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GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris. PLoS Genet 2014; 10:e1004169. [PMID: 24603708 PMCID: PMC3945215 DOI: 10.1371/journal.pgen.1004169] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/25/2013] [Indexed: 11/19/2022] Open
Abstract
The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.
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Liachko I, Youngblood RA, Keich U, Dunham MJ. High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 2012; 23:698-704. [PMID: 23241746 PMCID: PMC3613586 DOI: 10.1101/gr.144659.112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
DNA replication origins are necessary for the duplication of genomes. In addition, plasmid-based expression systems require DNA replication origins to maintain plasmids efficiently. The yeast autonomously replicating sequence (ARS) assay has been a valuable tool in dissecting replication origin structure and function. However, the dearth of information on origins in diverse yeasts limits the availability of efficient replication origin modules to only a handful of species and restricts our understanding of origin function and evolution. To enable rapid study of origins, we have developed a sequencing-based suite of methods for comprehensively mapping and characterizing ARSs within a yeast genome. Our approach finely maps genomic inserts capable of supporting plasmid replication and uses massively parallel deep mutational scanning to define molecular determinants of ARS function with single-nucleotide resolution. In addition to providing unprecedented detail into origin structure, our data have allowed us to design short, synthetic DNA sequences that retain maximal ARS function. These methods can be readily applied to understand and modulate ARS function in diverse systems.
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Affiliation(s)
- Ivan Liachko
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
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Knott SRV, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavaré S, Aparicio OM. Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell 2012; 148:99-111. [PMID: 22265405 DOI: 10.1016/j.cell.2011.12.012] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 10/11/2011] [Accepted: 12/09/2011] [Indexed: 12/28/2022]
Abstract
The replication of eukaryotic chromosomes is organized temporally and spatially within the nucleus through epigenetic regulation of replication origin function. The characteristic initiation timing of specific origins is thought to reflect their chromatin environment or sub-nuclear positioning, however the mechanism remains obscure. Here we show that the yeast Forkhead transcription factors, Fkh1 and Fkh2, are global determinants of replication origin timing. Forkhead regulation of origin timing is independent of local levels or changes of transcription. Instead, we show that Fkh1 and Fkh2 are required for the clustering of early origins and their association with the key initiation factor Cdc45 in G1 phase, suggesting that Fkh1 and Fkh2 selectively recruit origins to emergent replication factories. Fkh1 and Fkh2 bind Fkh-activated origins, and interact physically with ORC, providing a plausible mechanism to cluster origins. These findings add a new dimension to our understanding of the epigenetic basis for differential origin regulation and its connection to chromosomal domain organization.
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Affiliation(s)
- Simon R V Knott
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
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Liachko I, Tanaka E, Cox K, Chung SCC, Yang L, Seher A, Hallas L, Cha E, Kang G, Pace H, Barrow J, Inada M, Tye BK, Keich U. Novel features of ARS selection in budding yeast Lachancea kluyveri. BMC Genomics 2011; 12:633. [PMID: 22204614 PMCID: PMC3306766 DOI: 10.1186/1471-2164-12-633] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The characterization of DNA replication origins in yeast has shed much light on the mechanisms of initiation of DNA replication. However, very little is known about the evolution of origins or the evolution of mechanisms through which origins are recognized by the initiation machinery. This lack of understanding is largely due to the vast evolutionary distances between model organisms in which origins have been examined. RESULTS In this study we have isolated and characterized autonomously replicating sequences (ARSs) in Lachancea kluyveri - a pre-whole genome duplication (WGD) budding yeast. Through a combination of experimental work and rigorous computational analysis, we show that L. kluyveri ARSs require a sequence that is similar but much longer than the ARS Consensus Sequence well defined in Saccharomyces cerevisiae. Moreover, compared with S. cerevisiae and K. lactis, the replication licensing machinery in L. kluyveri seems more tolerant to variations in the ARS sequence composition. It is able to initiate replication from almost all S. cerevisiae ARSs tested and most Kluyveromyces lactis ARSs. In contrast, only about half of the L. kluyveri ARSs function in S. cerevisiae and less than 10% function in K. lactis. CONCLUSIONS Our findings demonstrate a replication initiation system with novel features and underscore the functional diversity within the budding yeasts. Furthermore, we have developed new approaches for analyzing biologically functional DNA sequences with ill-defined motifs.
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Affiliation(s)
- Ivan Liachko
- School of Mathematics and Statistics, University of Sydney, Sydney, Australia.
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Liachko I, Bhaskar A, Lee C, Chung SCC, Tye BK, Keich U. A comprehensive genome-wide map of autonomously replicating sequences in a naive genome. PLoS Genet 2010; 6:e1000946. [PMID: 20485513 PMCID: PMC2869322 DOI: 10.1371/journal.pgen.1000946] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 04/09/2010] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins. The machinery that initiates DNA synthesis is highly conserved, but the sites where the replication initiation proteins bind have diverged significantly. Functional comparative genomics is an obvious approach to study the evolution of replication origins. However, to date, the Saccharomyces cerevisiae replication origin map is the only genome map available. Using an iterative approach that combines computational prediction and functional validation, we have generated a high-resolution genome-wide map of DNA replication origins in Kluyveromyces lactis. Unlike other yeasts or metazoans, K. lactis autonomously replicating sequences (KlARSs) contain a 50 bp consensus motif suggestive of a dimeric structure. This motif is necessary and largely sufficient for initiation and was used to dependably identify 145 of the up to 156 non-repetitive intergenic ARSs projected for the K. lactis genome. Though similar in genome sizes, K. lactis has half as many ARSs as its distant relative S. cerevisiae. Comparative genomic analysis shows that ARSs in K. lactis and S. cerevisiae preferentially localize to non-syntenic intergenic regions, linking ARSs with loci of accelerated evolutionary change.
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Affiliation(s)
- Ivan Liachko
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Anand Bhaskar
- Department of Computer Science, Cornell University, Ithaca, New York, United States of America
| | - Chanmi Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Shau Chee Claire Chung
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Bik-Kwoon Tye
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Uri Keich
- School of Mathematics and Statistics F07, University of Sydney, Sydney, Australia
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Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha S. Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances. PLoS Comput Biol 2010; 6:e1000652. [PMID: 20126523 PMCID: PMC2813253 DOI: 10.1371/journal.pcbi.1000652] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 12/18/2009] [Indexed: 11/19/2022] Open
Abstract
We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif–function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations. We develop a computational pipeline for predicting the functions of transcription factor motifs, through DNA sequence analysis. The pipeline is applied to the newly sequenced genome of the jewel wasp, Nasonia vitripennis. It exploits the wealth of molecular data available in another insect species, the fruitfly Drosophila melanogaster, and uses cross-species comparison to its advantage. Our main contribution is to show how this can be done despite the large evolutionary divergence between the two species. The methodology presented here may be applied more generally to other scenarios (genomes) where comparative regulatory genomics must deal with large evolutionary divergences.
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Affiliation(s)
- Jaebum Kim
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ryan Cunningham
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Brian James
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Stefan Wyder
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Joshua D. Gibson
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Oliver Niehuis
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Evgeny M. Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gene E. Robinson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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