Yeast artificial chromosome

A YAC is built using an initial circular DNA plasmid, which is typically cut into a linear DNA molecule using restriction enzymes; DNA ligase is then used to ligate a DNA sequence or gene of interest into the linearized DNA, forming a single large, circular piece of DNA. [https://doi.org/10.1073/pnas.87.11.4256] The basic generation of linear yeast artificial chromosomes can be broken down into 6 main steps:

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|1= Ligation of selectable marker into plasmid vector: this allows for the differential selection of colonies with, or without the marker gene. An antibiotic resistance gene allows the YAC vector to be amplified and selected for in E. coli by enabling E. coli containing the YAC vector to survive in the presence of an antibiotic. The YAC vector cloning site for foreign DNA is located within the SUP4 gene. This gene compensates for a mutation in the yeast host cell that causes the accumulation of red pigment. The host cells are normally red, and those transformed with YAC only, will form colorless colonies. Cloning of a foreign DNA fragment into the YAC causes insertional inactivation of the gene, restoring the red color. Therefore, the colonies that contain the foreign DNA fragment are red.Strachan T. (2011). Human molecular genetics / Tom Strachan and Andrew Read, 4th ed.

|2= Ligation of necessary centromeric sequences for mitotic stability{{cite journal | vauthors = Clarke L, Carbon J | title = Isolation of a yeast centromere and construction of functional small circular chromosomes | journal = Nature | volume = 287 | issue = 5782 | pages = 504–9 | date = October 1980 | pmid = 6999364 | doi = 10.1038/287504a0 | bibcode = 1980Natur.287..504C | s2cid = 4348814 }}

|3= Ligation of Autonomously Replicating Sequences (ARS) providing an origin of replication to undergo mitotic replication. This allows the plasmid to replicate extrachromosomally, but renders the plasmid highly mitotically unstable, and easily lost without the centromeric sequences.{{cite journal | vauthors = Struhl K, Stinchcomb DT, Scherer S, Davis RW | title = High-frequency transformation of yeast: autonomous replication of hybrid DNA molecules | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 76 | issue = 3 | pages = 1035–9 | date = March 1979 | pmid = 375221 | pmc = 383183 | doi = 10.1073/pnas.76.3.1035 | bibcode = 1979PNAS...76.1035S | doi-access = free }}

|4= Ligation of artificial telomeric sequences to convert circular plasmid into a linear piece of DNA {{cite journal | vauthors = Kiss GB, Amin AA, Pearlman RE | title = Two separate regions of the extrachromosomal ribosomal deoxyribonucleic acid of Tetrahymena thermophila enable autonomous replication of plasmids in Saccharomyces cerevisiae | journal = Molecular and Cellular Biology | volume = 1 | issue = 6 | pages = 535–43 | date = June 1981 | pmid = 6765606 | doi = 10.1128/mcb.1.6.535 | pmc = 369696 }}

|5= Insertion of DNA sequence to be amplified (up to 1000kb)

|6= Transformation yeast colony{{cite journal | vauthors = Burke DT, Carle GF, Olson MV | title = Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors | journal = Science | volume = 236 | issue = 4803 | pages = 806–12 | date = May 1987 | pmid = 3033825 | doi = 10.1126/science.3033825| bibcode = 1987Sci...236..806B }}

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Chromosome III is the third smallest chromosome in S. cerevisiae; its size was estimated from pulsed-field gel electro- phoresis studies to be 300–360 kb{{cite journal | title = The complete DNA sequence of yeast chromosome III | journal = Nature| date = May 1992 | doi = 10.1038/357038a0 | last1 = Oliver| first1 = S. G.| last2 = Van Der Aart| first2 = Q. J. M.| last3 = Agostoni-Carbone| first3 = M. L.| last4 = Aigle| first4 = M.| last5 = Alberghina| first5 = L.| last6 = Alexandraki| first6 = D.| last7 = Antoine| first7 = G.| last8 = Anwar| first8 = R.| last9 = Ballesta| first9 = J. P. G.| last10 = Benit| first10 = P.| last11 = Berben| first11 = G.| last12 = Bergantino| first12 = E.| last13 = Biteau| first13 = N.| last14 = Bolle| first14 = P. A.| last15 = Bolotin-Fukuhara| first15 = M.| last16 = Brown| first16 = A.| last17 = Brown| first17 = A. J. P.| last18 = Buhler| first18 = J. M.| last19 = Carcano| first19 = C.| last20 = Carignani| first20 = G.| last21 = Cederberg| first21 = H.| last22 = Chanet| first22 = R.| last23 = Contreras| first23 = R.| last24 = Crouzet| first24 = M.| last25 = Daignan-Fornier| first25 = B.| last26 = Defoor| first26 = E.| last27 = Delgado| first27 = M.| last28 = Demolder| first28 = J.| last29 = Doira| first29 = C.| last30 = Dubois| first30 = E.| volume = 357| issue = 6373| pages = 38–46| pmid = 1574125| bibcode = 1992Natur.357...38O| s2cid = 4271784| display-authors = 1}}

This chromosome has been the subject of intensive study, not least because it contains the three genetic loci involved in mating-type control: MAT, HML and HMR.{{cite journal | title = The complete DNA sequence of yeast chromosome III | journal = Nature| date = May 1992 | author = Strathern, J. N., Newlon, C. S., Herskowitz, I. & Hicks, J. B. | series = Cell | volume = 18 | issue = 6373| pages = 309–319 | publication-date = 1979 | doi = 10.1038/357038a0 | pmid = 1574125| bibcode = 1992Natur.357...38O| s2cid = 4271784}}

In March 2014, Jef Boeke of the Langone Medical Centre at New York University, published that his team has synthesized one of the S. cerevisiae 16 yeast chromosomes, the chromosome III, that he named synIII.{{cite news | last=Shukman | first=David | url=https://www.bbc.com/news/science-environment-26768445 | title=Scientists hail synthetic chromosome advance | work=BBC News | date=27 March 2014 | access-date=2014-03-28 }}24674868{{cite journal | vauthors = Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, etal | title = Total synthesis of a functional designer eukaryotic chromosome | journal = Science | volume = 344 | issue = 6179 | pages = 55–8 | date = April 2014 | pmid = 24674868 | pmc = 4033833 | doi = 10.1126/science.1249252 | bibcode = 2014Sci...344...55A }} The procedure involved replacing the genes in the original chromosome with synthetic versions and the finished synthesized chromosome was then integrated into a yeast cell. It required designing and creating 273,871 base pairs of DNA - fewer than the 316,667 pairs in the original chromosome.

Yeast expression vectors, such as YACs, YIps (yeast integrating plasmids), and YEps (yeast episomal plasmids), have an advantage over bacterial artificial chromosomes (BACs) in that they can be used to express eukaryotic proteins that require posttranslational modification. By being able to insert large fragments of DNA, YACs can be utilized to clone and assemble the entire genomes of an organism.Burke, D., Carle, G. & Olson, M. Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236, 806–812 (1987). With the insertion of a YAC into yeast cells, they can be propagated as linear artificial chromosomes, cloning the inserted regions of DNA in the process. With this completed, two processes can be used to obtain a sequenced genome, or region of interest:

1. Physical Mapping [https://doi.org/10.1128/mcb.8.2.595-604.1988]
2. Chromosome Walking{{cite journal | last1 = Kere | first1 = J. | last2 = Nagaraja | first2 = R. | last3 = Mumm | first3 = S. | last4 = Ciccodicola | first4 = A. | last5 = D'Urso | first5 = M. | year = 1992 | title = Mapping human chromosomes by walking with sequence-tagged sites from end fragments of yeast artificial chromosome inserts | journal = Genomics | volume = 14 | issue = 2| pages = 241–248 | doi=10.1016/s0888-7543(05)80212-5| pmid = 1427839 }}

This is significant in that it allows for the detailed mapping of specific regions of the genome. Whole human chromosomes have been examined, such as the X chromosome,{{cite journal | last1 = Ross | first1 = M. T. | display-authors = etal | year = 2005 | title = The DNA sequence of the human X chromosome | journal = Nature | volume = 434 | issue = 7031| pages = 325–337 | doi = 10.1038/nature03440 | pmid = 15772651 | pmc = 2665286 | bibcode = 2005Natur.434..325R }} generating the location of genetic markers for numerous genetic disorders and traits.{{cite journal | vauthors = Petrukhin K, Fischer SG, Pirastu M, Tanzi RE, Chernov I, Devoto M, Brzustowicz LM, Cayanis E, Vitale E, Russo JJ | title = Mapping, cloning and genetic characterization of the region containing the Wilson disease gene | journal = Nature Genetics | volume = 5 | issue = 4 | pages = 338–43 | date = December 1993 | pmid = 8298640 | doi = 10.1038/ng1293-338 | s2cid = 12997875 }}

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In the United States, the Human Genome Project first took clear form in February of 1988, with the release of the National Research Council (NRC) report Mapping and Sequencing the Human Genome.{{cite journal | last1 = Olson | first1 = M V | title = The Human Genome Project. | journal = Proceedings of the National Academy of Sciences | date = 15 May 1993 | volume = 90 | issue = 10 | pages = 4338–4344 | issn = 0027-8424 | eissn = 1091-6490 | doi = 10.1073/pnas.90.10.4338 | pmid = 8506271 | pmc = 46506 | bibcode = 1993PNAS...90.4338O | url = | doi-access = free }} YACs are significantly less stable than BACs, producing "chimeric effects" : artifacts where the sequence of the cloned DNA actually corresponds not to a single genomic region but to multiple regions. Chimerism may be due to either co-ligation of multiple genomic segments into a single YAC, or recombination of two or more YACs transformed in the same host Yeast cell.{{cite journal | vauthors = Haldi M, Perrot V, Saumier M, Desai T, Cohen D, Cherif D, Ward D, Lander ES | title = Large human YACs constructed in a rad52 strain show a reduced rate of chimerism | journal = Genomics | volume = 24 | issue = 3 | pages = 478–84 | date = December 1994 | pmid = 7713499 | doi = 10.1006/geno.1994.1656 | doi-access = free }} The incidence of chimerism may be as high as 50%.{{cite journal | vauthors = Bronson SK, Pei J, Taillon-Miller P, Chorney MJ, Geraghty DE, Chaplin DD | title = Isolation and characterization of yeast artificial chromosome clones linking the HLA-B and HLA-C loci | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 88 | issue = 5 | pages = 1676–80 | date = March 1991 | pmid = 2000377 | pmc = 51087 | doi = 10.1073/pnas.88.5.1676 | bibcode = 1991PNAS...88.1676B | doi-access = free }} Other artifacts are deletion of segments from a cloned region, and rearrangement of genomic segments (such as inversion). In all these cases, the sequence as determined from the YAC clone is different from the original, natural sequence, leading to inconsistent results and errors in interpretation if the clone's information is relied upon. Due to these issues, the Human Genome Project ultimately abandoned the use of YACs and switched to bacterial artificial chromosomes, where the incidence of these artifacts is very low. In addition to stability issues, specifically the relatively frequent occurrence of chimeric events, YACs proved to be inefficient when generating the minimum tiling path covering the entire human genome. Generating the clone libraries is time consuming. Also, due to the nature of the reliance on sequence tagged sites (STS) as a reference point when selecting appropriate clones, there are large gaps that need further generation of libraries to span. It is this additional hindrance that drove the project to utilize BACs instead.Rowen, L., Mahairas, G. & Hood, L. Sequencing the Human Genome. Science (1997). This is due to two factors:{{cite journal | vauthors = McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, etal | title = A physical map of the human genome | journal = Nature | volume = 409 | issue = 6822 | pages = 934–41 | date = February 2001 | pmid = 11237014 | doi = 10.1038/35057157 | bibcode = 2001Natur.409..934M | doi-access = free }}

1. BACs are much quicker to generate, and when generating redundant libraries of clones, this is essential
2. BACs allow more dense coverage with STSs, resulting in more complete and efficient minimum tiling paths generated in silico.

However, it is possible to utilize both approaches, as was demonstrated when the genome of the nematode, C. elegans. There majority of the genome was tiled with BACs, and the gaps filled in with YACs.

• Bacterial artificial chromosome (BAC)
• Cosmid
• Fosmid
• Genetic engineering
• Human artificial chromosome
• Autonomously replicating sequence(ARS)
• Cloning Vector

{{reflist|2}}

• {{MeshName|Yeast+Artificial+Chromosomes}}
• North Dakota State University [http://www.ndsu.edu/pubweb/~mcclean/plsc731/cloning/cloning1.htm Cloning and Cloning Vectors Resource]
• Molecular Cell Biology 4th Edition [NCBI Database]: [https://www.ncbi.nlm.nih.gov/books/NBK21498/ DNA Cloning with Plasmid Vectors, Ch. 7]
• [http://genome.wustl.edu/ Washington University Genome Institute]
• [http://www.yeastgenome.org/ Saccharomyces Genome Database]

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Category:Molecular biology