Distinct epigenomes in CD4 + T cells of newborns, middle-ages and centenarians

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Zhao, Ming ^a   Qin, Jian ^b   Yin, Hanqi ^c   Tan, Yixin ^a   Liao, Wei ^a   Liu, Qian ^a   Luo, Shuangyan ^a   He, Min ^b   Liang, Gongping ^a   Shi, Yajing ^a   Zhang, Qing ^a   Cai, Wenjun ^d   Yin, Guangliang ^d   Zhou, Yin ^a   Wang, Jing ^a   Li, Mengying ^a   Huang, Yi ^a   Liu, Aiyun ^a   Wu, Haijing ^a   Zhang, Zhiyong ^b   Lu, Qianjin ^a   more..

^a CENTRAL SOUTH UNIVERSITY   (China)

^b GUANGXI MEDICAL UNIVERSITY   (China)

^c SUN YAT SEN UNIVERSITY   (China)

^d BGI SHENZHEN   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTOME;

AGING; CD4+ T LYMPHOCYTE; CYTOLOGY; DNA METHYLATION; FEMALE; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETIC EPIGENESIS; GENETICS; HUMAN; MALE; METABOLISM; MIDDLE AGED; MOLECULAR GENETICS; NEWBORN; VERY ELDERLY;

AGED, 80 AND OVER; AGING; CD4-POSITIVE T-LYMPHOCYTES; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENE ONTOLOGY; GENE REGULATORY NETWORKS; HUMANS; INFANT, NEWBORN; MALE; MICRORNAS; MIDDLE AGED; MOLECULAR SEQUENCE ANNOTATION; TRANSCRIPTOME;

EID: 85002273549     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep38411     Document Type: Article

References (40)

1. Montesanto, A., Dato, S., Bellizzi, D., Rose, G., Passarino, G. Epidemiological, genetic and epigenetic aspects of the research on healthy ageing and longevity. Immun. Ageing 9, 6 (2012).
2. Bjornsson, H. T. et al. Intra-individual change over time in DNA methylation with familial clustering. JAMA 299, 2877-2883 (2008).
3. Bollati, V. et al. Decline in genomic DNA methylation through aging in a cohort of elderly subjects. Mech. Ageing Dev. 130, 234-239 (2009).
4. Wilson, V. L., Smith, R. A., Ma, S., Cutler, R. G. Genomic 5-methyldeoxycytidine decreases with age. J. Biol. Chem. 262, 9948-9951 (1987).
5. Reynolds, L. M. et al. Age-related variations in the methylome associated with gene expression in human monocytes and T cells. Nat. Commun. 5, 5366 (2014).
6. Horvath, S. et al. Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol 13, R97 (2012).
7. Bell, J. T. et al. Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet. 8, e1002629 (2012).
8. Hitt, R., Young-Xu, Y., Silver, M., Perls, T. Centenarians: the older you get, the healthier you have been. Lancet 354, 652 (1999).
9. Perls, T. T. The different paths to 100. Am. J. Clin. Nutr. 83, 484S-487S (2006).
10. Yang, X. et al. Mitochondrial DNA polymorphisms are associated with the longevity in the Guangxi Bama population of China. Mol. Biol. Rep. 39, 9123-9131 (2012).
11. Vlieghe, D. et al. A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. 34, D95-97 (2006).
12. Kang, H. S. et al. Early growth response protein 1 upregulation and nuclear translocation by 2-benzoyloxycinnamaldehyde induces prostate cancer cell death. Cancer Lett. 329, 217-227 (2013).
13. Iyirhiaro, G. O. et al. Regulation of ischemic neuronal death by E2F4-p130 protein complexes. J. Biol. Chem. 289, 18202-18213 (2014).
14. Galvagni, F., Orlandini, M., Oliviero, S. Role of the AP-1 transcription factor FOSL1 in endothelial cells adhesion and migration. Cell Adh. Migr. 7, 408-411 (2013).
15. Lin, C. et al. Serum response factor controls transcriptional network regulating epidermal function and hair follicle morphogenesis. J. Invest. Dermatol. 133, 608-617 (2013).
16. Papetti, M., Wontakal, S. N., Stopka, T., Skoultchi, A. I. GATA-1 directly regulates p21 gene expression during erythroid differentiation. Cell Cycle 9, 1972-1980 (2010).
17. Langfelder, P., Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008).
18. Franceschini, A. et al. STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41, D808-815 (2013).
19. Uittenboogaard, L. M. et al. BACH2: a marker of DNA damage and ageing. DNA Repair (Amst) 12, 982-992 (2013).
20. Kuwahara, M. et al. The Menin-Bach2 axis is critical for regulating CD4 T-cell senescence and cytokine homeostasis. Nat. Commun. 5, 3555 (2014).
21. Wang, C. Q. et al. Runx3 deficiency results in myeloproliferative disorder in aged mice. Blood 122, 562-566 (2013).
22. Devireddy, L. R., Hart, D. O., Goetz, D. H., Green, M. R. A mammalian siderophore synthesized by an enzyme with a bacterial homolog involved in enterobactin production. Cell 141, 1006-1017 (2010).
23. Reznick, R. M. et al. Aging-associated reductions in AMP-activated protein kinase activity and mitochondrial biogenesis. Cell Metab. 5, 151-156 (2007).
24. Reynolds, L. M. et al. Transcriptomic profiles of aging in purified human immune cells. BMC Genomics 16, 333 (2015).
25. Zhang, R., Epstein, H. F. Homodimerization through coiled-coil regions enhances activity of the myotonic dystrophy protein kinase. FEBS Lett. 546, 281-287 (2003).
26. Loro, E. et al. Normal myogenesis and increased apoptosis in myotonic dystrophy type-1 muscle cells. Cell Death Differ. 17, 1315-1324 (2010).
27. Hata, T. et al. DSCP1, a novel TP53-inducible gene, is upregulated by strong genotoxic stresses and its overexpression inhibits tumor cell growth in vitro. Int. J. Oncol. 24, 513-520 (2004).
28. Barsotti, A. M. et al. p53-Dependent induction of PVT1 and miR-1204. J. Biol. Chem. 287, 2509-2519 (2012).
29. Seoudi, A. M., Lashine, Y. A., Abdelaziz, A. I. MicroRNA-181a-a tale of discrepancies. Expert. Rev. Mol. Med. 14, e5 (2012).
30. Mondal, A. M. et al. p53 isoforms regulate aging-and tumor-associated replicative senescence in T lymphocytes. J. Clin. Invest. 123, 5247-5257 (2013).
31. Ohkusu-Tsukada, K., Tsukada, T., Isobe, K. Accelerated development and aging of the immune system in p53-deficient mice. J. Immunol. 163, 1966-1972 (1999).
32. Feber, A. et al. Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. Genome Res. 21, 515-524 (2011).
33. Attwood, J. T., Yung, R. L., Richardson, B. C. DNA methylation and the regulation of gene transcription. Cell Mol. Life Sci. 59, 241-257 (2002).
34. Tacutu, R. et al. Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing. Nucleic Acids Res. 41, D1027-1033 (2013).
35. Roychoudhuri, R. et al. BACH2 represses effector programs to stabilize T(reg)-mediated immune homeostasis. Nature 498, 506-510 (2013).
36. Zhang, G. et al. FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads. Nucleic Acids Res. 40, e83 (2012).
37. Anders, S., Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
38. Langmead, B., Trapnell, C., Pop, M., Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
39. Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
40. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).