Skip to main content
Log in

An epigenetic view of developmental diseases: new targets, new therapies

  • Review Article
  • Published:
World Journal of Pediatrics Aims and scope Submit manuscript

Abstract

Background

Function of epigenetic modifications is one of the most competitive fields in life science. Over the past several decades, it has been revealed that epigenetic modifications play essential roles in development and diseases including developmental diseases. In the present review, we summarize the recent progress about the function of epigenetic regulation, especially DNA and RNA modifications in developmental diseases.

Data sources

Original research articles and literature reviews published in PubMed-indexed journals.

Results

DNA modifications including methylation and demethylation can regulate gene expression, and are involved in development and multiple diseases including Rett syndrome, Autism spectrum disorders, congenital heart disease and cancer, etc. RNA methylation and demethylation play important roles in RNA processing, reprogramming, circadian, and neuronal activity, and then modulate development.

Conclusions

DNA and RNA modifications play important roles in development and diseases through regulating gene expression. Epigenetic components could serve as novel targets for the treatment of developmental diseases.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Li X, Zhao X. Epigenetic regulation of mammalian stem cells. Stem Cells Dev 2008;17:1043–1052.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002;16:6–21.

    Article  CAS  PubMed  Google Scholar 

  3. Sun W, Zang L, Shu Q, Li X. From development to diseases: the role of 5hmC in brain. Genomics 2014;104:347–351.

    Article  CAS  PubMed  Google Scholar 

  4. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003;33 Suppl:245–254.

    Article  CAS  PubMed  Google Scholar 

  5. Chang CP, Bruneau BG. Epigenetics and cardiovascular development. Annu Rev Physiol 2012;74:41–68.

    Article  CAS  PubMed  Google Scholar 

  6. Wouters BJ, Delwel R. Epigenetics and approaches to targeted epigenetic therapy in acute myeloid leukemia. Blood 2016;127:42–52.

    Article  PubMed  Google Scholar 

  7. Zhang C, Zhong JF, Stucky A, Chen XL, Press MF, Zhang X. Histone acetylation: novel target for the treatment of acute lymphoblastic leukemia. Clin Epigenetics 2015;7:117.

    Article  PubMed  PubMed Central  Google Scholar 

  8. Kouzarides T. Chromatin modifications and their function. Cell 2007;128:693–705.

    Article  CAS  PubMed  Google Scholar 

  9. Zhang QJ, Liu ZP. Histone methylations in heart development, congenital and adult heart diseases. Epigenomics 2015;7:321–330.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. LaPlant Q, Vialou V, Covington HE, 3rd, Dumitriu D, Feng J, Warren BL, et al. Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nat Neurosci 2010;13:1137–1143.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Feng J, Zhou Y, Campbell SL, Le T, Li E, Sweatt JD, et al. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 2010;13:423–430.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, et al. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci 2011;14:1345–1351.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009;324:929–930.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009;324:930–935.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 2011;333:1303–1307.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Gu TP, Guo F, Yang H, Wu HP, Xu GF, Liu W, et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 2011;477:606–610.

    Article  CAS  PubMed  Google Scholar 

  17. Szulwach KE, Li X, Li Y, Song CX, Wu H, Dai Q, et al. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci 2011;14:1607–1616.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Nestor CE, Ottaviano R, Reddington J, Sproul D, Reinhardt D, Dunican D, et al. Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res 2012;22:467–477.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Cimmino L, Abdel-Wahab O, Levine RL, Aifantis I. TET family proteins and their role in stem cell differentiation and transformation. Cell Stem Cell 2011;9:193–204.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Li S, Mason CE. The pivotal regulatory landscape of RNA modifications. Annu Rev Genomics Hum Genet 2014;15:127–150.

    Article  CAS  PubMed  Google Scholar 

  21. Yue Y, Liu J, He C. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev 2015;29:1343–1355.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive analysis of mRNA methylation reveals enrichment in 3’ UTRs and near stop codons. Cell 2012;149:1635–1646.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 2012;485:201–206.

    Article  CAS  PubMed  Google Scholar 

  24. Bokar JA, Shambaugh ME, Polayes D, Matera AG, Rottman FM. Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA 1997;3:1233–1247.

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Liu X, McEachron TA, Schwartzentruber J, Wu G. Histone H3 mutations in pediatric brain tumors. Cold Spring Harb Perspect Biol 2014;6:a018689.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 2011;7:885–887.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell 2013;49:18–29.

    Article  CAS  PubMed  Google Scholar 

  28. Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, Zhao JC. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat Cell Biol 2014;16:191–198.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 1999;23:185–188.

    Article  CAS  PubMed  Google Scholar 

  30. Chahrour M, Zoghbi HY. The story of Rett syndrome: from clinic to neurobiology. Neuron 2007;56:422–437.

    Article  CAS  PubMed  Google Scholar 

  31. Mellen M, Ayata P, Dewell S, Kriaucionis S, Heintz N. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 2012;151:1417–1430.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 2014;515:209–215.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Iossifov I, O’Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 2014;515:216–221.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, et al. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun 2015;6:6404.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. James SJ, Shpyleva S, Melnyk S, Pavliv O, Pogribny IP. Complex epigenetic regulation of engrailed-2 (EN-2) homeobox gene in the autism cerebellum. Transl Psychiatry 2013;3:e232.

  36. James SJ, Shpyleva S, Melnyk S, Pavliv O, Pogribny IP. Elevated 5-hydroxymethylcytosine in the Engrailed-2 (EN-2) promoter is associated with increased gene expression and decreased MeCP2 binding in autism cerebellum. Transl Psychiatry 2014;4:e460.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Zhubi A, Chen Y, Dong E, Cook EH, Guidotti A, Grayson DR. Increased binding of MeCP2 to the GAD1 and RELN promoters may be mediated by an enrichment of 5-hmC in autism spectrum disorder (ASD) cerebellum. Transl Psychiatry 2014;4:e349.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Wang T, Pan Q, Lin L, Szulwach KE, Song CX, He C, et al. Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum. Hum Mol Genet 2012;21:5500–5510.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Papale LA, Zhang Q, Li S, Chen K, Keles S, Alisch RS. Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism. Hum Mol Genet 2015;24:7121–7131.

    CAS  PubMed  Google Scholar 

  40. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell 2012;151:206–220.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Gilsbach R, Preissl S, Gruning BA, Schnick T, Burger L, Benes V, et al. Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease. Nat Commun 2014;5:5288.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Sheng W, Qian Y, Wang H, Ma X, Zhang P, Diao L, et al. DNA methylation status of NKX2-5, GATA4 and HAND1 in patients with tetralogy of fallot. BMC Med Genomics 2013;6:46.

    Article  PubMed  PubMed Central  Google Scholar 

  43. van Driel LM, de Jonge R, Helbing WA, van Zelst BD, Ottenkamp J, Steegers EA, et al. Maternal global methylation status and risk of congenital heart diseases. Obstet Gynecol 2008;112:277–283.

    Article  PubMed  Google Scholar 

  44. Obermann-Borst SA, van Driel LM, Helbing WA, de Jonge R, Wildhagen MF, Steegers EA, et al. Congenital heart defects and biomarkers of methylation in children: a case-control study. Eur J Clin Invest 2011;41:143–150.

    Article  CAS  PubMed  Google Scholar 

  45. He A, Ma Q, Cao J, von Gise A, Zhou P, Xie H, et al. Polycomb repressive complex 2 regulates normal development of the mouse heart. Circ Res 2012;110:406–415.

    Article  CAS  PubMed  Google Scholar 

  46. Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, et al. De novo mutations in histone-modifying genes in congenital heart disease. Nature 2013;498:220–223.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Batista PJ, Molinie B, Wang J, Qu K, Zhang J, Li L, et al. m(6) A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 2014;15:707–719.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Geula S, Moshitch-Moshkovitz S, Dominissini D, Mansour AA, Kol N, Salmon-Divon M, et al. Stem cells. m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation. Science 2015;347:1002–1006.

    CAS  PubMed  Google Scholar 

  49. Alarcon CR, Lee H, Goodarzi H, Halberg N, Tavazoie SF. N6-methyladenosine marks primary microRNAs for processing. Nature 2015;519:482–485.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Chen T, Hao YJ, Zhang Y, Li MM, Wang M, Han W, et al. m(6) A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. Cell Stem Cell 2015;16:289–301.

    Article  CAS  PubMed  Google Scholar 

  51. Dina C, Meyre D, Gallina S, Durand E, Korner A, Jacobson P, et al. Variation in FTO contributes to childhood obesity and severe adult obesity. Nat Genet 2007;39:724–726.

    Article  CAS  PubMed  Google Scholar 

  52. Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, Lindgren CM, et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 2007;316:889–894.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Fischer J, Koch L, Emmerling C, Vierkotten J, Peters T, Bruning JC, et al. Inactivation of the Fto gene protects from obesity. Nature 2009;458:894–898.

    Article  CAS  PubMed  Google Scholar 

  54. Church C, Moir L, McMurray F, Girard C, Banks GT, Teboul L, et al. Overexpression of Fto leads to increased food intake and results in obesity. Nat Genet 2010;42:1086–1092.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Boissel S, Reish O, Proulx K, Kawagoe-Takaki H, Sedgwick B, Yeo GS, et al. Loss-of-function mutation in the dioxygenaseencoding FTO gene causes severe growth retardation and multiple malformations. Am J Hum Genet 2009;85:106–111.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Hess ME, Hess S, Meyer KD, Verhagen LA, Koch L, Bronneke HS, et al. The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry. Nat Neurosci 2013;16:1042–1048.

    Article  CAS  PubMed  Google Scholar 

  57. Fustin JM, Doi M, Yamaguchi Y, Hida H, Nishimura S, Yoshida M, et al. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell 2013;155:793–806.

    Article  CAS  PubMed  Google Scholar 

  58. Maze I, Shen L, Zhang B, Garcia BA, Shao N, Mitchell A, et al. Analytical tools and current challenges in the modern era of neuroepigenomics. Nat Neurosci 2014;17:1476–1490.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Sweatt JD. The emerging field of neuroepigenetics. Neuron 2013;80:624–632.

    Article  CAS  PubMed  Google Scholar 

  60. Shin J, Ming GL, Song H. Seeking a roadmap toward neuroepigenetics. Neuron 2015;86:12–15.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Qiang Shu.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Xie, P., Zang, LQ., Li, XK. et al. An epigenetic view of developmental diseases: new targets, new therapies. World J Pediatr 12, 291–297 (2016). https://doi.org/10.1007/s12519-016-0020-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12519-016-0020-3

Key words

Navigation