Information

32.2: Reading and Writing Genomes - Biology

32.2: Reading and Writing Genomes - Biology


We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

As a motivation, consider the following question: Is there any technology that is not biologically motivated or inspired? Biology and our observations of it influence our lives pervasively. Even in telecommunications, the potential of quantum-level molecular computing is promising, and is expected to be a major player in the future.

Church has been involved in molecular computing in his own research, and claims that once harnessed, it has great advantages over their current silicon counterparts. For example, molecular computing can provide at least 10% greater efficiency per Joule in computation. More profound perhaps is its potential effect on data storage. Current data storage media (magnetic disk, solid-state drives, etc.) is much less (billions times) dense than DNA. The limitation of DNA as data storage is that it has a high error rate. Church is currently involved in a project exploring reliable storage through the use of error correction and other techniques.

In a 2009 Nature Biotechnology review article [1], Church explores the potential for efficient methods to read and write to DNA. He observes that in the past decade there has been a 10( imes) exponential curve in both sequencing and oligo synthesis, with double-stranded synthesis lagging behind but steadily increasing. Compared to the 1.5( imes) exponential curve for VLSI (Moore’s Law), the increase on the biological side is more dramatic, and there is no theoretical argument yet for why the trend should taper off. In summary, there is great potential for genome synthesis and engineering.

Did You Know?

George Church was an early pioneer of genome sequencing. In 1978, Church was able to sequence plasmids at $10 per base. By 1984, together with Walter Gilbert, he developed the first direct genomic sequencing method [3]. With this breakthrough, he helped initiate the Human Genome Project in 1984. This proposal aimed to sequence an entire human haploid genome at $1 per base, requiring a total budget of $3 billion. This quickly played out into the well-known race between Celera and UCSC-Broad-Sanger. Although the latter barely won in the end, their sequence had many errors and gaps, whereas Celera’s version was much higher quality. Celera initially planned on releasing the genome in 50 kb fragments, which researchers could perform alignments on, much like BLAST. Church once approached Celera’s founder, Craig Venter, and received a promise to obtain the entire genome on DVD after release. However, questioning the promise, Church decided instead to download the genome directly from Celera by taking advantage of the short fragment releases. Using automated crawl and download scripts, Church managed to download the entire genome in 50 kb fragments within three days!


The Down syndrome 'super genome'

Down syndrome -- also known as trisomy 21 -- is a genetic disorder caused by an additional third chromosome 21. Although this genetic abnormality is found in one out of 700 births, only 20% of fetuses with trisomy 21 reach full term. But how do they manage to survive the first trimester of pregnancy despite this heavy handicap? Researchers from the Universities of Geneva (UNIGE) and Lausanne (UNIL) have found that children born with Down syndrome have an excellent genome in many ways -- better, in fact, than the average genome of people without the genetic abnormality. It is possible that this genome offsets the disabilities caused by the extra chromosome, helping the fetus to survive and the child to grow and develop. You can find out more about these discoveries in the journal Genome Research.

Trisomy 21 is a serious genetic disorder, with four pregnancies out of five not reaching term naturally if the fetus is affected. However, 20% of conceptuses with Down syndrome are born live, grow up and can reach the age of 65. How is this possible? Researchers from UNIGE and UNIL hypothesised that individuals born with Down syndrome possess a high quality genome that has the ability to compensate for the effects of the third chromosome 21.

Variation, regulation and expression all tested

"The genome consists of all the genetic material that makes up an individual," explains Stylianos Antonarakis, the honorary professor in UNIGE's Faculty of Medicine who led the research. "It's the genome that determines what becomes of a person, and makes him or her grow up and grow old, with or without disease. Some genomes are of better quality than others, and can also be less prone to illnesses such as cancer." Basing their work on the hypothesis of a the quality of the genome, the geneticists tested the gene variation, regulation and expression of 380 individuals with Down syndrome and compared them to people without the genetic disorder.

The first test consisted of observing the presence of rare variants, i.e. potentially harmful genetic mutations, in people with Down. It is known that the a chromosome can have different rare variants in its two copies. In a person with Down, however, the rare mutations that are identical for all three copies of chromosome 21 and limited in number, thereby reducing the total of potentially deleterious variants.

In a next step the geneticists have studied the regulation of genes on chromosome 21. Each gene has switches that regulate its expression either positively or negatively. Since people with Down have three chromosomes 21, most of these genes are overexpressed. "But we discovered that people with Down syndrome have more regulators that diminish the expression of the 21 genes, making it possible to compensate for the surplus induced by the third copy," says Konstantin Popadin, a researcher at UNIL's Center for Integrative Genomics.

Finally, the researchers focused on the variation gene expression for the chromosomes of the entire genome. Each gene expression on a scale from 0 to 100 forms part of a global spread curve, with the median -- 50 -- considered the ideal expression. "For a normal genome, the expressions oscillate between 30 and 70, while for a person with Down syndrome, the curve is narrower around the peak that is very close to 50 for genes on all the chromosomes," continues professor Antonarakis. "In other words, this means that the genome of someone with Down leans towards the average -- optimal functioning." Indeed, the smaller the gene expression variations are, the better the genome.

A superior genome that compensates for the disability

The UNIGE and UNIL geneticists were thus able to test the three functions of genomes of people suffering from Down syndrome. "The research has shown that for a child with Down to survive pregnancy and then grow, his or her genome must be of a higher quality so that it can compensate for the disabilities caused by the extra copy of chromosome 21," concludes Popadin. These conclusions may also apply to other serious genetic disorders where pregnancies reach full term.


Genetic Engineering and Synthetic Genomics in Yeast to Understand Life and Boost Biotechnology

The field of genetic engineering was born in 1973 with the "construction of biologically functional bacterial plasmids in vitro". Since then, a vast number of technologies have been developed allowing large-scale reading and writing of DNA, as well as tools for complex modifications and alterations of the genetic code. Natural genomes can be seen as software version 1.0 synthetic genomics aims to rewrite this software with "build to understand" and "build to apply" philosophies. One of the predominant model organisms is the baker's yeast Saccharomyces cerevisiae. Its importance ranges from ancient biotechnologies such as baking and brewing, to high-end valuable compound synthesis on industrial scales. This tiny sugar fungus contributed greatly to enabling humankind to reach its current development status. This review discusses recent developments in the field of genetic engineering for budding yeast S. cerevisiae, and its application in biotechnology. The article highlights advances from Sc1.0 to the developments in synthetic genomics paving the way towards Sc2.0. With the synthetic genome of Sc2.0 nearing completion, the article also aims to propose perspectives for potential Sc3.0 and subsequent versions as well as its implications for basic and applied research.

Keywords: Saccharomyces cerevisiae Sc2.0 Sc3.0 biotechnology cell factory genetic engineering synthetic biology synthetic genomics yeast.

Conflict of interest statement

The author declares no conflict of interest.

Figures

Established yeast 1.0 applications. (…

Established yeast 1.0 applications. ( A ) Yeast has been widely used to…

The Sc2.0 project and its applications. ( A ) Step by step replacement…

Potential design principles for the…

Potential design principles for the Sc3.0 genome. ( A ) Recent data suggest…


References

Gibson, D.G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56 (2010).

Gibson, D.G. Oligonucleotide assembly in yeast to produce synthetic DNA fragments. Methods Mol. Biol. 852, 11–21 (2012).

Gibson, D.G. Enzymatic assembly of overlapping DNA fragments. Methods Enzymol. 498, 349–361 (2011).

Gibson, D.G. Gene and genome construction in yeast. Curr. Protoc. Mol. Biol. 94, 3.22 (2011).

Gibson, D.G. Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res. 37, 6984–6990 (2009).

Gibson, D.G. et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215–1220 (2008).

Gibson, D.G. et al. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc. Natl. Acad. Sci. USA 105, 20404–20409 (2008).

Gibson, D.G., Smith, H.O., Hutchison, C.A. III., Venter, J.C. & Merryman, C. Chemical synthesis of the mouse mitochondrial genome. Nat. Methods 7, 901–903 (2010).

Gibson, D.G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).

Benders, G.A. et al. Cloning whole bacterial genomes in yeast. Nucleic Acids Res. 38, 2558–2569 (2010).

Lartigue, C. et al. Genome transplantation in bacteria: changing one species to another. Science 317, 632–638 (2007).

Lartigue, C. et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325, 1693–1696 (2009).

Venter, J.C. Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life (Viking, 2013).

Ma, S., Tang, N. & Tian, J. DNA synthesis, assembly and applications in synthetic biology. Curr. Opin. Chem. Biol. 16, 260–267 (2012).

Ellis, T., Adie, T. & Baldwin, G.S. DNA assembly for synthetic biology: from parts to pathways and beyond. Integr. Biol. (Camb.) 3, 109–118 (2011).

Itaya, M., Tsuge, K., Koizumi, M. & Fujita, K. Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc. Natl. Acad. Sci. USA 102, 15971–15976 (2005).

Smailus, D.E., Warren, R.L. & Holt, R.A. Constructing large DNA segments by iterative clone recombination. Syst. Synth. Biol. 1, 139–144 (2007).

Ma, H., Kunes, S., Schatz, P.J. & Botstein, D. Plasmid construction by homologous recombination in yeast. Gene 58, 201–216 (1987).

Tagwerker, C. et al. Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast. Nucleic Acids Res. 40, 10375–10383 (2012).

Karas, B.J., Tagwerker, C., Yonemoto, I.T., Hutchison, C.A. III. & Smith, H.O. Cloning the Acholeplasma laidlawii PG-8A genome in Saccharomyces cerevisiae as a yeast centromeric plasmid. ACS Synth. Biol. 1, 22–28 (2012).

Karas, B.J. et al. Direct transfer of whole genomes from bacteria to yeast. Nat. Methods 10, 410–412 (2013).

Schwartz, D.C. & Cantor, C.R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37, 67–75 (1984).

Noskov, V.N. et al. Assembly of large, high G+C bacterial DNA fragments in yeast. ACS Synth. Biol. 1, 267–273 (2012).

Kouprina, N. & Larionov, V. Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat. Protoc. 3, 371–377 (2008).

Kornberg, R.D. Eukaryotic transcriptional control. Trends Cell Biol. 9, M46–M49 (1999).

Kozak, M. Initiation of translation in prokaryotes and eukaryotes. Gene 234, 187–208 (1999).

Marschall, P., Malik, N. & Larin, Z. Transfer of YACs up to 2.3 Mb intact into human cells with polyethylenimine. Gene Ther. 6, 1634–1637 (1999).

van Brabant, A.J., Buchanan, C.D., Charboneau, E., Fangman, W.L. & Brewer, B.J. An origin-deficient yeast artificial chromosome triggers a cell cycle checkpoint. Mol. Cell 7, 705–713 (2001).

Carr, P.A. & Church, G.M. Genome engineering. Nat. Biotechnol. 27, 1151–1162 (2009).

Wang, H.H. et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460, 894–898 (2009).

Isaacs, F.J. et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348–353 (2011).

Ellis, H.M., Yu, D., DiTizio, T. & Court, D.L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl. Acad. Sci. USA 98, 6742–6746 (2001).

Dymond, J.S. et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477, 471–476 (2011).

Gaj, T., Gersbach, C.A. & Barbas, C.F. III. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 31, 397–405 (2013).

Gurdon, J.B. & Byrne, J.A. The first half-century of nuclear transplantation. Proc. Natl. Acad. Sci. USA 100, 8048–8052 (2003).

Gurdon, J.B. & Wilmut, I. Nuclear transfer to eggs and oocytes. Cold Spring Harb. Perspect. Biol. 3, a002659 (2011).

Forster, A.C. & Church, G.M. Towards synthesis of a minimal cell. Mol. Syst. Biol. 2, 45 (2006).

Forster, A.C. & Church, G.M. Synthetic biology projects in vitro. Genome Res. 17, 1–6 (2007).

Jewett, M.C. & Forster, A.C. Update on designing and building minimal cells. Curr. Opin. Biotechnol. 21, 697–703 (2010).

Medema, M.H., van Raaphorst, R., Takano, E. & Breitling, R. Computational tools for the synthetic design of biochemical pathways. Nat. Rev. Microbiol. 10, 191–202 (2012).

Chan, L.Y., Kosuri, S. & Endy, D. Refactoring bacteriophage T7. Mol. Syst. Biol. 1, 2005.0018 (2005).

Jaschke, P.R., Lieberman, E.K., Rodriguez, J., Sierra, A. & Endy, D. A fully decompressed synthetic bacteriophage oX174 genome assembled and archived in yeast. Virology 434, 278–284 (2012).

Fraser, C.M. et al. The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403 (1995).

Karr, J.R. et al. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401 (2012).

Dormitzer, P.R. et al. Synthetic generation of influenza vaccine viruses for rapid response to pandemics. Sci. Transl. Med. 5, 185ra68 (2013).

Guye, P., Li, Y., Wroblewska, L., Duportet, X. & Weiss, R. Rapid, modular and reliable construction of complex mammalian gene circuits. Nucleic Acids Res. 41, e156 (2013).

Temme, K., Zhao, D. & Voigt, C.A. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc. Natl. Acad. Sci. USA 109, 7085–7090 (2012).

O'Neill, B.M. et al. An exogenous chloroplast genome for complex sequence manipulation in algae. Nucleic Acids Res. 40, 2782–2792 (2012).

Smith, H.O., Hutchison, C.A. III., Pfannkoch, C. & Venter, J.C. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 100, 15440–15445 (2003).


Access options

Get full journal access for 1 year

All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.

Get time limited or full article access on ReadCube.

All prices are NET prices.


Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses

D. Prangishvili, R.A. Garrett Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses. Biochem Soc Trans 1 April 2004 32 (2): 204–208. doi: https://doi.org/10.1042/bst0320204

The remarkable diversity of the morphologies of viruses found in terrestrial hydrothermal environments with temperatures >80°C is unprecedented for aquatic ecosystems. The best-studied viruses from these habitats have been assigned to novel viral families: Fuselloviridae, Lipothrixviridae and Rudiviridae. They all have double-stranded DNA genomes and infect hyperthermophilic crenarchaea of the orders Sulfolobales and Thermoproteales. Representatives of the different viral families share a few homologous ORFs (open reading frames). However, about 90% of all ORFs in the seven sequenced genomes show no significant matches to sequences in public databases. This suggests that these hyperthermophilic viruses have exceptional biochemical solutions for biological functions. Specific features of genome organization, as well as strategies for DNA replication, suggest that phylogenetic relationships exist between crenarchaeal rudiviruses and the large eukaryal DNA viruses: poxviruses, the African swine fever virus and Chlorella viruses. Sequence patterns at the ends of the linear genome of the lipothrixvirus AFV1 are reminiscent of the telomeric ends of linear eukaryal chromosomes and suggest that a primitive telomeric mechanism operates in this virus.


Frequently bought together

Review

“This third edition is absolutely necessary to incorporate the recent advances, such as genome sequencing, polymerase chain reaction, and microarray technology, in this field.” (Doody’s, 19 October 2012)

About the Author

Jeremy W. Dale is a professor emeritus in the Microbial and Cellular Sciences Department at the University of Surrey, UK.

Malcolm von Schantz is Professor of Chronobiology at the University of Surrey. He is an internationally recognised researcher and an experienced educator, who received his training in Sweden, the United States, and the UK.

Nicholas Plant is the author of From Genes to Genomes: Concepts and Applications of DNA Technology, 3rd Edition, published by Wiley.


Genetics, genes, and genomes

My sister is convinced I have a 100% chance of having red headed children because my wife is red headed and we have red heads on either side of my family. My hair color is dark brown and my parents had no red headed children.

For context, I don’t care about what color hair my children will have. I just want to settle the record with regards to how my family understands how red heads are determined via their genetics.

35 18 26 22

Dominate the game. Destroy their Nexus. Experience Wild Rift on the big screen with BlueStacks. Download Now!

Are deletions or duplications worse? Or is it "depends"?

Are people the most heterogenously mating species?

Let me explain what i mean - usually there are major extinction or bottleneck events for specie every thousand or so years. This usually means that in confined area, all mating partners are descendent from a small population that survived that drought, epidemic or something like that. However, in case of people, we have been extremely successful for hundreds of thousands of years thus there are regularly intermixing populations with a very heterogenous background.

My question is are our mating partners usually way more distantly related than other animal species? Is there a paper that checked this thing?


Reproductive genome from the laboratory

The field of synthetic biology does not only observe and describe processes of life but also mimics them. A key characteristic of life is the ability to ability for replication, which means the maintenance of a chemical system. Scientists at the Max Planck Institute of Biochemistry in Martinsried generated a system, which is able to regenerate parts of its own DNA and protein building blocks.

In the field of synthetic biology, researchers investigate so-called "bottom-up" processes, which means the generation of life mimicking systems from inanimate building blocks. One of the most fundamental characteristics of all living organism is the ability to conserve and reproduce itself as distinct entities. However, the artificial "bottom-up" approach to create a system, which is able to replicate itself, is a great experimental challenge. For the first time, scientists have succeeded in overcoming this hurdle and synthesizing such a system.

Hannes Mutschler, head of the research group "Biomimetic Systems" at the Max Planck Institute for Biochemistry, and his team are dedicated to imitate the replication of genomes and protein synthesis with a "bottom-up" approach. Both processes are fundamental for the self-preservation and reproduction of biological systems. The researchers now succeeded in producing an in vitro system, in which both processes could take place simultaneously. "Our system is able to regenerate a significant proportion of its molecular components itself," explains Mutschler.

In order to start this process, the researchers needed a construction manual as well as various molecular "machines" and nutrients. Translated into biological terms, this means the construction manual is DNA, which contains the information to produce proteins. Proteins are often referred to as "molecular machines" because they often act as catalysts, which accelerate biochemical reactions in organisms. The basic building blocks of DNA are the so-called nucleotides. Proteins are made of amino acids.

Modular structure of the construction manual

Specifically, the researchers have optimized an in vitro expression system that synthesizes proteins based on a DNA blueprint. Due to several improvements, the in vitro expression system is now able to synthesize proteins, known as DNA polymerases, very efficiently. These DNA polymerases then replicate the DNA using nucleotides. Kai Libicher, first author of the study, explains: "Unlike previous studies, our system is able to read and copy comparatively long DNA genomes.

The scientists assembled the artificial genomes from up to eleven ring-shaped pieces of DNA. This modular structure enables them to insert or remove certain DNA segments easily. The largest modular genome reproduced by the researchers in the study consists of more than 116,000 base pairs, reaching the genome length of very simply cells.

Regeneration of proteins

Apart from encoding polymerases that are important for DNA replication, the artificial genome contains blueprints for further proteins, such as 30 translation factors originating from the bacterium Escherischia coli. Translation factors are important for the translation of the DNA blueprint into the respective proteins. Thus, they are essential for self-replicating systems, which imitate biochemical processes. In order to show that the new in vitro expression system is not only able to reproduce DNA, but is also able to produce its own translation factors, the researchers used mass spectrometry. With this analytic method, they determined the amount of proteins produced by the system.

Surprisingly, some of the translation factors were even present in larger quantities after the reaction than added before. According to the researchers, this is an important step towards a continuously self-replicating system that mimics biological processes.

In the future, the scientists want to extend the artificial genome with additional DNA segments. In cooperation with colleagues from the research network MaxSynBio, they want to produce an enveloped system that is able to remain viable by adding nutrients and disposing of waste products. Such a minimal cell could then be used, for example, in biotechnology as a tailor-made production machine for natural substances or as a platform for building even more complex life-like systems.


32.2: Reading and Writing Genomes - Biology

Research Area:
Genetics, Cell, and Developmental Biology
Computational Biology

B.A., Boston University, 2004
Ph.D. Johns Hopkins University, 2013

Mammalian development relies on a complex interplay between genetic and epigenetic factors to create trillions of highly specialized cells from the same genetic blueprint. This process is orchestrated in part by gene regulatory sequences encoded in DNA, which in turn are influenced by epigenetic properties including DNA methylation, DNA packaging, and modifications of DNA packaging proteins. Mammalian genomes contain hundreds of epigenetic regulators -- collectively referred to as the &ldquoepigenetic machinery&rdquo -- which are responsible for reading, writing, and erasing this epigenetic information. Our research seeks to understand how the epigenetic machinery works, and how its malfunction contributes to disease.

Current directions in the lab seek to answer the following key questions about the epigenetic machinery:

1. What are the specific regulatory sequences and target genes influenced by components of the epigenetic machinery, and in what cell types/contexts?

2. How are components of the epigenetic machinery recruited to specific regions of the genome (e.g. regulatory sequences) in specific cellular contexts?

3. By what mechanisms do disease-causing mutations in components of the epigenetic machinery give rise to phenotypes at the molecular, cellular, and organismal levels.

To answer these questions, we use a variety of tools including epigenomics, genome-editing, single-cell genomics, and computational biology, with a focus on mouse developmental and human cell culture models.


Watch the video: Δείγμα υλικού πρώτης γραφής και ανάγνωσης (December 2022).