Functional complementation between transcriptional methylation regulation and post-transcriptional microRNA regulation in the human genome

BMC Genomics

Volumn 12, Issue SUPPL. 5, 2011, Pages

  Su, Zhixi ^a,b   Xia, Junfeng ^a   Zhao, Zhongming ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DNA METHYLATION; GENE EXPRESSION REGULATION; GENE LOCATION; GENETIC COMPLEMENTATION; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; PROMOTER REGION; TRANSCRIPTION FACTOR BINDING SITE; TRANSCRIPTION REGULATION; TUMOR GENE; 3' UNTRANSLATED REGION; ANIMAL; CPG ISLAND; GENETIC DATABASE; GENETIC EPIGENESIS; METABOLISM; MOUSE;

3' UNTRANSLATED REGIONS; ANIMALS; CPG ISLANDS; DATABASES, GENETIC; DNA METHYLATION; EPIGENESIS, GENETIC; GENOME, HUMAN; HUMANS; MICE; MICRORNAS; PROMOTER REGIONS, GENETIC;

EID: 84255188918     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-S5-S15     Document Type: Article

References (65)

1. Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. Nature 2004, 429:457-463. 10.1038/nature02625, 15164071.
2. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 2004, 430:471-476. 10.1038/nature02651, 15269773.
3. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007, 39:457-466. 10.1038/ng1990, 17334365.
4. Han L, Su B, Li W-H, Zhao Z. CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol 2008, 9:R79. 10.1186/gb-2008-9-5-r79, 2441465, 18477403.
5. Han L, Zhao Z. Contrast features of CpG islands in the promoter and other regions in the dog genome. Genomics 2009, 94:117-124. 10.1016/j.ygeno.2009.04.007, 2729786, 19409480.
6. Zhao Z, Han L. CpG islands: algorithms and applications in methylation studies. Biochem Biophys Res Commun 2009, 382:643-645. 10.1016/j.bbrc.2009.03.076, 2679166, 19302978.
7. Robertson KD. DNA methylation and human disease. Nat Rev Genet 2005, 6:597-610.
8. Szyf M. The role of DNA hypermethylation and demethylation in cancer and cancer therapy. Curr Oncol 2008, 15:72-75. 2365485, 18454186.
9. Szyf M, Pakneshan P, Rabbani SA. DNA methylation and breast cancer. Biochem Pharmacol 2004, 68:1187-1197. 10.1016/j.bcp.2004.04.030, 15313416.
10. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003, 33:245-254. 10.1038/ng1089, 12610534.
11. Murrell A, Rakyan VK, Beck S. From genome to epigenome. Hum Mol Genet 2005, 14:R3-R10. 10.1093/hmg/ddi110, 15809270.
12. Perez-Iratxeta C, Palidwor G, Porter CJ, Sanche NA, Huska MR, Suomela BP, Muro EM, Krzyzanowski PM, Hughes E, Campbell PA. Study of stem cell function using microarray experiments. FEBS Lett 2005, 579:1795-1801. 10.1016/j.febslet.2005.02.020, 15763554.
13. Wu X, Schmidt JA, Avarbock MR, Tobias JW, Carlson CA, Kolon TF, Ginsberg JP, Brinster RL. Prepubertal human spermatogonia and mouse gonocytes share conserved gene expression of germline stem cell regulatory molecules. Proc Natl Acad Sci USA 2009, 106:21672-21677. 10.1073/pnas.0912432106, 2799876, 20018717.
14. Li Y, Zhu J, Tian G, Li N, Li Q, Ye M, Zheng H, Yu J, Wu H, Sun J, et al. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol 2010, 8(11):e1000533. 10.1371/journal.pbio.1000533, 2976721, 21085693.
15. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322. 10.1038/nature08514, 2857523, 19829295.
16. Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 2011, 471(7336):68-73. 10.1038/nature09798, 3100360, 21289626.
17. Su Z, Han L, Zhao Z. Conservation and divergence of DNA methylation in eukaryotes: New insights from single base-resolution DNA methylomes. Epigenetics 2011, 6:134-140. 10.4161/epi.6.2.13875, 20962593.
18. Filipowicz W, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?. Nat Rev Genet 2008, 9:102-114.
19. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-D157. 10.1093/nar/gkq1027, 3013655, 21037258.
20. Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-D158. 10.1093/nar/gkn221, 2238936, 17991681.
21. Friedman LM, Dror AA, Mor E, Tenne T, Toren G, Satoh T, Biesemeier DJ, Shomron N, Fekete DM, Hornstein E, Avraham KB. MicroRNAs are essential for development and function of inner ear hair cells in vertebrates. Proc Natl Acad Sci USA 2009, 106:7915-7920. 10.1073/pnas.0812446106, 2683084, 19416898.
22. Bushati N, Cohen SM. microRNA functions. Annu Rev Cell Dev Biol 2007, 23:175-205. 10.1146/annurev.cellbio.23.090506.123406, 17506695.
23. Jiang C, Han L, Su B, Li WH, Zhao Z. Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol 2007, 24:1991-2000. 10.1093/molbev/msm128, 17591602.
24. Elango N, Hunt BG, Goodisman MA, Yi SV. DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera. Proc Natl Acad Sci USA 2009, 106:11206-11211. 10.1073/pnas.0900301106, 2708677, 19556545.
25. R package RmiR.hsa. , http://www.bioconductor.org/packages/2.8/data/annotation/html/RmiR.hsa.html
26. McVicker G, Green P. Genomic signatures of germline gene expression. Genome Res 2010, 20:1503. 10.1101/gr.106666.110, 2963814, 20686123.
27. Barberi T, Willis LM, Socci ND, Studer L. Derivation of multipotent mesenchymal precursors from human embryonic stem cells. PLoS Med 2005, 2:e161. 10.1371/journal.pmed.0020161, 1160574, 15971941.
28. Chalmel F, Rolland AD, Niederhauser-Wiederkehr C, Chung SSW, Demougin P, Gattiker A, Moore J, Patard JJ, Wolgemuth DJ, Jégou B. The conserved transcriptome in human and rodent male gametogenesis. Proc Natl Acad Sci USA 2007, 104:8346-8351. 10.1073/pnas.0701883104, 1864911, 17483452.
29. Ge X, Yamamoto S, Tsutsumi S, Midorikawa Y, Ihara S, Wang SM, Aburatani H. Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues. Genomics 2005, 86:127-141. 10.1016/j.ygeno.2005.04.008, 15950434.
30. Houmard B, Small C, Yang L, Naluai-Cecchini T, Cheng E, Hassold T, Griswold M. Global gene expression in the human fetal testis and ovary. Biol Reprod 2009, 81:438-443. 10.1095/biolreprod.108.075747, 2849816, 19369649.
31. Looijenga LHJ, Hersmus R, Gillis AJM, Pfundt R, Stoop HJ, van Gurp RJ, Veltman J, Beverloo HB, van Drunen E, Geurts van Kessel A. Genomic and expression profiling of human spermatocytic seminomas: primary spermatocyte as tumorigenic precursor and DMRT1 as candidate chromosome 9 gene. Cancer Res 2006, 66:290-302. 10.1158/0008-5472.CAN-05-2936, 16397242.
32. Kocabas AM, Crosby J, Ross PJ, Otu HH, Beyhan Z, Can H, Tam WL, Rosa GJM, Halgren RG, Lim B. The transcriptome of human oocytes. Proc Natl Acad Sci USA 2006, 103:14027-14032. 10.1073/pnas.0603227103, 1599906, 16968779.
33. Korkola JE, Houldsworth J, Chadalavada RSV, Olshen AB, Dobrzynski D, Reuter VE, Bosl GJ, Chaganti R. Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13. 31, is associated with in vivo differentiation of human male germ cell tumors. Cancer Res 2006, 66:820-827. 10.1158/0008-5472.CAN-05-2445, 16424014.
34. Sato N, Sanjuan IM, Heke M, Uchida M, Naef F, Brivanlou AH. Molecular signature of human embryonic stem cells and its comparison with the mouse. Dev Biol 2003, 260:404-413. 10.1016/S0012-1606(03)00256-2, 12921741.
35. Skottman H, Mikkola M, Lundin K, Olsson C, Strömberg AM, Tuuri T, Otonkoski T, Hovatta O, Lahesmaa R. Gene expression signatures of seven individual human embryonic stem cell lines. Stem Cells 2005, 23:1343-1356. 10.1634/stemcells.2004-0341, 16081666.
36. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101:6062-6067. 10.1073/pnas.0400782101, 395923, 15075390.
37. Hubbell E, Liu WM, Mei R. Robust estimators for expression analysis. Bioinformatics 2002, 18:1585-1592. 10.1093/bioinformatics/18.12.1585, 12490442.
38. BioGPS. , http://biogps.org
39. Yang J, Su AI, Li WH. Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol 2005, 22:2113-2118. 10.1093/molbev/msi206, 15987875.
40. The Cancer Gene Census database. , http://www.sanger.ac.uk/genetics/CGP/Census/
41. Volinia S, Mascellani N, Marchesini J, Veronese A, Ormondroyd E, Alder H, Palatini J, Negrini M, Croce CM. Genome wide identification of recessive cancer genes by combinatorial mutation analysis. PLoS One 2008, 3:e3380. 10.1371/journal.pone.0003380, 2557123, 18846217.
42. Xia J, Sun J, Jia P, Zhao Z. Do cancer proteins really interact strongly in the human protein-protein interaction network?. Comput Biol Chem 2011, 35:121-125. 10.1016/j.compbiolchem.2011.04.005, 21666777.
43. Chen FC, Chen CJ, Li WH, Chuang TJ. Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Res 2007, 17:16-22. 1716262, 17095709.
44. 17-Way vertebrate alignment in the UCSC Genome Browser. , http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz17way/
45. Deaton AM, Bird A. CpG islands and the regulation of transcription. Genes Dev 2011, 25:1010-1022. 10.1101/gad.2037511, 3093116, 21576262.
46. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr ARW, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP. Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 2010, 6:e1001134.
47. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002, 16:6-21. 10.1101/gad.947102, 11782440.
48. Walsh CP, Bestor TH. Cytosine methylation and mammalian development. Genes Dev 1999, 13:26-34. 10.1101/gad.13.1.26, 316374, 9887097.
49. Warnecke PM, Clark SJ. DNA methylation profile of the mouse skeletal alpha-actin promoter during development and differentiation. Mol Cell Biol 1999, 19:164-172. 83875, 9858541.
50. Wang X, El Naqa IM. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 2008, 24:325-332. 10.1093/bioinformatics/btm595, 18048393.
51. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M. Combinatorial microRNA target predictions. Nat Genet 2005, 37:495-500. 10.1038/ng1536, 15806104.
52. Rajewsky N. microRNA target predictions in animals. Nat Genet. 2006, 38(Suppl:):S8-S13.
53. Cheng C, Bhardwaj N, Gerstein M. The relationship between the evolution of microRNA targets and the length of their UTRs. BMC Genomics 2009, 10:431. 10.1186/1471-2164-10-431, 2758905, 19751524.
54. Kim SH, Yi SV. Understanding relationship between sequence and functional evolution in yeast proteins. Genetica 2007, 131:151-156. 10.1007/s10709-006-9125-2, 17160620.
55. Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends Genet 2003, 19:362-365. 10.1016/S0168-9525(03)00140-9, 12850439.
56. Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM. Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell 2005, 123:1133-1146. 10.1016/j.cell.2005.11.023, 16337999.
57. Cui Q, Yu Z, Pan Y, Purisima EO, Wang E. MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochem Biophys Res Commun 2007, 352:733-738. 10.1016/j.bbrc.2006.11.080, 17141185.
58. Xie X, Lu J, Kulbokas E, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. Systematic discovery of regulatory motifs in human promoters and 3 UTRs by comparison of several mammals. Nature 2005, 434:338-345. 10.1038/nature03441, 2923337, 15735639.
59. PACdb. , http://harlequin.jax.org/pacdb/
60. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
61. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120. 10.1007/BF01731581, 7463489.
62. Sun J, Zhao Z. A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics 2010, 11(Suppl):S3-S5. 10.1186/1471-2164-11-S3-S5, 2999350, 21143787.
63. Gu X, Su Z, Huang Y. Simultaneous expansions of microRNAs and protein-coding genes by gene/genome duplications in early vertebrates. J Exp Zool B Mol Dev Evol 2009, 312B:164-170. 10.1002/jez.b.21273, 19214983.
64. Heimberg AM, Sempere LF, Moy VN, Donoghue PC, Peterson KJ. MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci USA 2008, 105:2946-2950. 10.1073/pnas.0712259105, 2268565, 18287013.
65. Mandrioli M. A new synthesis in epigenetics: towards a unified function of DNA methylation from invertebrates to vertebrates. Cell Mol Life Sci 2007, 64:2522-2524. 10.1007/s00018-007-7231-7, 17712527.