DOI QR코드

DOI QR Code

The Principles and Applications of High-Throughput Sequencing Technologies

  • Jun-Yeong Lee (School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University)
  • Received : 2022.12.12
  • Accepted : 2023.02.20
  • Published : 2023.03.15

Abstract

The advancement in high-throughput sequencing (HTS) technology has revolutionized the field of biology, including genomics, epigenomics, transcriptomics, and metagenomics. This technology has become a crucial tool in many areas of research, allowing scientists to generate vast amounts of genetic data at a much faster pace than traditional methods. With this increased speed and scale of data generation, researchers can now address critical questions and gain new insights into the inner workings of living organisms, as well as the underlying causes of various diseases. Although the first HTS technology have been introduced about two decades ago, it can still be challenging for those new to the field to understand and use effectively. This review aims to provide a comprehensive overview of commonly used HTS technologies these days and their applications in terms of genome sequencing, transcriptome, DNA methylation, DNA-protein interaction, chromatin accessibility, three-dimensional genome organization, and microbiome.

Keywords

Acknowledgement

I appreciate my lab colleagues, Yeongjae Shin and Donghyeon Kim, for providing feedback regarding the readability and helpfulness of this information for those new to this field.

References

  1. Abdellah Z, Ahmadi A, Ahmed S, Aimable M, Ainscough R, Almeida J, et al. (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945. https://doi.org/10.1038/nature03001
  2. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061-1073. https://doi.org/10.1038/nature09534
  3. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM. 2009. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27:361-368. https://doi.org/10.1038/nbt.1533
  4. Barras F, Marinus MG (1989) The great GATC: DNA methylation in E. coli. Trends Genet. 5:139-143. https://doi.org/10.1016/0168-9525(89)90054-1
  5. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59. https://doi.org/10.1038/nature07517
  6. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell. 132:311-322. https://doi.org/10.1016/j.cell.2007.12.014
  7. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10:1213-1218. https://doi.org/10.1038/nmeth.2688
  8. Chen S, Lake BB, Zhang K (2019) High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nat Biotechnol 37:1452-1457. https://doi.org/10.1038/s41587-019-0290-0
  9. Cho I, Blaser MJ (2012) The human microbiome: At the interface of health and disease. Nat Rev Genet 13:260-270. https://doi.org/10.1038/nrg3182
  10. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 44:667-678. https://doi.org/10.1016/j.molcel.2011.08.027
  11. Churchman LS, Weissman JS (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469:368-373. https://doi.org/10.1038/nature09652
  12. Collins FS, Morgan M, Patrinos A (2003) The human genome project: Lessons from large-scale biology. Science 300:286-290. https://doi.org/10.1126/science.1084564
  13. Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845-1848. https://doi.org/10.1126/science.1162228
  14. Cui P, Lin Q, Ding F, Xin C, Gong W, Zhang L, Geng J, Zhang B, Yu X, Yang J, Hu S, Yu J (2010) A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics 96:259-265. https://doi.org/10.1016/j.ygeno.2010.07.010
  15. Dekker J, Marti-Renom MA, Mirny LA (2013) Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data. Nat Rev Genet 14:390-403. https://doi.org/10.1038/nrg3454
  16. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306-1311. https://doi.org/10.1126/science.1067799
  17. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J (2006) Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res 16:1299-1309. https://doi.org/10.1101/gr.5571506
  18. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Graf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Backdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJP, Durbin R, Tavare S, Beck S (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26:779-785. https://doi.org/10.1038/nbt1414
  19. Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74. https://doi.org/10.1038/nature11247
  20. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133-138. https://doi.org/10.1126/science.1162986
  21. Esteller M (2011) Non-coding RNAs in human disease. Nat Rev Genet 12:861-874. https://doi.org/10.1038/nrg3074
  22. Fatica A, Bozzoni I (2014) Long non-coding RNAs: New players in cell differentiation and development. Nat Rev Genet 15:7-21. https://doi.org/10.1038/nrg3606
  23. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, et al. (2009) An oestrogen-receptor-α-bound human chromatin interactome. Nature 462:58-64. https://doi.org/10.1038/nature08497
  24. Galas DJ, Schmitz A (1978) DNAase footprinting a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5:3157-3170. https://doi.org/10.1093/nar/5.9.3157
  25. Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, Berney T, Montanya E, Mohlke KL, Lieb JD, Ferrer J (2010) A map of open chromatin in human pancreatic islets. Nat Genet 42:255-259. https://doi.org/10.1038/ng.530
  26. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD (2007) FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin. Genome Res 17:877-885. https://doi.org/10.1101/gr.5533506
  27. Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74:481-514. https://doi.org/10.1146/annurev.biochem.74.010904.153721
  28. Grewal SIS, Jia S (2007) Heterochromatin revisited. Nat Rev Genet 8:35-46. https://doi.org/10.1038/nrg2008
  29. Guo J, Xu N, Li Z, Zhang S, Wu J, Kim DH, Marma MS, Meng Q, Cao H, Li X, Shi S, Yu L, Kalachikov S, Russo JJ, Turro NJ, Ju J (2008) Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc Natl Acad Sci USA 105:9145-9150. https://doi.org/10.1073/pnas.0804023105
  30. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, DiMeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z (2008) Single-molecule DNA sequencing of a viral genome. Science 320:106-109. https://doi.org/10.1126/science.1150427
  31. Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, et al. (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207-214. https://doi.org/10.1038/nature11234
  32. Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-223. https://doi.org/10.1126/science.1168978
  33. Jacinto FV, Ballestar E, Esteller M (2008) Methyl-DNA immunoprecipitation (MeDIP): Hunting down the DNA methylome. Biotechniques 44:35-43. https://doi.org/10.2144/000112708
  34. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502. https://doi.org/10.1126/science.1141319
  35. Jones PA, Takai D (2001) The role of DNA methylation in mammalian epigenetics. Science 293:1068-1070. https://doi.org/10.1126/science.1063852
  36. Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93:13770-13773. https://doi.org/10.1073/pnas.93.24.13770
  37. Khodor YL, Rodriguez J, Abruzzi KC, Tang CHA, Marr MT, Rosbash M (2011) Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Genes Dev 25:2502-2512. https://doi.org/10.1101/gad.178962.111
  38. Klein DC, Hainer SJ (2020) Genomic methods in profiling DNA accessibility and factor localization. Chromosome Res 28:69-85. https://doi.org/10.1007/s10577-019-09619-9
  39. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921. https://doi.org/10.1038/35057062
  40. Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299:682-686. https://doi.org/10.1126/science.1079700
  41. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289-293. https://doi.org/10.1126/science.1181369
  42. Lister R, Pelizzola M, Dowen RH, David Hawkins R, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Harvey Millar A, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315-322. https://doi.org/10.1038/nature08514
  43. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380. https://doi.org/10.1038/nature03959
  44. Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci 74:560-564. https://doi.org/10.1073/pnas.74.2.560
  45. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766-770. https://doi.org/10.1038/nature07107
  46. Minshall N, Chernukhin I, Carroll JS, Git A (2022) ncRNAseq: Simple modifications to RNA-seq library preparation allow recovery and analysis of mid-sized non-coding RNAs. Biotechniques 72:21-28. https://doi.org/10.2144/btn-2021-0035
  47. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349. https://doi.org/10.1126/science.1158441
  48. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272-276. https://doi.org/10.1038/nature08250
  49. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37:e123.
  50. Pennisi E (2012a) Search for pore-fection. Science 336:534-537. https://doi.org/10.1126/science.336.6081.534
  51. Pennisi E (2012b) Single-cell sequencing tackles basic and biomedical questions. Science 336:976-977. https://doi.org/10.1126/science.336.6084.976
  52. Peterson D, Bonham KS, Rowland S, Pattanayak CW, Resonance Consortium, Klepac-Ceraj V (2021) Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes. Front Microbiol 12:670336.
  53. Quick J, Quinlan AR, Loman NJ (2014) A reference bacterial genome dataset generated on the MinIONTM portable single-molecule nanopore sequencer. GigaScience 3:22.
  54. Regnier P, Marujo PE (2013) Polyadenylation and Degradation of RNA in Prokaryotes. Madame Curie Bioscience Database, Landes Bioscience, Austin, TX.
  55. Reuter JA, Spacek DV, Snyder MP (2015) High-throughput sequencing technologies. Mol Cell 58:586-597. https://doi.org/10.1016/j.molcel.2015.05.004
  56. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317-330. https://doi.org/10.1038/nature14248
  57. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651-657. https://doi.org/10.1038/nmeth1068
  58. Robertson KD (2005) DNA methylation and human disease. Nat Rev Genet 6:597-610. https://doi.org/10.1038/nrg1655
  59. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348-352. https://doi.org/10.1038/nature10242
  60. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74:5463-5467. https://doi.org/10.1073/pnas.74.12.5463
  61. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887-898. https://doi.org/10.1016/j.cell.2008.02.022
  62. Scott Hansen R, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA (2010) Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci USA 107:139-144. https://doi.org/10.1073/pnas.0912402107
  63. Sephton CF, Cenik C, Kucukural A, Dammer EB, Cenik B, Han YH, Dewey CM, Roth FP, Herz J, Peng J, Moore MJ, Yu G (2011) Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. J Biol Chem 286:1204-1215. https://doi.org/10.1074/jbc.M110.190884
  64. Serre D, Lee BH, Ting AH (2010) MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 38:391-399. https://doi.org/10.1093/nar/gkp992
  65. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728-1732. https://doi.org/10.1126/science.1117389
  66. Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers H, Kawai J, Carninci P, Hayashizaki Y (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci USA 100:15776-15781. https://doi.org/10.1073/pnas.2136655100
  67. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38:1348-1354. https://doi.org/10.1038/ng1896
  68. Skene PJ, Henikoff S (2017) An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6:e21856.
  69. Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G (2014) Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat Methods 11:817-820. https://doi.org/10.1038/nmeth.3035
  70. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Nicholas Ornston L, Gerstein M, Snyder M (2007) New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev 21:601-614. https://doi.org/10.1101/gad.1510307
  71. Stackebrandt E, Goebel BM (1994) Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846-849. https://doi.org/10.1099/00207713-44-4-846
  72. Stratton M (2008) Genome resequencing and genetic variation. Nat Biotechnol 26:65-66. https://doi.org/10.1038/nbt0108-65
  73. Takahashi H, Lassmann T, Murata M, Carninci P (2012) 5' End-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 7:542-561. https://doi.org/10.1038/nprot.2012.005
  74. Travers KJ, Chin CS, Rank DR, Eid JS, Turner SW (2010) A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 38:e159.
  75. Tuck AC, Tollervey D (2011) RNA in pieces. Trends Genet 27:422-432. https://doi.org/10.1016/j.tig.2011.06.001
  76. van Opijnen T, Bodi KL, Camilli A (2009) Tn-seq: High-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat Methods 6:767-772. https://doi.org/10.1038/nmeth.1377
  77. van Steensel B, Belmont AS (2017) Lamina-associated domains: Links with chromosome architecture, heterochromatin, and gene repression. Cell 169:780-791. https://doi.org/10.1016/j.cell.2017.04.022
  78. van Steensel B, Henikoff S (2000) Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18:424-428. https://doi.org/10.1038/74487
  79. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18:1051-1063. https://doi.org/10.1101/gr.076463.108
  80. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. (2001) The sequence of the human genome. Science 291:1304-1351. https://doi.org/10.1126/science.1058040
  81. Wen L, Tang F (2018) Boosting the power of single-cell analysis. Nat Biotechnol 36:408-409. https://doi.org/10.1038/nbt.4131
  82. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090. https://doi.org/10.1073/pnas.74.11.5088
  83. Yong WS, Hsu FM, Chen PY (2016) Profiling genome-wide DNA methylation. Epigenetics Chromatin 9:26.
  84. Yu M, Ren B (2017) The three-dimensional organization of mammalian genomes. Annu Rev Cell Dev Biol 33:265-289. https://doi.org/10.1146/annurev-cellbio-100616-060531
  85. Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM (2014) Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. BMC Genom 15:419.