Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase

Nucleic Acids Research

Volumn 45, Issue 10, 2017, Pages

  Gansauge, Marie Theres ^a   Gerber, Tobias ^a   Glocke, Isabelle ^a   Korlević, Petra ^a   Lippik, Laurin ^a   Nagel, Sarah ^a   Riehl, Lara Maria ^b   Schmidt, Anna ^a   Meyer, Matthias ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b UNIVERSITY HOSPITAL ULM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA LIGASE; DNA POLYMERASE; DOUBLE STRANDED DNA; EXONUCLEASE; GENOMIC DNA; SINGLE STRANDED DNA; DNA; OLIGONUCLEOTIDE; PRIMER DNA;

ARTICLE; DNA BASE COMPOSITION; DNA DAMAGE; DNA DEGRADATION; DNA HAIRPIN; DNA LIBRARY; DNA STRAND; DNA SYNTHESIS; ENZYME ACTIVITY; ENZYME MECHANISM; HUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; TEMPERATURE; ANIMAL; BONE; CHEMISTRY; DNA SEQUENCE; FOSSIL; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; HORSE; LIVER; METABOLISM; NUCLEIC ACID HYBRIDIZATION; PIG; POLYMERASE CHAIN REACTION;

ANIMALS; BONE AND BONES; DNA; DNA LIGASES; DNA PRIMERS; DNA, SINGLE-STRANDED; FOSSILS; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HORSES; HUMANS; LIVER; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SWINE;

EID: 85022068287     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx033     Document Type: Article

References (39)

1. Ke, R., Mignardi, M., Pacureanu, A., Svedlund, J., Botling, J., Wahlby, C. and Nilsson, M. (2013) In situ sequencing for RNA analysis in preserved tissue and cells. Nat. Methods, 10, 857-860.
2. Lee, J.H., Daugharthy, E.R., Scheiman, J., Kalhor, R., Yang, J.L., Ferrante, T.C., Terry, R., Jeanty, S.S., Li, C., Amamoto, R. et al. (2014) Highly multiplexed subcellular RNA sequencing in situ. Science, 343, 1360-1363.
3. Meyer, M., Kircher, M., Gansauge, M.T., Li, H., Racimo, F., Mallick, S., Schraiber, J.G., Jay, F., Prufer, K., de Filippo, C. et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science, 338, 222-226.
4. Gansauge, M.T. and Meyer, M. (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc., 8, 737-748.
5. Prufer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P.H., de Filippo, C. et al. (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505, 43-49.
6. Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S.M., Bondarev, A.A., Johnson, P.L., Aximu-Petri, A., Prufer, K., de Filippo, C. et al. (2014) Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514, 445-449.
7. Dabney, J., Knapp, M., Glocke, I., Gansauge, M.T., Weihmann, A., Nickel, B., Valdiosera, C., Garcia, N., Paabo, S., Arsuaga, J.L. et al. (2013) Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. U.S.A., 110, 15758-15763.
8. Meyer, M., Arsuaga, J.L., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martinez, I., Gracia, A., Bermudez de Castro, J.M., Carbonell, E. et al. (2016) Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature, 531, 504-507.
9. Bennett, E.A., Massilani, D., Lizzo, G., Daligault, J., Geigl, E.M. and Grange, T. (2014) Library construction for ancient genomics: single strand or double strand? Biotechniques, 56, 289-300.
10. Wales, N., Caroe, C., Sandoval-Velasco, M., Gamba, C., Barnett, R., Samaniego, J.A., Madrigal, J.R., Orlando, L. and Gilbert, M.T. (2015) New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA. Biotechniques, 59, 368-371.
11. Snyder, M.W., Kircher, M., Hill, A.J., Daza, R.M. and Shendure, J. (2016) Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell, 164, 57-68.
12. Burnham, P., Kim, M.S., Agbor-Enoh, S., Luikart, H., Valantine, H.A., Khush, K.K. and De Vlaminck, I. (2016) Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma. Sci. Rep., 6, 27859.
13. Stiller, M., Sucker, A., Griewank, K., Aust, D., Baretton, G.B., Schadendorf, D. and Horn, S. (2016) Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA. Oncotarget., 7, 59115-59128.
14. Blondal, T., Thorisdottir, A., Unnsteinsdottir, U., Hjorleifsdottir, S., Aevarsson, A., Ernstsson, S., Fridjonsson, O.H., Skirnisdottir, S., Wheat, J.O., Hermannsdottir, A.G. et al. (2005) Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties. Nucleic Acids Res., 33, 135-142.
15. Karlsson, K., Sahlin, E., Iwarsson, E., Westgren, M., Nordenskjold, M. and Linnarsson, S. (2015) Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations. Genomics, 105, 150-158.
16. Turchinovich, A., Surowy, H., Serva, A., Zapatka, M., Lichter, P. and Burwinkel, B. (2014) Capture and Amplification by Tailing and Switching (CATS). An ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA. RNA Biol., 11, 817-828.
17. Tin, M.M., Economo, E.P. and Mikheyev, A.S. (2014) Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics. PLoS One, 9, e96793.
18. Kuhn, H. and Frank-Kamenetskii, M.D. (2005) Template-independent ligation of single-stranded DNA by T4 DNA ligase. FEBS J., 272, 5991-6000.
19. Kwok, C.K., Ding, Y., Sherlock, M.E., Assmann, S.M. and Bevilacqua, P.C. (2013) A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation. Anal. Biochem., 435, 181-186.
20. Ding, J., Taylor, M.S., Jackson, A.P. and Reijns, M.A. (2015) Genome-wide mapping of embedded ribonucleotides and other noncanonical nucleotides using emRiboSeq and EndoSeq. Nat. Protoc., 10, 1433-1444.
21. Petryk, N., Kahli, M., d'Aubenton-Carafa, Y., Jaszczyszyn, Y., Shen, Y., Silvain, M., Thermes, C., Chen, C.L. and Hyrien, O. (2016) Replication landscape of the human genome. Nat. Commun., 7, 10208.
22. Korlevic, P., Gerber, T., Gansauge, M.T., Hajdinjak, M., Nagel, S., Aximu-Petri, A. and Meyer, M. (2015) Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques, 59, 87-93.
23. Meyer, M. and Kircher, M. (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc., 2010, doi:10.1101/pdb.prot5448.
24. Maricic, T. and Paabo, S. (2009) Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands. Biotechniques, 46, 51-57.
25. Dabney, J. and Meyer, M. (2012) Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques, 52, 87-94.
26. Kircher, M., Sawyer, S. and Meyer, M. (2012) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res., 40, e3.
27. Renaud, G., Stenzel, U. and Kelso, J. (2014) leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res., 42, e141.
28. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
29. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. and Genome Project Data Processing, S. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
30. Briggs, A.W., Stenzel, U., Johnson, P.L., Green, R.E., Kelso, J., Prufer, K., Meyer, M., Krause, J., Ronan, M.T., Lachmann, M. et al. (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. U.S.A., 104, 14616-14621.
31. Li, T.W. and Weeks, K.M. (2006) Structure-independent and quantitative ligation of single-stranded DNA. Anal. Biochem., 349, 242-246.
32. Yang, W. (2003) Damage repair DNA polymerases Y. Curr. Opin. Struct. Biol., 13, 23-30.
33. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
34. Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K. et al. (2015) Massive migration from the steppe was a source for Indo-European languages in Europe. Nature, 522, 207-211.
35. Allentoft, M.E., Sikora, M., Sjogren, K.G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P.B., Schroeder, H., Ahlstrom, T., Vinner, L. et al. (2015) Population genomics of Bronze Age Eurasia. Nature, 522, 167-172.
36. Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., Smith, G.P., Milton, J., Brown, C.G., Hall, K.P., Evers, D.J., Barnes, C.L., Bignell, H.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
37. Star, B., Nederbragt, A.J., Hansen, M.H., Skage, M., Gilfillan, G.D., Bradbury, I.R., Pampoulie, C., Stenseth, N.C., Jakobsen, K.S. and Jentoft, S. (2014) Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA. PLoS One, 9, e89676.
38. Meyer, M., Briggs, A.W., Maricic, T., Hober, B., Hoffner, B., Krause, J., Weihmann, A., Paabo, S. and Hofreiter, M. (2008) From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res., 36, e5.
39. Jonsson, H., Ginolhac, A., Schubert, M., Johnson, P.L. and Orlando, L. (2013) mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics, 29, 1682-1684.