THE TELOMERATOR-A TOOL FOR CHROMOSOME ENGINEERING

[0001] This application claims the benefit of U.S. Provisional Application No. 61/773,206, filed Mar. 6, 2013, which is incorporated herein by reference in its entirety.

[0002] This invention was made with government support under grant number MCB1026068, awarded by the National Science Foundation. The government has certain rights in the invention.

[0003] The present invention relates to the field of chromosome engineering. More specifically, the present invention provides methods and compositions useful for inducibly linearizing circular DNA molecules in vivo in yeast.

[0004] This application contains a sequence listing. It has been submitted electronically via EFS-Web as an ASCII text file entitled “P12280-02_Sequence_Listing.txt.” The sequence listing is 8,462 bytes in size, and was created on Mar. 6, 2014. It is hereby incorporated by reference in its entirety.

[0005] Chromosome engineering is the study of genetic modifications that affect large segments of chromosomes. Top down approaches start with pre-existing chromosomes and modify them in vivo by introducing, for instance, large deletions, inversions, or duplications. Bottom up approaches, on the other hand, attempt to design and build chromosomes de novo. In either case, we need a strong understanding not only of chromosomal features that confer mitotic stability, including centromeres, telomeres, and origins of replication, but also the effect of the spatial relationships of these elements with one another and with other chromosomal features like genes.

[0006] The Saccharomyces cerevisiae genome is an excellent platform to develop tools for chromosome engineering given the ease of genetic manipulation and similarity to higher eukaryotes. The S. cerevisiae genome is composed of 12 Mb of DNA inherited via 16 linear chromosomes ranging in size from 270 kb to over 1 Mb (1). Two important cis elements are required to maintain chromosome stability through mitosis and meiosis: compact point centromeres (˜125 bp) ensure faithful segregation of sister chromatids (2), and conserved telomere sequences protect the ends of each chromosome and guarantee the maintenance of chromosome length during replication (3, 4). With these elements intact, many lines of evidence indicate budding yeast tolerates a high degree of chromosomal modifications without affecting viability, for instance: (a) the largest yeast chromosome (IV) can be sub-divided into 11 separate mini-chromosomes (5); (b) more than 500 kb, including 247 non-essential genes, can be deleted in a single haploid strain (6); (c) any of the 16 chromosomes can be individually destabilized in a diploid cell to generate a chromosomal complement of 2n−1 (7); (d) a designer, synthetic chromosome arm, synIXR, was shown to power growth of budding yeast in the absence of the native chromosome sequence (8).

[0007] The present invention is based, at least in part, on the development of compositions and methods to inducibly convert circular DNA molecules in yeast into stably maintained linear chromosomes. We call this genetic system “The Telomerator.” In brief, we can introduce a “telomerator cassette” by homologous recombination into any circular DNA intended to be linearized, in principle, at any position. The cassette encodes a selectable marker gene sequence interrupted by an intron that harbors a homing endonuclease recognition site such as I-SceI. The recognition site is flanked by telomere seed sequences (TeSS), short stretches of minimal yeast telomere sequences. When the endonuclease is inducibly expressed, circular DNA is efficiently linearized and subsequently stably maintained due to the presence of the terminal TeSSs.

[0008] Accordingly, in one aspect, the present invention provides a telomerator cassette. In one embodiment, a telomerator cassette comprises a nucleic acid encoding a selectable marker, wherein the nucleic acid encoding a selectable marker comprises an intron comprising an endonuclease recognition site flanked by telomere seed sequences. In a specific embodiment, the intron is the ACT1 intron. A telomerator cassette can also be referred to as a cassette, an expression cassette, a nucleic acid construct, a construct or simply, a composition.

[0009] In another embodiment, a telomerator cassette comprises a nucleic acid encoding a selectable marker, wherein the nucleic acid encoding a selectable marker comprises an endonuclease recognition site flanked by telomere seed sequences. The site and flanking sequences are inserted in-frame into the nucleic acid sequence encoding the selectable marker to allow expression. In a specific embodiment, the endonuclease recognition site flanked by telomere seed sequences comprises SEQ ID NO:4. In another embodiment, a telomerator cassette comprises a nucleic acid encoding a selectable marker, wherein the nucleic acid encoding the selectable marker comprises an endonuclease recognition site flanked by telomere seed sequences such that the selectable marker retains its function. In a further embodiment, a telomerator cassette comprises a nucleic acid encoding a selectable marker, wherein the nucleic acid encoding a selectable marker comprises the original marker sequence operably linked as a protein fusion with an endonuclease recognition site flanked by telomere seed sequences.

[0010] In one embodiment, the marker is an auxotrophic marker. Auxotrophic markers can include, but are not limited to, LEU2, URA3, TRP1, MET15, LYS1, and HIS3. In a specific embodiment, the auxotrophic marker is the URA3 gene. In another embodiment, the marker is a drug selection marker and may include, but is not limited to, nourseothrecin (NAT), geneticin, and hygromycin

[0011] In particular embodiments, the selectable marker is both selectable and counterselectable. Examples in yeast include URA3, LYS2 and TRP1, counterselectable using 5-fluoro-orotic acid, alpha-amino-adipate, and 5-fluoro-anthranilic acid, respectively. In other embodiments, a counterselectable marker, e.g., CYH2 (counterselectable on cycloheximide), can be fused to any other selectable marker by joining the two open reading frames in such a way that both moieties are functional.

[0012] In another embodiment, the endonuclease recognition site is specific for I-SceI. In a more specific embodiment, the I-SceI endonuclease recognition site comprises SEQ ID NO:2. In other embodiments, the endonuclease may comprise restriction endonucleases, Zinc finger nucleases, TALENs or other meganucleases.

[0013] In certain embodiments, the telomere seed sequences comprise minimal telomere seed sequences. In general, the telomere seed sequences for yeast comprise [(TG_(1-3))₁₆ . . . (C_(1-3)A)₁₆]. In a specific embodiment, the telomere seed sequences comprise SEQ ID NO:1 and SEQ ID NO:3.

[0014] In particular embodiments, a circular chromosome comprises a telomerator cassette described herein. In other embodiments, a eukaryotic host cell comprises a circular chromosome of the present invention. In a specific embodiment, the eukaryote is yeast. In a more specific embodiment, the yeast is S. cerevisiae. In other embodiments, the yeast is Hansenula polymorpha, Pichia pastoris or Schizosaccharomyces pombe.

[0015] In specific embodiments, the eukaryotic host cell comprises a vector encoding the endonuclease under the control of an inducible promoter. In a particular embodiment, the inducible promoter is the GAL1 promoter. Other promoters can include, but are not limited to, pMET15, pCUP2, other pGAL sequences, and TetON/TetOFF systems.

[0016] In a specific embodiment, a telomerator cassette of the present invention comprises a nucleic acid that encodes the auxotrophic marker URA3, wherein the nucleic acid comprises an intron that comprises the I-SceI endonuclease recognition site flanked by telomere seed sequences. In a more specific embodiment, the telomere seed sequences comprise SEQ ID NO:1 and SEQ ID NO:3. In another embodiment, the I-SceI endonuclease recognition site comprises SEQ ID NO:2. A circular chromosome can comprise a telomerator cassette described herein. In another embodiment, a yeast host cell comprises a circular chromosome described herein. The yeast host cell may comprise a vector encoding the I-SceI endonuclease under the control of an inducible promoter. More specifically, the inducible promoter can be the GAL1 promoter.

[0017] In one embodiment, a yeast host cell comprises a circular chromosome comprising a telomerator cassette encoding a selectable marker, wherein the nucleic acid encoding the selectable marker comprises an intron that comprises an endonuclease recognition site flanked by telomere seed sequences; and a vector encoding the endonuclease under the control of an inducible promoter. In a specific embodiment, the selectable marker is an auxotrophic marker. In a more specific embodiment, the auxotrophic marker is the URA3 gene. In the yeast host the endonuclease recognition site is specific for I-SceI. More specifically, the I-SceI endonuclease recognition site comprises SEQ ID NO:2. Moreover, the telomere seed sequences can comprise SEQ ID NO:1 and SEQ ID NO:3.

[0018] In another aspect, the present invention provides methods for chromosome engineering. In one embodiment, a method for engineering a circular chromosome capable of being inducibly linearized comprises the step of integrating a telomerator cassette into a circular chromosome, wherein the telomerator cassette comprises a nucleic acid encoding a selectable marker, wherein the nucleic acid encoding a selectable marker comprises an intron comprising an endonuclease recognition site flanked by telomere seed sequences. In a specific embodiment, the integrating step is accomplished by transforming a telomerator cassette into a host cell comprising the circular chromosome. In another embodiment, the host cell comprises a vector encoding the endonuclease under the control of an inducible promoter.

[0026] It is understood that the present invention is not limited to the particular methods and components, etc., described herein, as these may vary. It is also to be understood that the terminology used herein is used for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention. It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include the plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to a “protein” is a reference to one or more proteins, and includes equivalents thereof known to those skilled in the art and so forth.

[0027] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Specific methods, devices, and materials are described, although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention.

[0028] All publications cited herein are hereby incorporated by reference including all journal articles, books, manuals, published patent applications, and issued patents. In addition, the meaning of certain terms and phrases employed in the specification, examples, and appended claims are provided. The definitions are not meant to be limiting in nature and serve to provide a clearer understanding of certain aspects of the present invention.

[0029] Chromosome engineering is an emerging focus in the fields of systems biology, genetics, synthetic biology, and the functional analysis of genomes. Here we describe the ‘telomerator’, a new synthetic biology device designed to inducibly linearize circular DNA molecules in vivo in Saccharomyces cerevisiae. To demonstrate the functionality and utility of the telomerator, we generate linear variants of a synthetic yeast chromosome originally built as a circular molecule, synIXR BAC. By circularly permuting synIXR BAC using the telomerator, we generated an array of 53 different linearized chromosome structures, many of which confer novel phenotypic properties. This tool offers a new way to study the effect of gene placement on chromosomes (i.e. telomere proximity), the essentiality of 3′ non-coding regions of genes, and the plasticity of gene order and chromosome structure on cell fitness. The telomerator will be an important tool to generate artificial, linear chromosomes in yeast and the concept could be extended to other eukaryotes including mammals and human cells.

[0030] The term “nucleic acid” or “polynucleotide” refers to a polymeric form of nucleotides of any length, either ribonucleotides and/or deoxyribonucleotides. These terms include a single-, double- or triple-stranded DNA, genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases. The backbone of the nucleic acid can comprise sugars and phosphate groups (as may typically be found in RNA or DNA), or modified or substituted sugar or phosphate groups. Alternatively, the backbone of the nucleic acid can comprise a polymer of synthetic subunits such as phosphoramidates and thus can be an oligodeoxynucleoside phosphoramidate (P—NH₂) or a mixed phosphoramidate-phosphodiester oligomer. In addition, a double-stranded nucleic acid can be obtained from the single stranded nucleic acid product of chemical synthesis either by synthesizing the complementary strand and annealing the strands under appropriate conditions, or by synthesizing the complementary strand de novo using a DNA polymerase with an appropriate primer.

[0031] The following are non-limiting examples of nucleic acids: a gene or gene fragment, exons, introns, mRNA, tRNA, rRNA, ribozymes, cDNA, recombinant nucleic acids, branched nucleic acids, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A nucleic acid may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs, uracyl, other sugars and linking groups such as fluororibose and thioate, and nucleotide branches. The sequence of nucleotides may be interrupted by non-nucleotide components. A nucleic acid may be further modified after polymerization, such as by conjugation with a labeling component. Other types of modifications included in this definition are caps, substitution of one or more of the naturally occurring nucleotides with an analog, and introduction of means for attaching the nucleic acid to proteins, metal ions, labeling components, other nucleic acids, or a solid support.

[0032] As used herein, the term “operably linked” means that nucleic acid sequences or proteins are operably linked when placed into a functional relationship with another nucleic acid sequence or protein. For example, a promoter sequence is operably linked to a coding sequence if the promoter promotes transcription of the coding sequence. As a further example, a repressor protein and a nucleic acid sequence are operably linked if the repressor protein binds to the nucleic acid sequence. Additionally, a protein may be operably linked to a first and a second nucleic acid sequence if the protein binds to the first nucleic acid sequence and so influences transcription of the second, separate nucleic acid sequence. Generally, “operably linked” means that the DNA sequences being linked are contiguous, although they need not be, and that a gene and a regulatory sequence or sequences (e.g., a promoter) are connected in such a way as to permit gene expression when the appropriate molecules (e.g., transcriptional activator proteins—transcription factors—or proteins which include transcriptional activator domains) are bound to the regulatory sequence or sequences.

[0033] The term “plasmid” refers to an extrachromosomal circular DNA capable of autonomous replication in a given cell. In certain embodiments, the plasmid is designed for amplification and expression in bacteria. Plasmids can be engineered by standard molecular biology techniques. See Sambrook et al., Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), N.Y. The term “expression vector” is used interchangeably herein with the term “plasmid” and refers to a recombinant DNA molecule containing a desired coding sequence and appropriate nucleic acid sequences necessary for expression of the operably linked coding sequence (e.g. an insert sequence that codes for a product) in a particular host cell. Nucleic acid sequences necessary for expression in prokaryotes usually include a promoter, an operator (optional), and a ribosome binding site, often along with other sequences.

[0034] The term “promoter” refers to the DNA region, usually upstream of the coding sequence of a gene or operon, which binds RNA polymerase and directs the enzyme to the correct transcriptional start site.

[0035] The terms “endonuclease” refers to any wild-type or variant enzyme capable of catalyzing the hydrolysis (cleavage) of bonds between nucleic acids within a DNA or RNA molecule, preferably a DNA molecule. Endonucleases do not cleave the DNA or RNA molecule irrespective of its sequence, but recognize and cleave the DNA or RNA molecule at specific polynucleotide sequences, further referred to as “target sequences” or “target sites”. Endonucleases can for example be a homing endonuclease (Paques et al., Curr Gen Ther. 2007 7:49-66), a chimeric Zinc-Finger nuclease (ZFN) resulting from the fusion of engineered zinc-finger domains with the catalytic domain of a restriction enzyme such as Fokl (Porteus et al., Nat Biotechnol. 2005 23:967-973) or a chemical endonuclease (Arimondo et al., Mol Cell Bioi. 2006 26:324-333; Simon et al., NAR 2008 36:3531-3538; Eisenschmidt et al., NAR 2005 33:7039-7047; Cannata et al., PNAS 2008 105:9576-9581). In chemical endonucleases, a chemical or peptidic cleaver is conjugated either to a polymer of nucleic acids or to another DNA recognizing a specific target sequence, thereby targeting the cleavage activity to a specific sequence. Chemical endonucleases also encompass synthetic nucleases like conjugates of orthophenanthroline, a DNA cleaving molecule, and triplex-forming oligonucleotides (TFOs), known to bind specific DNA sequences (Kalish and Glazer Ann NY Acad Sci 2005 1058: 151-61). Such chemical endonucleases are considered to fall within the scope of the term “endonuclease” according to the present invention. Also within the scope of the present invention is intended any fusion between molecules able to bind DNA specific sequences and agent/reagent/chemical able to cleave DNA or interfere with cellular proteins implicated in the double strand break (DSB) repair (Majumdar et al., J. Bioi. Chem 2008 283, 17:11244-11252; Liu et al. NAR 2009 37:6378-6388); as a non-limiting example such a fusion can be constituted by a specific DNA-sequence binding domain linked to a chemical inhibitor known to inhibit re-ligation activity of a topoisomerase after DSB cleavage. Endonucleases can comprise a homing endonuclease, also known under the name of meganuclease. The term “meganuclease” refers to an endonuclease having a double-stranded DNA target sequence of about 12 to about 45 base pairs (bp). Such homing endonucleases are well-known to the art (see e.g. Stoddard, Quarterly Reviews of Biophysics, 2006, 38:49-95). Homing endonucleases recognize a DNA target sequence and generate a single- or double-strand break. Homing endonucleases are highly specific, recognizing DNA target sites ranging from 12 to 45 base pairs (bp) in length, usually ranging from about 14 to about 40 bp in length. The homing endonuclease according to the invention may for example correspond to a LAGLIDADG endonuclease, to a HNH endonuclease, or to a GIY-YIG endonuclease. In certain embodiments, a meganuclease is either a dimeric enzyme, wherein each domain is on a monomer or a monomeric enzyme comprising the two domains on a single polypeptide.

[0036] Endonucleases according to the invention can also be derived from TALENs, a new class of chimeric nucleases using a Fokl catalytic domain and a DNA binding domain derived from Transcription Activator Like Effector (TALE), a family of proteins used in the infection process by plant pathogens of the Xanthomonas genus (Boch, Scholze et al. 2009; Moscou and Bogdanove 2009; Christian, Cermak et al., 2010; Li, Huang et al., 2011) (Boch, Scholze et al., 2009; Moscou and Bogdanove 2009; Christian, Cermak et al., 2010; Li, Huang et al., 2010). The functional layout of a Fokl-based TALE-nuclease (TALEN) is essentially that of a ZFN, with the Zinc-finger DNA binding domain being replaced by the TALE domain. As such, DNA cleavage by a TALEN requires two DNA recognition regions flanking an unspecific central region. Endonucleases encompassed in the present invention can also be derived from TALENs. An endonuclease according to the present invention can be derived from a TALE-nuclease (TALEN), i. e. a fusion between a DNA-binding domain derived from a Transcription Activator Like Effector (TALE) and one or two catalytic domains. In other embodiments, CRISPR/Cas systems may be used. See Mali P, Yang L, Esvelt K M, Aach J, Guell M, Dicarlo J E, Norville J E, Church G M: RNA-guided human genome engineering via Cas9. Science 2013; Cong L, Ran F A, Cox D, Lin S, Barretto R, Habib N, Hsu P D, Wu X, Jiang W, Marraffini L A, Zhang F: Multiplex genome engineering using CRISPR/Cas systems. Science 2013; Cho S W, Kim S, Kim J M, Kim J S: Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 2013; Hwang W Y, Fu Y, Reyon D, Maeder M L, Tsai S Q, Sander J D, Peterson R T, Yeh J R, Joung J K: Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 2013; and Jiang W, Bikard D, Cox D, Zhang F, Marraffini L A: RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 2013.

[0037] As used herein, a “selectable marker” refers to a phenotypic trait conferred on transformed cells that protects them from a selective agent in their environment, i.e., the growth media. Examples of selectable markers include, but are not limited to, antibiotic resistance markers (e.g., genes encoding resistance to kanamycin, ampicillin, chloramphenicol, gentamycin, or tetracycline), metabolic markers (e.g., amino acid synthesis genes or transfer RNA genes) and auxotrophic markers.

[0038] As used herein, the term “vector” refers to a nucleic acid construct designed for transduction/transfection of one or more cell types. Vectors may be, for example, “cloning vectors” which are designed for isolation, propagation and replication of inserted nucleotides, “expression vectors” which are designed for expression of a nucleotide sequence in a host cell. The term “replication” means duplication of a vector.

[0039] Any yeast cell can be used in the methods of the present invention. In particular embodiments, a yeast species within the genus of Saccharomyces, particularly Saccharomyces cerevisiae, are used. Other examples of suitable yeast species include, but are not limited to, Hansenula polymorpha, Pichia pastoris, and Schizosaccharomyces pombe. Indeed, numerous yeast strains or derivative strains are known in the art. The application and optional modification of such strains for purposes of the present invention should be apparent to a skilled artisan apprised of the present disclosure.

[0040] Our goal was to systematically perturb order and orientation of genetic elements on linear chromosomes in S. cerevisiae. To achieve this, we have developed the telomerator, a genetic tool that can inducibly linearize circular DNA molecules in vivo. We use the telomerator to circularly permute the synIXR synthetic chromosome, which is encoded as a bacterial artificial chromosome (BAC, herein referred to synIXR BAC). Our results support that telomerator-induced linearization generates linear chromosomes with functional telomeres on which heterochromatin is fully established.

[0041] At least two previous methods have been used to construct artificial linear chromosomes in yeast. First, non-native chromosomes were generated by in vitro ligation of synthetic telomere sequences onto linear DNA followed by transformation and selection in yeast (20, 21). This approach overcomes the complicating factor that linear DNA molecules cannot be replicated in E. coli and can therefore be difficult to construct. Secondly, a circular derivative of chromosome three (22) was linearized by integrating into it synthetic telomere sequences; over time these sequences resolved in vivo to generate a linear molecule (23). Together these studies shed light on important features about the mitotic stability of chromosomes. First, the overall length of linear DNA molecules is a major contributing factor to mitotic stability (16, 20, 21, 23). Second, the spatial relationship between the centromere and telomeres has very little impact on mitotic stability (16, 23). Finally, X and Y′ elements located in subtelomeric regions of native S. cerevisiae chromosomes have little or no impact on mitotic stability (23).

[0042] The telomerator represents a new and convenient way to linearize circular DNA molecules in vivo in S. cerevisiae and can be applied to the construction of artificial chromosomes. Here we demonstrate its utility by circularly permuting a pre-existing circular synthetic chromosome in yeast—synIXR. In terms of chromosome engineering, the telomerator presents four major advantages over the approaches described above: (i) the use of telomere seed sequences that correspond to native yeast telomeres; (ii) the ease with which a telomerator construct can be PCR amplified and thus integrated at multiple unique loci; (iii) the method gives virtually 100% correct clones with no requirement for cumbersome screening approaches; and (iv) the inducible control over timing of linearization in vivo.

[0043] Linear Permutations of synIXR.

[0044] In our work, we linearized circular chromosomes to generate minimal telomere sequences. Based on the SIR2-dependent phenotypes observed, we conclude that heterochromatin is forming on the linearized chromosomes. In native chromosomes, subtelomeric sequences can buffer these effects, as can insulators. Future telomerator designs could incorporate such elements.

[0045] With the exception of effects on gene expression, the panel of permuted chromosomes displays surprisingly little variation in behavior, suggesting that the relative placement of telomeres and centromeres in S. cerevisiae is quite flexible. For instance, linearization at either YIL001 W or YIR001C produces telocentric versions of synIXR with only ˜1 kb separating the centromere from a telomere; that these permutations exhibit no apparent growth defect is consistent with previous work suggesting telocentric chromosomes in budding yeast are mitotically stable (16, 23).

[0046] Other Applications for Telomerator.

[0047] The telomerator provides a flexible new strategy to aid in the construction and expression of supernumerary chromosomes encoding non-native pathways that give a multitude of new functions to the cell. In principle, this technology can be extended to other eukaryotic organisms, especially those with point/small centromeres like budding yeast. Applying the telomerator to chromosome engineering in mammalian cells will be more challenging as ‘regional’ mammalian centromeres can extend for hundreds of kilobases and include repetitive sequences. Artificially generated human minichromosomes, existing as either linear or circular constructs, have been described and they may serve as a starting point for mammalian artificial chromosome engineering (24-30). We ultimately envision such artificial chromosomes as valuable platforms for gene targeting that will allow delivery of large DNAs to recipient cells and provide a means by which to investigate the incorporation of complex segments of DNA encoding networks and pathways.

[0048] Prospects for Telomerators in Other Systems/Organisms.

[0049] The linearization function of the telomerator can obviously be achieved with a wide variety of restriction endonucleases, Zinc finger nucleases, TALENs or meganucleases besides I-SceI. One important consideration is that the recognition sequence of the enzyme must be sufficiently rare within the sequence of the host genome (i.e., no or few existing sites) to work without causing “collateral damage” in the rest of the genome. In this regard the I-SceI site is not present in yeast nuclear genome (31). A wide variety of selectable/counterselectable markers could also be employed.

[0050] Another approach to introduce the Telomerator sequence into a circular DNA molecule for linearization is to include the TeSS-I-SceI-TeSS sequence as part of the protein coding sequence of the selectable marker. In such embodiments, the TeSS-I-SceI-TeSS sequence is “in-frame” with the selectable marker sequence (i.e., a multiple of 3) such that the resulting protein translation would not be truncated. The TeSS-I-SceI-Tess sequence is inserted into the selectable marker in a position that would not disrupt function of the resulting protein product. Shorter TeSSs have been described in the literature (Yamagishi 2008 Appl Microbiol Biotechnol 79:699-706), and could be employed in this so-called Telomerator-fusion protein model in order to increase the stability of the highly repetitive TeSS sequences.

[0051] This work should be easily expandable to other yeast species. This is relevant in the academic setting, where fungal species other than S. cerevisiae are becoming increasingly commonplace (i.e., Ashbya gossypii, Candida glabrata, Pichia pastoris etc.). Furthermore, many yeast species are used industrially, exploiting unique properties beneficial to the process of interest (e.g., P. pastoris, high-level secreted protein production; A. gossypii, riboflavin production). Similarly, the approach could almost certainly be expanded to other eukaryotic microorganisms such as algae, and potentially to various tissue culture cells.

[0052] Without further elaboration, it is believed that one skilled in the art, using the preceding description, can utilize the present invention to the fullest extent. The following examples are illustrative only, and not limiting of the remainder of the disclosure in any way whatsoever.

[0053] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compounds, compositions, articles, devices, and/or methods described and claimed herein are made and evaluated, and are intended to be purely illustrative and are not intended to limit the scope of what the inventors regard as their invention. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.) but some errors and deviations should be accounted for herein. Unless indicated otherwise, parts are parts by weight, temperature is in degrees Celsius or is at ambient temperature, and pressure is at or near atmospheric. There are numerous variations and combinations of reaction conditions, e.g., component concentrations, desired solvents, solvent mixtures, temperatures, pressures and other reaction ranges and conditions that can be used to optimize the product purity and yield obtained from the described process. Only reasonable and routine experimentation will be required to optimize such process conditions.

[0054] Construction of the Telomerator.

[0055] The TeSS-I-SceI sequence was introduced by one-step isothermal assembly (32) into the unique XhoI site encoded centrally within the ACT1 intron that had been previously transplanted into URA3(12). Specifically, the TeSS-I-SceI-TeSS sequence (5′TGTGTGGTGTGTGGGTGTGTGTGGGTGTGTGGGTGTGTGGGTAGGGATAACAG GGTAATCACCCACCACACACACCCACACACACCACACACCCACCCA3′) (SEQ ID NO:4) flanked by 40 bp corresponding to sequence on either side of the XhoI site was ordered from IDT as an Ultramer. This sequence was exponentially amplified using external primers (F 5′ATCCCATTTAACTGTAAGAAGAATTGC3′ (SEQ ID NO:5); R 5′GGAGAGTGAAAAATAGTAAAAAAAGGT3′ (SEQ ID NO:6)). Expression of the URA3-intronACT1-TeSS-I-Sce-I-TeSS-intronACT1-URA3 cassette was verified by functional complementation assay as described in the text.

[0056] Integration of Telomerator into synIXR BAC.

[0057] Primers were designed to bind upstream of the URA3 promoter (5′CCCGGGGGATCCGGTGATTG3′) (SEQ ID NO:7) and downstream of the URA3 terminator (5′CCAAAGCTGGAGCTCCACCG3′) (SEQ ID NO:8) on the telomerator construct. 50 bp corresponding to either side of each unique integration site was then appended to these two primers. Standard PCR conditions were used to amplify the telomerator, which was then transformed into a synIXR BAC containing strain (yJS587 (8)). Integration was confirmed with a location specific primer in combination with a primer internal to the URA3 promoter sequence (FIG. 6).

[0058] Linearization of synIXR.

[0059] The pGAL1-I-SceI sequence was subcloned from a pre-existing plasmid (33) into the yeast shuttle vector pRS413 (14) at the SalI recognition site. This construct was transformed into strains to be linearized and selected on medium lacking histidine (SC-His). Linearization was induced in liquid culture in synthetic medium lacking histidine with 2% galactose for 24 hours. Strains were then transferred onto synthetic complete solid medium supplemented with Foa and extra uracil. Each strain was subjected to single round of colony purification on YPD medium and single isolates that had lost the pGAL-I-Sce-I construct, confirmed by replica-plating on SC-His, were selected for further analysis. Circular versus linear status of synIXR was tested by PCR using the primers originally designed to amplify the TeSS-I-Sce-I-TeSS ultramer (described above and FIG. 6).

[0060] Pulsed Field Gel Electrophoresis.

[0061] Full length yeast chromosomes were prepared in agarose plugs as previously described (34). Chromosomes were separated by clamped homogeneous electric field (CHEF) gel electrophoresis using the CHEF-DR III Pulsed Field Electrophoresis Systems (Biorad) with the following settings: 6V/cm, switch time 60-120 seconds over 24 hours, 14° C., 0.5×TBE, 1% gel prepared with low melting point agarose (Lonza, 50100). Gels were stained with 5 ug/ml ethidium bromide in water post-electrophoresis and then imaged.

[0062] SIR2 Gene Deletion.

[0063] The sir2ΔkanMX locus was amplified from the deletion mutant collection strain (35) using primers ˜500 bp flanking the gene deletion and subsequently transformed into the array of permutable strains by selection on YP supplemented with 200 μg/mL geneticin. SIR2 gene deletion was confirmed functionally by confirming the loss of mating proficiency.

[0064] The design of the telomerator includes several different elements (FIG. 1A). Centrally, the telomerator encodes an 18 base pair recognition sequence for the I-SceI homing endonuclease (9, 10). This site is flanked by a pair of convergent telomere seed sequences (TeSS) that encode ˜40 bp of conserved yeast telomere repeats [(TG_(1-3))₁₆ . . . (C_(1-3)A)₁₆] previously shown to serve as a minimal telomeric repeat (11) (FIG. 1B). The entire TeSS-I-SceI-TeSS sequence is encoded within an intron that interrupts the URA3 S. cerevisiae auxotrophic selectable marker coding sequence. Previous work showed that transplantation of the ACT1 gene intron into the middle of the URA3 coding sequence did not disrupt complementation on medium lacking uracil, indicating the mRNA was expressed and the non-native intron correctly spliced prior to translation of the URA3 gene product (12). Thus, the overall design of the telomerator is as follows: 5′-URA3exon1-intronACT1-TeSS-I-SceI-TeSS-intronACT1-URA3exon2-3′.

[0065] Expression of the I-SceI homing endonuclease, which recognizes and cleaves the 18 bp I-SceI recognition site, can linearize a circular DNA molecule encoding the telomerator. To facilitate inducible linearization, I-SceI expression can be placed under control of the inducible GAL1 promoter and thus linearization driven specifically by growth in medium containing galactose. Under standard growth conditions in glucose medium, the telomerator cassette should remain intact with cells expressing a functional Ura3 protein, complementing growth of a ura3Δ0 strain on medium lacking uracil. Following growth in galactose, the linearization reaction can be selected on 5-fluoroorotic acid (Foa) medium, which counterselects against URA3⁺ cells (13); a circular telomerator-containing molecule will grow on medium lacking uracil and die on FOA, but a cell harboring a linearized molecule, in which the URA3 gene component of the telomerator is literally split in two, should display the opposite growth phenotype (Ura⁻, Foa^R [uracil requiring and resistant to Foa]) (FIG. 1A).

[0066] While expression of the URA3 gene interrupted by the ACT1 intron was previously shown to complement growth of ura3 mutants on medium lacking uracil (12), the effect on complementation of further encoding the TeSS-I-SceI-TeSS sequence within the intron was unknown. To test this, we constructed the telomerator cassette in pRS413, a centromere-based yeast shuttle vector encoding the HIS3 selectable marker (14). The telomerator-containing construct was transformed into BY4741, a yeast strain with a complete URA3 deletion (ura3Δ0) (15), and plated on medium lacking uracil. Growth of the resulting transformants was compared to cells transformed with pRS416, another centromere-based yeast shuttle vector encoding a wild type URA3 gene, or a plasmid encoding the URA3exon1-intronACT1-URA3exon2 cassette (12), identical to the telomerator plasmid but lacking the TeSS-I-SceI-TeSS sequence. Growth of cells transformed with any of the three constructs on medium lacking uracil was indistinguishable (FIG. 2). Thus, the presence of the TeSS-I-SceI-TeSS sequence within the ACT1 intron interrupting the URA3 gene does not interfere with growth on medium lacking uracil.

[0067] Chromosome length has important consequences for mitotic stability as linear chromosomes shorter than 90 kb exhibit markedly decreased stability (16). Therefore, we tested the capacity of the telomerator to linearize circular DNA molecules in vivo using synIXR, a synthetic yeast chromosome arm corresponding to the right arm of chromosome nine previously constructed as a bacterial artificial chromosome (BAC) (8, 17) approximately 100 kb long. SynIXR encodes all 52 genes from the right arm of chromosome 9 (YIR001C-YIR044C), 2 genes from the left arm (YIL001W, YIL002C), the native chromosome 9 centromere (CEN9), a yeast selectable marker (LEU2), plus ˜10 kb of BAC vector sequence including the chloramphenicol resistance gene (FIG. 3A). synIXR, which encodes seven essential genes, was previously shown to be mitotically stable in vivo and power yeast cell growth at wild type levels in the absence of the wild type chromosome arm IXR (8). Two ‘gene-free’ regions of synIXR BAC were chosen as initial integration sites for the telomerator cassette, which was then introduced by homologous recombination to generate two new strains for linearization. Additionally, the URA3exon1-intronACT1-URA3exon2 cassette (12), lacking the TeSS-I-SceI-TeSS sequence, was integrated at the same two positions to generate equivalent, but non-linearizeable control strains. All four strains were transformed with a plasmid expressing pGAL1-I-SceI, grown in galactose medium for 24 hours, and finally ˜200 cells were plated on YPD, permissive yeast medium containing dextrose. These plates were replica printed onto medium containing Foa and uracil, or on medium lacking uracil (SC-Ura) or leucine (SC-Leu) (FIG. 3B). At either integration site 1 or 2, in cells expressing the functional telomerator cassette (+I-SceI), ˜50% of cells became resistant to growth on Foa and correspondingly lost ability to grow on SC-Ura, consistent with successful linearization (FIG. 3B, top row). The remaining half of cells that were sensitive to Foa was able to grow on SC-Ura, suggesting the synIXR BAC had not been linearized. When comparing cells harboring circular or linear synIXR molecules, there were no apparent changes to colony size or shape, suggesting the linearized construct was mitotically stable. Importantly, in cells lacking the I-SceI recognition site (−I-SceI), the Foa^R phenotype was not observed, demonstrating that linearization depends on this sequence (FIG. 3B, bottom row). Taken together, this work suggests that the telomerator efficient linearizes circular DNA molecules in vivo upon induction.

[0068] The telomerator enables fine control over the location at which a circular DNA molecule is linearized and thus represents a tool to probe the function of gene order, orientation, and chromosomal structure in vivo. For instance, if integrated between two genes, telomerator-driven linearization will yield novel telomere-promixal gene positioning that could lead to subtelomeric silencing. Furthermore, depending on the orientation of each gene with respect to the telomerator cassette, linearization could disrupt either 5′ or 3′ regulatory elements that drive their transcription. To test these ideas, we integrated the telomerator cassette three base pairs downstream of all 54 chromosome IX genes on synIXR BAC, generating an array of 54 permutable strains. We chose this position as it was previously shown to tolerate the insertion of synthetic sequences (8); indeed synIXR BAC encodes a 34 base pair site-specific recombination site (loxPsym) at this position downstream of every non-essential gene on the BAC with no effect on cell fitness (FIG. 3A). For the telomerator cassette integration, at each of the 47 non-essential genes we “overwrote” the loxPsym site, and for the 7 essential genes that had no pre-exiting loxPsym site we inserted the cassette cleanly 3 base pairs downstream of the stop codon (FIG. 4A). Integration at the correct locus was confirmed for all 54 permutable strains by PCR using a gene-specific primer in combination with a primer that annealed within the telomerator (FIG. 6). We found that at all 54 loci integration of the telomerator caused no noticeable change in fitness (FIG. 4B and data not shown). Notably, the promoter region of the telomerator-encoded URA3 contains a terminator sequence that would polyadenylate incoming transcripts; thus integration of the telomerator 3′ to any gene, while disrupting native 3′ end forming sequences, provides a built-in, non-native terminator sequence for the resulting transcript. Next, the pGAL-I-SceI construct was transformed into the 54 strains, which were grown in galactose medium for 24 hours to induce linearization. Foa resistant cells were selected, enabling isolation of the permuted array of linearized synIXR-containing strains. To investigate whether the synIXR BACs were linearized, full-length chromosomes from six permuted strains, pre- and post-linearization were chosen and separated by pulse-field gel electrophoresis. Only telomerator-integrated strains subjected to growth in galactose exhibited a band on the gel corresponding to the linearized form of synIXR (FIG. 4C). Of the 54 sites into which the telomerator had been integrated, 53 could be linearized and give rise to viable FoaR colonies. At just one position, YIR013C, linearization of synIXR was lethal (FIG. 4B). YIR013C encodes a non-essential, GATA family zinc finger motif containing protein with no annotated function. While not lethal, many other permuted chromosomes resulted in modest growth defects at 30° C. (FIG. 4B). At 37° C., almost half of all permuted strains grew very slowly. Together, the data indicate that telomerator-induced linearization provides a new way to generate novel phenotypes.

[0069] We hypothesized that telomeric silencing could underlie the fitness defects observed in many of the linear permutations of synIXR (FIG. 3B). Telomeric silencing, or the transcriptional repression of genes in proximity to telomeres, is an epigenetic phenomenon relying on the establishment of heterochromatin that spreads from the ends of chromosomes inwards. Linearization-dependent re-location of essential genes into sub-telomeric regions and the subsequent reduction in expression could have a major impact on impact cell fitness and/or survival. Indeed, mapping the position of the seven essential genes onto the array of linearized permutations of synIXR suggests that fitness defects tend to occur in strains in which one or more essential genes are re-located to within 10 kb of a telomere (FIG. 7). Consequently, they might be subject to silencing, a process mediated in part by the lysine deacetylase enzyme Sir2 (18), which deacetylates histone H4 (19). To test our hypothesis, we deleted SIR2 in each of the 54 linearizable synIXR strains. Following transformation of the pGAL1-I-SceI construct and growth in galactose, cells harboring linearized synIXR molecules were selected on medium containing Foa. We discovered that disruption of telomeric silencing by SIR2 deletion rescued nearly all growth defects associated linear permutations of synIXR (FIG. 5). Notably, this included the location at which we previously could not detect linearization, YIR013C (FIG. 3B) Importantly, these results are consistent with the conclusion that the telomerator-encoded 40 bp telomere seed sequences indeed generate functional telomeres complete with the appropriate establishment of heterochromatin. Moreover, the telomerator clearly provides a new means to probe epigenetic regulation and chromatin architecture as we show that proper gene expression can depend on the chromosomal location/environment in which a gene is positioned.

[0070] Another approach to introduce the Telomerator sequence into a circular DNA molecule for linearization is to include the TeSS-I-SceI-TeSS sequence as part of the protein coding sequence of the selectable marker. In such embodiments, the TeSS-I-SceI-TeSS sequence is “in-frame” with the selectable marker sequence (i.e., a multiple of 3) such that the resulting protein translation would not be truncated. The TeSS-I-SceI-Tess sequence is inserted into the selectable marker in a position that would not disrupt function of the resulting protein product.

[0071] SEQ ID NO:9 shows the TeSS-ISceI-TeSS sequence encoded within the native URA3 coding sequence:

(SEQ ID NO: 9)

atgTGTGTGGTGTGTGGGTGTGTGTGGGTGTGTGGGTGTGTGGGTAGGG

ATAACAGGGTAATCACCCACCACACACACCCACACACACCACACACCCA

CCCAtcgaaagctacatataaggaacgtgctgctactcatcctagtcct

gttgctgccaagctatttaatatcatgcacgaaaagcaaacaaacttgt

gtgcttcattggatgttcgtaccaccaaggaattactggagttagttga

agcattaggtcccaaaatttgtttactaaaaacacatgtggatatcttg

actgatttttccatggagggcacagttaagccgctaaaggcattatccg

ccaagtacaattttttactcttcgaagacagaaaatttgctgacattgg

taatacagtcaaattgcagtactctgcgggtgtatacagaatagcagaa

tgggcagacattacgaatgcacacggtgtggtgggcccaggtattgtta

gcggtttgaagcaggcggcagaagaagtaacaaaggaacctagaggcct

tttgatgttagcagaattgtcatgcaagggctccctatctactggagaa

tatactaagggtactgttgacattgcgaagagcgacaaagattttgtta

tcggctttattgctcaaagagacatgggtggaagagatgaaggttacga

ttggttgattatgacacccggtgtgggtttagatgacaagggagaTgca

ttgggtcaacagtatagaaccgtggatgatgtggtGtctacaggatctg

acattattattgttggaagaggactatttgcaaagggaagggatgctaa

ggtagagggtgaacgttacagaaaagcaggctgggaagcatatttgaga

agatgcggccagcaaaactaa

[0072] The TeSS-ISceI-TeSS sequence, which is 99 bp and thus should be in-frame, is inserted just past the start codon (ATG) of URA3. The lower case letters are native URA3 coding sequence and the upper case letters correspond to the TeSS-ISceI-TeSS

[0073] A construct encoding SEQ ID NO:9 was built and transformed into yeast. Plasmids were recovered from colonies that grew on SC-Ura plates and sequenced. Clone 1 has the following sequence:

(SEQ ID NO: 10)

atgTGTGTGGTGTGTGGGTGTGTGTGGGTGTGTGGGTGTGTGTGGGTG

TGTGGGTGTGTGGGTAGGGATAACAGGGTAATCACCCACCACACACAC

CCACACACACCACACACCCACCCAtcgaaagctacatataaggaacgt

gctgctactcatcctagtcctgttgctgccaagctatttaatatcatg

cacgaaaagcaaacaaacttgtgtgatcattggatgttcgtaccacca

aggaattactggagttagttgaagcattaggtcccaaaatttgtttac

taaaaacacatgtggatatcttgactgatttttccatggagggcacag

ttaagccgctaaaggcattatccgccaagtacaattttttactcttcg

aagacagaaaatttgctgacattggtaatacagtcaaattgcagtact

ctgcgggtgtatacagaatagcagaatgngcagacattacgaatgcac

acggtgtggtgggcccaggtattgttagcggtttgaagcaggcggcag

aagaagtaacaaaggaacctagaggccttttgatgttagcagaattgt

catgcaagggctccctatctactggagaatatactaagggtactgttg

acattgcgaagagcgacaaagattttgttatcggctttattgctcaaa

gagacatgggtggaagagatgaaggttacgattggttgattatgacac

ccggtgtgggtttagatgacaagggagacgcattgggtcaacagtata

gaaccgtggatgatgtggtctctacaggatctgacattattattgttg

gaagaggactatttgcaaagggaagggatgctaaggtagagggtgaac

gttacagaaaagcaggctgggaagcatatttgagaagatgcggccagc

aaaactaa

Clone 2 has the following sequence:

(SEQ ID NO: 11)

atgTGTGTGGTGTGTGGGTGTGTGTGGGTGTGTGGGTGTGTGGGTAGGGA

TAACAGGGTAATCACCCACCCAtcgaaagctacatataaggaacgtgctg

ctactcatcctagtcctgttgctgccaagctatttaatatcatgcacgaa

aagcaaacaaacttgtgtgatcattggatgttcgtaccaccaaggaatta

ctggagttagttgaagcattaggtcccaaaatttgtttactaaaaacaca

tgtggatatcttgactgatttttccatggagggcacagttaagccgctaa

aggcattatccgccaagtacaattttttactatcgaagacagaaaatttg

ctgacattggtaatacagtcaaattgcagtactctgcgggtgtatacaga

atagcagaatgggcagacattacgaatgcacacggtgtggtgggcccagg

tattgttagcggtttgaagcaggcggcagaagaagtaacaaaggaaccta

gaggccttttgatgttagcagaattgtcatgcaagggctccctatctact

ggagaatatactaagggtactgttgacattgcgaagagcgacaaagattt

tgttatcggattattgctcaaagagacatgggtggaagagatgaaggtta

cgattggttgattatgacacccggtgtgggtttagatgacaagggagacg

cattgggtcaacagtatagaaccgtggatgatgtggtctctacaggatct

gacattattattgttggaagaggactatttgcaaagggaagggatgctaa

ggtagagggtgaacgttacagaaaagcaggctgggaagcatatttgagaa

gatgcggccagcaaaactaa

[0074] Clone 3 has the following sequence:

(SEQ ID NO: 12)

atgTGTGTGGTGTGTGGGTGTGTGTGGGTGTGTGGGTGTGTGGGTAGGG

ATAACAGGGTAATCACCCACCACACACACCCACACACACCACACACCCA

CCCAtcgaaagctacatataaggaacgtgctgctactcatcctagtcct

gttgctgccaagctatttaatatcatgcacgaaaagcaaacaaacttgt

gtgcttcattggatgttcgtaccaccaaggaattactggagttagttga

agcattaggtcccaaaatttgtttactaaaaacacatgtggatatcttg

actgatttttccatggagggcacagttaagccgctaaaggcattatccg

ccaagtacaattttttactcttcgaagacagaaaatttgctgacattgg

taatacagtcaaattgcagtactctgcgggtgtatacagaatagcagaa

tgggcagacattacgaatgcacacggtgtggtgggcccaggtattgtta

gcggtttgaagcangcggcagaagaagtaacaaaggaacctagaggcct

tttgatgttagcagaattgtcatgcaagggctccctatctactggagaa

tatactaagggtactgttgacattgcgaagagcgacaaagattttgtta

tcggctttattgctcaaagagacatgggtggaagagatgaaggttacga

ttggttgattatgacacccggtgtgggtttagatgacaagggagacgca

ttgggtcaacagtatagaaccgtggatgatgtggtctctacaggatctg

acattattattgttggaagaggactatttgcaaagggaagggatgctaa

ggtagagggtgaacgttacagaaaagcaggctgggaagcatatttgaga

agatgcggccagcaaaactaa

[0075] Clone 4 has the following sequence:

(SEQ ID NO: 13)

atgTGTGTGGTGTGTGGGTGTGTGTGGGTGTGTGGGTGTGTGGGTAGGG

ATAACAGGGTAATCACCCACCCAtcgaaagctacatataaggaacgtgc

tgctactcatcctagtcctgttgctgccaagctatttaatatcatgcac

gaaaagcaaacaaacttgtgtgatcattggatgttcgtaccaccaagga

attactggagttagttgaagcattaggtcccaaaatttgtttactaaaa

acacatgtggatatcttgactgatttttccatggagggcacagttaagc

cgctaaaggcattatccgccaagtacaattttttactcttcgaagacag

aaaatttgctgacattggtaatacagtcaaattgcagtactctgcgggt

gtatacagaatagcagaatgggcagacattacgaatgcacacggtgtgg

tgggcccaggtattgttagcggtttgaagcaggcggcagaagaagtaac

aaaggaacctagaggccttttgatgttagcagaattgtcatgcaagggc

tccctatctactggngaatatactaagggtactgttgacattgcgaaga

gcgacaaagattttgttatcggctttattgctcaaagagacatgggtgg

aagagatgaaggttacgattggttgattatgacacccggtgtgggttta

gatgacaagggagacgcattgggtcaacagtatagaaccgtggatgatg

tggtctctacaggatctgacattattattgttggaagaggactatttgc

aaagggaagggatgctaaggtagagggtgaacgttacagaaaagcaggc

tgggaagcatatttgagaagatgcggccagcaaaactaa

[0076] The TeSS repeats are unstable in the absence of selection (i.e., growth on SC-Ura), likely due to slippage during DNA replication. Clone 3 matches exactly the designed sequence, suggesting this design can indeed complement growth. Two out of four clones have a truncated CA repeat, which likely increases the stability. Other embodiments of the telomerator can incorporate this design to generate a more stable construct.

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