.0030039] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Accepted: 01/26/2007] [Indexed: 11/18/2022] Open
Abstract
The human ABCB1 (MDR1)-encoded multidrug transporter P-glycoprotein (P-gp) plays a major role in disposition and efficacy of a broad range of drugs including anticancer agents. ABCB1 polymorphisms could therefore determine interindividual variability in resistance to these drugs. To test this hypothesis we developed a Saccharomyces-based assay for evaluating the functional significance of ABCB1 polymorphisms. The P-gp reference and nine variants carrying amino-acid-altering single nucleotide polymorphisms (SNPs) were tested on medium containing daunorubicin, doxorubicin, valinomycin, or actinomycin D, revealing SNPs that increased (M89T, L662R, R669C, and S1141T) or decreased (W1108R) drug resistance. The R669C allele's highly elevated resistance was compromised when in combination with W1108R. Protein level or subcellular location of each variant did not account for the observed phenotypes. The relative resistance profile of the variants differed with drug substrates. This study established a robust new methodology for identification of function-altering polymorphisms in human multidrug transporter genes, identified polymorphisms affecting P-gp function, and provided a step toward genotype-determined dosing of chemotherapeutics.
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Affiliation(s)
- Hotcherl Jeong
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Ira Herskowitz
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Deanna L Kroetz
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Ashby MN, Rine J, Mongodin EF, Nelson KE, Dimster-Denk D. Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl Environ Microbiol 2007; 73:4532-42. [PMID: 17526780 PMCID: PMC1932806 DOI: 10.1128/aem.02956-06] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The accurate description of a microbial community is an important first step in understanding the roles of its components in ecosystem function. A method for surveying microbial communities termed serial analysis of rRNA genes (SARD) is described here. Through a series of molecular cloning steps, short DNA sequence tags are recovered from the fifth variable (V5) region of the prokaryotic 16S rRNA genes from microbial communities. These tags are ligated to form concatemers comprised of 20 to 40 tags which are cloned and identified by DNA sequencing. Four agricultural soil samples were profiled with SARD to assess the method's utility. A total of 37,008 SARD tags comprising 3,127 unique sequences were identified. A comparison of duplicate profiles from one soil genomic DNA preparation revealed that the method was highly reproducible. The large numbers of singleton tags, together with nonparametric richness estimates, indicated that a significant amount of sequence tag diversity remained undetected with this level of sampling. The abundance classes of the observed tags were scale-free and conformed to a power law distribution. Numerically, the majority of the total tags observed belonged to abundance classes that were each present at less than 1% of the community. Over 99% of the unique tags individually made up less than 1% of the community. Therefore, from either a numerical or diversity standpoint, taxa with low abundance comprised a significant proportion of the microbial communities examined and could potentially make a large contribution to ecosystem function. SARD may provide a means to explore the ecological roles of these rare members of microbial communities in qualitative and quantitative terms.
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