OpenLB
Open Library of Bioscience
Advanced Search
Methods (San Diego, Calif.)
03, 2021;187 104-113.

Modern epigenetics methods in biological research.

Yuanyuan Li
Author Information
  1. Yuanyuan Li: Department of Obstetrics, Gynecology & Women's Heath, University of Missouri, Columbia, MO 65212, USA; Department of Surgery, University of Missouri, Columbia, MO 65212, USA. Electronic address: ylgrk@missouri.edu.
PMID: 32645449 DOI: 10.1016/j.ymeth.2020.06.022

Abstract

The definition of epigenetics refers that molecular modifications on DNA that can regulate gene activity are independent of DNA sequence and mitotically stable. Notably, epigenetics studies have grown exponentially in the past few years. Recent progresses that lead to exciting discoveries and groundbreaking nature of this area demand thorough methodologies and advanced technologies to move epigenetics to the forefront of molecular biology. The most recognized epigenetic regulations are DNA methylation, histone modifications, and non-coding RNAs (ncRNAs). This review will discuss the modern techniques that are available to detect locus-specific and genome-wide changes for all epigenetic codes. Furthermore, updated analysis of technologies, newly developed methods, recent breakthroughs and bioinformatics pipelines in epigenetic analysis will be presented. These methods, as well as many others presented in this specific issue, provide comprehensive guidelines in the area of epigenetics that facilitate further developments in this promising and rapidly developing field.

Keywords

Advanced technologies DNA methylation Epigenetics Histone modifications Methods Non-coding RNAs

References

  1. Mol Biotechnol. 2010 May;45(1):87-100 [PMID: 20077036]
  2. Nat Rev Genet. 2009 Aug;10(8):578-85 [PMID: 19609263]
  3. Epigenetics. 2006 Apr-Jun;1(2):76-80 [PMID: 17998809]
  4. Methods Mol Biol. 2016;1402:19-26 [PMID: 26721480]
  5. Cell. 2007 Feb 23;128(4):693-705 [PMID: 17320507]
  6. Nat Rev Genet. 2012 Mar 13;13(4):271-82 [PMID: 22411466]
  7. Appl Microbiol Biotechnol. 2020 Apr;104(8):3445-3457 [PMID: 32088759]
  8. Genome Res. 2013 Jan;23(1):129-41 [PMID: 23093720]
  9. Nat Rev Genet. 2014 Jan;15(1):7-21 [PMID: 24296535]
  10. Nat Methods. 2015 Nov;12(11):1061-3 [PMID: 26366987]
  11. BMC Bioinformatics. 2018 Apr 3;19(1):111 [PMID: 29614954]
  12. Nature. 2004 May 27;429(6990):457-63 [PMID: 15164071]
  13. Nucleic Acids Res. 2015 Dec 2;43(21):e146 [PMID: 26202974]
  14. Cell Res. 2016 Mar;26(3):304-19 [PMID: 26902283]
  15. Nat Rev Cancer. 2006 Feb;6(2):107-16 [PMID: 16491070]
  16. Nature. 2009 Jul 23;460(7254):479-86 [PMID: 19536157]
  17. Science. 2001 Aug 10;293(5532):1068-70 [PMID: 11498573]
  18. Mol Cell. 2016 May 19;62(4):618-26 [PMID: 27184080]
  19. Biochim Biophys Acta. 2009 Jan;1789(1):58-68 [PMID: 18722564]
  20. PLoS Comput Biol. 2019 Jun 10;15(6):e1007024 [PMID: 31181064]
  21. Methods Mol Biol. 2012;809:85-104 [PMID: 22113270]
  22. Genome Biol. 2012 Oct 03;13(10):R83 [PMID: 23034175]
  23. Nat Rev Genet. 2014 Jun;15(6):394-408 [PMID: 24805120]
  24. Adv Exp Med Biol. 2017;978:489-512 [PMID: 28523562]
  25. Epigenomics. 2011 Oct;3(5):521-3 [PMID: 22126239]
  26. Bioinformatics. 2019 Nov 1;35(22):4586-4595 [PMID: 30994904]
  27. Cell. 2014 Nov 20;159(5):985-994 [PMID: 25416940]
  28. Nature. 1986 May 15-21;321(6067):209-13 [PMID: 2423876]
  29. Cell. 2012 Jun 8;149(6):1368-80 [PMID: 22608086]
  30. Biology (Basel). 2016 Jan 06;5(1): [PMID: 26751487]
  31. J Integr Bioinform. 2019 Jul 13;16(3): [PMID: 31301674]
  32. Nat Rev Genet. 2012 Apr 18;13(5):358-69 [PMID: 22510765]
  33. Nat Methods. 2014 Aug;11(8):817-820 [PMID: 25042786]
  34. Genes (Basel). 2019 Jan 18;10(1): [PMID: 30669388]
  35. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1827-31 [PMID: 1542678]
  36. Methods Mol Biol. 2011;791:11-21 [PMID: 21913068]
  37. Nat Rev Genet. 2015 Dec;16(12):716-26 [PMID: 26460349]
  38. Nat Methods. 2019 Oct;16(10):991-993 [PMID: 31384045]
  39. Nat Methods. 2017 Apr;14(4):411-413 [PMID: 28218897]
  40. Biomed Pharmacother. 2019 Mar;111:395-401 [PMID: 30594777]
  41. Sci Adv. 2017 Sep 27;3(9):eaao2110 [PMID: 28959731]
  42. Nat Commun. 2015 Jun 15;6:7438 [PMID: 26074426]
  43. Methods Mol Biol. 2015;1343:249-64 [PMID: 26420722]
  44. Nucleic Acids Res. 2012 Sep 1;40(17):e136 [PMID: 22649061]
  45. Cell Res. 2011 Mar;21(3):381-95 [PMID: 21321607]
  46. Cell Chem Biol. 2016 Jan 21;23(1):74-85 [PMID: 26933737]
  47. Nat Rev Genet. 2014 Dec;15(12):814-27 [PMID: 25297728]
  48. Methods. 2021 Mar;187:44-53 [PMID: 32240773]
  49. Methods. 2002 Jun;27(2):114-20 [PMID: 12095268]
  50. Trends Biotechnol. 2018 Sep;36(9):952-965 [PMID: 29724495]
  51. BMC Genomics. 2018 Jun 15;19(1):463 [PMID: 29907088]
  52. Bull World Health Organ. 1976;54(2):129-39 [PMID: 798633]
  53. Nat Rev Genet. 2000 Oct;1(1):11-9 [PMID: 11262868]
  54. Methods Mol Biol. 2011;791:1-10 [PMID: 21913067]
  55. PLoS One. 2019 Apr 4;14(4):e0214368 [PMID: 30946758]
  56. Front Genet. 2019 May 22;10:496 [PMID: 31178900]
  57. Genes Cells. 2013 Jul;18(7):589-601 [PMID: 23672187]
  58. PLoS Biol. 2020 Apr 10;18(4):e3000684 [PMID: 32275660]
  59. Methods Mol Biol. 2015;1262:183-97 [PMID: 25555582]
  60. Genome Res. 2012 Jun;22(6):1120-7 [PMID: 22466171]
  61. Cell Oncol. 2004;26(5-6):291-9 [PMID: 15623939]
  62. Genomics. 2011 Oct;98(4):288-95 [PMID: 21839163]
  63. Cell. 2019 Nov 14;179(5):1033-1055 [PMID: 31730848]
  64. Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):12126-12131 [PMID: 29087948]
  65. Methods Mol Biol. 2018;1767:311-349 [PMID: 29524144]
  66. Genome Biol. 2008;9(9):R137 [PMID: 18798982]
  67. Front Mol Biosci. 2018 Nov 08;5:90 [PMID: 30467545]
  68. Nat Rev Mol Cell Biol. 2011 Apr;12(4):246-58 [PMID: 21427766]
  69. Cell. 2010 Apr 2;141(1):129-41 [PMID: 20371350]
  70. Methods Mol Biol. 2009;523:341-66 [PMID: 19381927]
  71. Bioinform Biol Insights. 2020 Jan 31;14:1177932219899051 [PMID: 32076369]
  72. Nucleic Acids Res. 2008 Dec;36(22):e150 [PMID: 18984622]
  73. Mol Cell. 2011 Nov 18;44(4):667-78 [PMID: 21963238]
  74. Methods Mol Biol. 2011;791:239-51 [PMID: 21913084]
  75. Yonsei Med J. 2009 Aug 31;50(4):455-63 [PMID: 19718392]
  76. Epigenomics. 2011 Dec;3(6):771-84 [PMID: 22126295]
  77. Nucleic Acids Res. 2005 Jun 08;33(10):e93 [PMID: 15944447]
  78. Genome Biol. 2013 Jul 03;14(7):405 [PMID: 23822731]
  79. Nucleic Acids Res. 2005 Oct 13;33(18):5868-77 [PMID: 16224102]
  80. Nat Protoc. 2013 Oct;8(10):1841-51 [PMID: 24008380]
  81. Nat Struct Mol Biol. 2019 Jan;26(1):3-13 [PMID: 30532059]
  82. Front Cell Dev Biol. 2018 Apr 20;6:28 [PMID: 29732369]
  83. Hum Mol Genet. 2010 Oct 15;19(R2):R227-40 [PMID: 20858600]
  84. Nat Rev Genet. 2016 Dec;17(12):719-732 [PMID: 27795564]
  85. Epigenetics Chromatin. 2016 Jun 29;9:26 [PMID: 27358654]
  86. Nat Methods. 2017 Jan 31;14(2):125-134 [PMID: 28139673]
  87. Cell. 2015 May 7;161(4):893-906 [PMID: 25936838]
  88. Essays Biochem. 2019 Dec 20;63(6):639-648 [PMID: 31755932]
  89. Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18904-9 [PMID: 24167255]
  90. Nature. 2007 May 24;447(7143):396-8 [PMID: 17522671]
  91. Bioinformatics. 2011 Jun 1;27(11):1571-2 [PMID: 21493656]
  92. Genes (Basel). 2019 May 29;10(6): [PMID: 31146487]
  93. Nat Rev Genet. 2015 Feb;16(2):71-84 [PMID: 25554358]
  94. Nat Rev Genet. 2012 Oct;13(10):705-19 [PMID: 22986265]
  95. Nat Rev Genet. 2017 Sep;18(9):517-534 [PMID: 28555658]
  96. Nat Rev Genet. 2012 May 29;13(7):484-92 [PMID: 22641018]
  97. Nature. 2007 May 24;447(7143):407-12 [PMID: 17522673]
  98. Epigenetics Chromatin. 2013 Oct 11;6(1):33 [PMID: 24279302]
  99. Biotechniques. 2008 Jan;44(1):35, 37, 39 passim [PMID: 18254377]
  100. Nat Rev Genet. 2012 Dec;13(12):840-52 [PMID: 23090257]
  101. Clin Epigenetics. 2019 Dec 12;11(1):193 [PMID: 31831061]
  102. Proc Natl Acad Sci U S A. 2013 May 7;110(19):7772-7 [PMID: 23610441]
  103. Bioinformation. 2010 Jan 23;4(7):331-7 [PMID: 20978607]
  104. Science. 2009 Jan 2;323(5910):133-8 [PMID: 19023044]
  105. Genome Med. 2017 Sep 30;9(1):87 [PMID: 28964259]
  106. Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20497-502 [PMID: 22143764]

Grants

  1. K01 AT009373/NCCIH NIH HHS

MeSH Term

Biomedical Research
DNA Methylation
Epigenesis, Genetic
Epigenomics
Histone Code
Humans
RNA, Untranslated

Chemicals

RNA, Untranslated
Journal Article Research Support, N.I.H., Extramural Review
Article has an altmetric score of 10

Word Cloud

Created with Highcharts 10.0.0epigeneticsDNAmodificationstechnologiesepigeneticmethodsmolecularareamethylationRNAswillanalysispresenteddefinitionreferscanregulategeneactivityindependentsequencemitoticallystableNotablystudiesgrownexponentiallypastyearsRecentprogressesleadexcitingdiscoveriesgroundbreakingnaturedemandthoroughmethodologiesadvancedmoveforefrontbiologyrecognizedregulationshistonenon-codingncRNAsreviewdiscussmoderntechniquesavailabledetectlocus-specificgenome-widechangescodesFurthermoreupdatednewlydevelopedrecentbreakthroughsbioinformaticspipelineswellmanyothersspecificissueprovidecomprehensiveguidelinesfacilitatedevelopmentspromisingrapidlydevelopingfieldModernbiologicalresearchAdvancedEpigeneticsHistoneMethodsNon-coding

Similar Articles

Cited By