Book contents
- Single-Molecule Science
- Single-Molecule Science
- Copyright page
- Dedication
- Contents
- Contributors
- Foreword
- Preface
- Part I Super-Resolution Microscopy and Molecular Imaging Techniques to Probe Biology
- 1 Introduction on Single-Molecule Science
- 2 One Molecule, Two Molecules, Red Molecules, Blue Molecules
- 3 Multiscale Fluorescence Imaging
- 4 Long-Read Single-Molecule Optical Maps
- Part II Protein Folding, Structure, Confirmation, and Dynamics
- Part III Mapping DNA Molecules at the Single-Molecule Level
- Part IV Single-Molecule Biology to Study Gene Expression
- Index
- References
4 - Long-Read Single-Molecule Optical Maps
from Part I - Super-Resolution Microscopy and Molecular Imaging Techniques to Probe Biology
Published online by Cambridge University Press: 05 May 2022
Book contents
- Single-Molecule Science
- Single-Molecule Science
- Copyright page
- Dedication
- Contents
- Contributors
- Foreword
- Preface
- Part I Super-Resolution Microscopy and Molecular Imaging Techniques to Probe Biology
- 1 Introduction on Single-Molecule Science
- 2 One Molecule, Two Molecules, Red Molecules, Blue Molecules
- 3 Multiscale Fluorescence Imaging
- 4 Long-Read Single-Molecule Optical Maps
- Part II Protein Folding, Structure, Confirmation, and Dynamics
- Part III Mapping DNA Molecules at the Single-Molecule Level
- Part IV Single-Molecule Biology to Study Gene Expression
- Index
- References
Summary
More than 150 years after the discovery of DNA (Dahm, 2005) and 50 years after the determination of a DNA duplex structure (Choudhuri, 2003), our understanding of genomics is still lacking. Despite a massive effort in genetic studies, there are still missing pieces in the puzzle: many traits have no corresponding genetic features, the reasons for variations among different individuals within a species are still a mystery, and the lack of single-molecule resolution hinders many types of analysis. These gaps are exemplified by inherent limitations in the currently leading technique for DNA studies, next generation sequencing (NGS). The initial “input” for NGS consists of genomes extracted from a large number of cells, and the final “output” is a single sequence. Thus, the produced data represents an average sequence of the majority of the sequenced cells. This results in oversight of several significant biological aspects, since variations within the population and rare cellular populations are not detected.
- Type
- Chapter
- Information
- Single-Molecule ScienceFrom Super-Resolution Microscopy to DNA Mapping and Diagnostics, pp. 49 - 64Publisher: Cambridge University PressPrint publication year: 2022
References
Anon., (n.d.) GeneCards. Human Genes | Gene Database | Gene Search. www.genecards.org/.Google Scholar
Baday, M., et al. (2012). Multi-Color Super-Resolution DNA Imaging for Genetic Analysis. Nano Letters, 12, 3861–3866.Google Scholar
Batzer, M. A. and Deininger, P. L. (2002). Alu Repeats and Human Genomic Diversity. Nature Reviews. Genetics, 3(5), 370–379. http://dx.doi.org/10.1038/nrg798.Google Scholar
Bensimon, A., et al. (1994). Alignment and Sensitive Detection of DNA by a Moving Interface. Science, 265(5181), 2096–2098.Google Scholar
Cabianca, D. S. and Gabellini, D. (2010). The Cell Biology of Disease: FSHD: Copy Number Variations on the Theme of Muscular Dystrophy. The Journal of Cell Biology, 191(6), 1049–1060. www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3002039&tool=pmcentrez&rendertype=abstract.CrossRefGoogle ScholarPubMed
Cai, W., Jing, J., Irvin, B., et al. (1998). High-Resolution Restriction Maps of Bacterial Artificial Chromosome Constructed by Optical Mapping. Proceedings of the National Academy of Science USA, 95(March), 3390–3395.Google Scholar
Choudhuri, S. (2003). The Path from Nuclein to Human Genome: A Brief History of DNA with a Note on Human Genome Sequencing and Its Impact on Future Research in Biology. Bulletin of Science, Technology and Society, 23(5), 360–367. http://bst.sagepub.com/cgi/doi/10.1177/0270467603259770.Google Scholar
Dahm, R. (2005). Friedrich Miescher and the Discovery of DNA. Developmental Biology, 278(2), 274–288.Google Scholar
Dinsdale, E. A., et al. (2008). Functional Metagenomic Profiling of Nine Biomes. Nature, 452(7187), 629–632. www.ncbi.nlm.nih.gov/pubmed/18337718.CrossRefGoogle ScholarPubMed
Gaillard, M.-C., et al. (2014). Differential DNA Methylation of the D4Z4 Repeat in Patients with FSHD and Asymptomatic Carriers. Neurology, 83(8), 733–742. www.ncbi.nlm.nih.gov/pubmed/25031281.CrossRefGoogle ScholarPubMed
Grönlund, M. M., et al. (2000). Importance of Intestinal Colonisation in the Maturation of Humoral Immunity in Early Infancy: A Prospective Follow Up Study of Healthy Infants Aged 0–6 Months. Archives of Disease in Childhood. Fetal and Neonatal Edition, 83(3), F186–F192. www.ncbi.nlm.nih.gov/pubmed/11040166.Google Scholar
Grunwald, A., et al. (2015). Bacteriophage Strain Typing by Rapid Single Molecule Analysis. Nucleic Acids Research, 43(18), 1–8. www.ncbi.nlm.nih.gov/pubmed/26019180.Google Scholar
Handelsman, J. (2004). Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiology and Molecular Biology Reviews, 68(4), 669–685.Google Scholar
Hansen, K. D., et al. (2011). Increased Methylation Variation in Epigenetic Domains across Cancer Types. Nature Genetics, 43(8), 768–775. http://dx.doi.org/10.1038/ng.865.Google Scholar
Hanz, G. M., et al. (2014). Sequence-Specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues. Journal of Visualized Experiments: JoVE, (93), 3–12. www.ncbi.nlm.nih.gov/pubmed/25490674.Google Scholar
Herrick, J. and Bensimon, A. (2009). Introduction to Molecular Combing: Genomics, DNA Replication, and Cancer. Methods in Molecular Biology, 521, 71–101.Google Scholar
Huichalaf, C., et al. (2014). DNA Methylation Analysis of the Macrosatellite Repeat Associated with FSHD Muscular Dystrophy at Single Nucleotide Level. PloS One, 9(12), p.e115278. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115278#s6.CrossRefGoogle ScholarPubMed
Jeffet, J., et al. (2016). Super-Resolution Genome Mapping in Silicon Nanochannels. ACS Nano, 10(11), 9823–9830. http://pubs.acs.org/doi/abs/10.1021/acsnano.6b05398.Google Scholar
Jones, P. A. and Takai, D. (2001). The Role of DNA Methylation in Mammalian Epigenetics. Science, 293(5532), 1068–1070.CrossRefGoogle ScholarPubMed
Kidd, J. M. et al. (2008). Mapping and Sequencing of Structural Variation from Eight Human Genomes. Nature, 453(7191), 56–64.Google Scholar
Kinkley, S., et al. (2009). SPOC1: A Novel PHD-Containing Protein Modulating Chromatin Structure and Mitotic Chromosome Condensation. Journal of Cell Science, 122(16), 2946–2956.Google Scholar
Klimasauskas, S. and Weinhold, E. (2007). A New Tool for Biotechnology: AdoMet-Dependent Methyltransferases. Trends in Biotechnology, 25(3), 99–104. www.ncbi.nlm.nih.gov/pubmed/17254657.Google Scholar
Laird, P. W. (2010). Principles and Challenges of Genome-Wide DNA Methylation Analysis. Nature Reviews Genetics, 11(3), 191. www.ncbi.nlm.nih.gov/pubmed/20125086.CrossRefGoogle Scholar
Lam, E. T., et al. (2012). Genome Mapping on Nanochannel Arrays for Structural Variation Analysis and Sequence Assembly. Nature Biotechnology, 30(8), 771–776. www.nature.com/doifinder/10.1038/nbt.2303.Google Scholar
Landan, G., et al. (2012). Epigenetic Polymorphism and the Stochastic Formation of Differentially Methylated Regions in Normal and Cancerous Tissues. Nature Genetics, 44(11), 1207–1214. www.nature.com/doifinder/10.1038/ng.2442.Google Scholar
Landau, D. A. et al. (2014). Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia. Cancer Cell, 26(6), 813–825. www.ncbi.nlm.nih.gov/pubmed/25490447.Google Scholar
Levy-Sakin, M. and Ebenstein, Y. (2013). Beyond Sequencing: Optical Mapping of DNA in the Age of Nanotechnology and Nanoscopy. Current Opinion in Biotechnology, 24, 690–698. www.ncbi.nlm.nih.gov/pubmed/23428595.Google Scholar
van der Maarel, S. M., et al. (2000). De Novo Facioscapulohumeral Muscular Dystrophy: Frequent Somatic Mosaicism, Sex-Dependent Phenotype, and the Role of Mitotic Transchromosomal Repeat Interaction between Chromosomes 4 and 10. American Journal of Human Genetics, 66(1), 26–35. www.sciencedirect.com/science/article/pii/S0002929707622307.Google Scholar
Mak, A. C. Y., et al. (2016). Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays. Genetics, 202(1), 351–362. www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4701098&tool=pmcentrez&rendertype=abstract.CrossRefGoogle ScholarPubMed
Mather, K. A., et al. (2011). Is Telomere Length a Biomarker of Aging? A Review. The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences, 66(2), 202–213. www.ncbi.nlm.nih.gov/pubmed/21030466.CrossRefGoogle ScholarPubMed
Mostovoy, Y., et al. (2016). A Hybrid Approach for De Novo Human Genome Sequence Assembly and Phasing. Nature Methods, 13(7), 587–590. www.nature.com/doifinder/10.1038/nmeth.3865%5Cnhttp://www.ncbi.nlm.nih.gov/pubmed/27159086.Google Scholar
Nilsson, A. N., et al. (2014). Competitive Binding-Based Optical DNA Mapping for Fast Identification of Bacteria – Multi-Ligand Transfer Matrix Theory and Experimental Applications on Escherichia Coli. Nucleic Acids Research, 42(15), E118.Google Scholar
Noble, C., et al. (2013). A Fast and Scalable Algorithm for Alignment of Optical DNA Mappings. PLoS One, 10(4), e0121905.CrossRefGoogle Scholar
O'Boyle, C. J., et al. (1998). Microbiology of Bacterial Translocation in Humans. Gut, 42(1), 29–35. http://gut.bmj.com/cgi/doi/10.1136/gut.42.1.29.Google Scholar
Pendleton, M., et al. (2015a). Assembly and Diploid Architecture of an Individual Human Genome via Single-Molecule Technologies. Nature Methods, 12(8), 780–786. www.nature.com/nmeth/journal/v12/n8/full/nmeth.3454.html#affil-auth.Google Scholar
Pendleton, M., et al. (2015b). Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature Methods, 12(8), 780–786. http://dx.doi.org/10.1038/nmeth.3454.Google Scholar
Petell, C. J., et al. (2016). An Epigenetic Switch Regulates De Novo DNA Methylation at a Subset of Pluripotency Gene Enhancers during Embryonic Stem Cell Differentiation. Nucleic Acids Research, 44(16), 7605–7617.CrossRefGoogle Scholar
Reinius, L. E., et al. (2012). Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility. PLoS One, 7(7), e41361.CrossRefGoogle ScholarPubMed
Schmid, C. W. and Prescott, L. D. (1975). Organization of the Human Genome Transcription. Cell, 6(November), 345–358.Google Scholar
Sender, R., Fuchs, S., and Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology, 14(8), e1002533.CrossRefGoogle ScholarPubMed
Thakur, A. K., et al. (2014). Gut-Microbiota and Mental Health: Current and Future Perspectives. Journal of Pharmacology and Clinical Toxicology, 2(1), 1–15.Google Scholar
Thomas Anantharaman, B. M., 2001. False Positives in Genomic Map Assembly and Sequence Validation. In Gascuel, O. and Moret, B. M. E., eds., Algorithms in Bioinformatics, Lecture Notes in Computer Science. Berlin, Heidelberg: Springer Berlin Heidelberg. http://link.springer.com/10.1007/3-540-44696-6.Google Scholar
Treangen, T. J. and Salzberg, S. L. (2012). Repetitive DNA and Next-Generation Sequencing: Computational Challenges and Solutions. Nature Reviews. Genetics, 13(1), 36–46. www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3324860&tool=pmcentrez&rendertype=abstract.Google Scholar
Valinluck, V. and Sowers, L. C. (2007). Endogenous Cytosine Damage Products Alter the Site Selectivity of Human DNA Maintenance Methyltransferase DNMT1. Cancer Research, 67(3), 946–950.Google Scholar
Wooley, J. C. and Ye, Y. (2009). Metagenomics: Facts and Artifacts, and Computational Challenges. National Institutes of Health Public Access, 25(1), 71–81.Google ScholarPubMed
Xi, Y., et al. (2009). BSMAP: Whole Genome Bisulfite Sequence MAPping Program. BMC Bioinformatics, 10(1), 232. www.biomedcentral.com/1471-2105/10/232.CrossRefGoogle ScholarPubMed
Zirkin, S., et al. (2014). Lighting Up Individual DNA Damage Sites by In Vitro Repair Synthesis. Journal of the American Chemical Society, 136(21), 7771–7776.Google Scholar
Zohar, H. and Muller, S. J. (2011). Labeling DNA for Single-Molecule Experiments: Methods of Labeling Internal Specific Sequences on Double-Stranded DNA. Nanoscale, 3(8), 3027–3039.CrossRefGoogle ScholarPubMed