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Divergence of transcription factor binding sites across related yeast species (2007)

A. R. Borneman ; T. A. Gianoulis ; Z. D. Zhang ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 317(5839): 815-9. doi: 10.1126/science.1140748.

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Publication Date: 2007-08-11

Description: Characterization of interspecies differences in gene regulation is crucial for understanding the molecular basis of both phenotypic diversity and evolution. By means of chromatin immunoprecipitation and DNA microarray analysis, the divergence in the binding sites of the pseudohyphal regulators Ste12 and Tec1 was determined in the yeasts Saccharomyces cerevisiae, S. mikatae, and S. bayanus under pseudohyphal conditions. We have shown that most of these sites have diverged across these species, far exceeding the interspecies variation in orthologous genes. A group of Ste12 targets was shown to be bound only in S. mikatae and S. bayanus under pseudohyphal conditions. Many of these genes are targets of Ste12 during mating in S. cerevisiae, indicating that specialization between the two pathways has occurred in this species. Transcription factor binding sites have therefore diverged substantially faster than ortholog content. Thus, gene regulation resulting from transcription factor binding is likely to be a major cause of divergence between related species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borneman, Anthony R -- Gianoulis, Tara A -- Zhang, Zhengdong D -- Yu, Haiyuan -- Rozowsky, Joel -- Seringhaus, Michael R -- Wang, Lu Yong -- Gerstein, Mark -- Snyder, Michael -- New York, N.Y. -- Science. 2007 Aug 10;317(5839):815-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690298" target="_blank"〉PubMed〈/a〉

Keywords: Base Sequence ; Binding Sites ; Candida albicans/genetics/growth & development/metabolism ; Chromatin Immunoprecipitation ; DNA-Binding Proteins/genetics/metabolism ; *Evolution, Molecular ; Fungal Proteins/genetics/*metabolism ; Gene Expression Regulation, Fungal ; Gene Regulatory Networks ; Genes, Fungal ; Oligonucleotide Array Sequence Analysis ; *Regulatory Sequences, Nucleic Acid ; Saccharomyces/*genetics/growth & development/metabolism ; Saccharomyces cerevisiae/*genetics/growth & development/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Transcription Factors/genetics/*metabolism

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Precise manipulation of chromosomes in vivo enables genome-wide codon replacement (2011)

F. J. Isaacs ; P. A. Carr ; H. H. Wang ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 333(6040): 348-53. doi: 10.1126/science.1205822.

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Publication Date: 2011-07-19

Description: We present genome engineering technologies that are capable of fundamentally reengineering genomes from the nucleotide to the megabase scale. We used multiplex automated genome engineering (MAGE) to site-specifically replace all 314 TAG stop codons with synonymous TAA codons in parallel across 32 Escherichia coli strains. This approach allowed us to measure individual recombination frequencies, confirm viability for each modification, and identify associated phenotypes. We developed hierarchical conjugative assembly genome engineering (CAGE) to merge these sets of codon modifications into genomes with 80 precise changes, which demonstrate that these synonymous codon substitutions can be combined into higher-order strains without synthetic lethal effects. Our methods treat the chromosome as both an editable and an evolvable template, permitting the exploration of vast genetic landscapes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Isaacs, Farren J -- Carr, Peter A -- Wang, Harris H -- Lajoie, Marc J -- Sterling, Bram -- Kraal, Laurens -- Tolonen, Andrew C -- Gianoulis, Tara A -- Goodman, Daniel B -- Reppas, Nikos B -- Emig, Christopher J -- Bang, Duhee -- Hwang, Samuel J -- Jewett, Michael C -- Jacobson, Joseph M -- Church, George M -- K99 GM081450/GM/NIGMS NIH HHS/ -- R00 GM081450/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 15;333(6040):348-53. doi: 10.1126/science.1205822.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. farren.isaacs@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764749" target="_blank"〉PubMed〈/a〉

Keywords: Chromosomes, Bacterial/*genetics ; *Codon, Terminator ; *Conjugation, Genetic ; Directed Molecular Evolution ; Escherichia coli/*genetics/growth & development/physiology ; Genetic Engineering/*methods ; *Genome, Bacterial ; Genomic Instability ; Mutagenesis, Site-Directed ; Mutation ; Phenotype ; Recombination, Genetic ; Templates, Genetic

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics