Epigenetic mechanisms in MDS
Συγγραφέας Αρετή Ρέγκλη Γράφτηκε στις ,
1 Department of Haematology and of Internal Medicine , General Hospital
of Athens <
2 TEI of Athens,Department of medical laboratorys,Athens,Greece
3Department of Molecular Biology,School of Natural Sciences,University of Athens
(EKPA),Athens,Greece
___________________________________________________________________________________
The cause of myelodysplasia is unknown in majority of patients, but mostly by exposure to radiation, chemotherapeutic agents, benzene or other organic compounds. In the past few years transcriptional inactivation of tumour suppressor genes by promoter CpG island hypermethylation has been a subject of intense interest as a causal factor in haematological malignancies.Because these epigenetic events and the molecular alterations that might cause them and/or underlie altered gene expression in malignancies.Recent advances have connected DNA methylation to chromatin-remodelling enzymes,and understanding this link will be central to the design of new therapeutic tools.No truly effective treatment exists for MDS,and therapy usually focuses on reducing or preventing compications of the disease.The fact that changes in the epigenome are potentially reversible makes them important targets for therapeutic intervention,and an exciting goal will be to identify those key steps at which it is possible to reprogram a cancer cell to terminally differentiate or apoptose rather than proliferate.In this direction the advent of targeted therapy has increased the repertoire of therapeutic options.In particular the methyl transferase and histone deacetylase inhibitors has been licensed by the US Food and Drug Administration for use in all subtypes of MDS.Given the current pace of research in the field of epigenetics,it is likely that great strides will continue to be made towards these goals in the next decade,which may revolutionize how we think about and treat the disease process.
Key words:MDS,epigenetics,HATS,HDACS,HMTs, lysine
____________________________________________________________________
INTRODUCTION
2
One of the mechanism controlling gene expression is suppressing the expression of the gene by methylating the cytosine. It’s a rare phenomenon in the lower organisms, but is observed in vertebrates at a percentage of above 10% of the whole number of cytosines. The original methylation is not accidental but occurs in C particular copies and more precisely in the 5’ mCpG 3’ dinucleotide sequences across the DNA structure. The CpG groups are named also CpG islands.The active genes are usually non methylated on the cytosines. The methylated situation transferred to the daughter cell with the homocentric way of replicating on only one chain, developing one semimethylated domain. Methylotransferase will add further a methylated group to the newly-synthesized chain14,121. The mechanism of methylating cytosine which modify the gene expression was for a long time an enigma. Today it is known that methylation is not an independent phenomenon of the chromatin with the histones since CpG islands are prone to the enzyme deacetylase of the histone (HDAC) which
develops a complex that modifies the chromatin making it a target, thus deactivating the surrounding genes63,102.The methylation of DNA is involved in two other phenomenons,the gene footprinting and the deactivation of the X chromosome7,14,25,27. The case of gene footprinting is not a common phenomenon and concerns the silencing of one from two homologue alleles of the gene7,32,113 .
It is always the same allele which is activated by methylation, and is always transferred by one parent. It is known that methylation provokes activation of the gene. Alternatively in hypersensitive DNA polymerase regions, where the gene is situated in an epigenetic state, and is observed of ten that is a partial demethylation of CpG islands within and near the gene. The epigenetic methylation of the cytosine as a control mechanism of the eukaryotic gene action is a hereditary situation7. Thus it can affect the modification against the embryonic development, where the cells follow a certain pathway, developing demorphysised clones. The changes in the prototypes of methylating the DNA during the embryo development have not fully clarified , it is hypothesized that embryonic cells following the hereditary procedures while they develop, they have no return back7.The expression of a cell is defined by its constituent proteins, which are the result of specific gene expression patterns. The suppression of the transcription activate a chain of events, which, involve usually changes in the chromatin other occurrence which make changes in the expression of the cells, except the genetic mutation processes , are the epigenetic changes. A large interest has been concentrated on the epigenetic mechanism, especially in diseases related to hematology and oncology, which are based in epigenetics, irreversal after pharmaceutical intake83. The epigenetic rhythm is determined by the change which provokes the gene expression, such as modification of histones, changes in methylation and acetylation of the DNA7,19,78,103.
Histone Acetyltransferases-HATS
The acetylation of histones in eukaryotic organisms was discovered quite a few years ago, and the identification as well as the characterization of enzymes which create have revealed their remarkable diversity in different organisms.
3
Histone Acetyltransferases-HATS, the factors which allocate enzyme activation in the transportation of an acetylation team from the acetyl-CoA to the e-amino of the group of amino-acids lysine, usually found in the basic region of N-terminal end of histones. The total number of enzymes-HATS are separated in two categories: type A found in the core19 and type B found in cytoplasm 9,93. HATS type B are considered to catalyse the acetylation of newly- composed proteins in the cytoplasm, while HATS type A considered to participate in the nuclear acetylation of the histone related to the transcription.
The acetyltransferase type B HAT1 was discovered in sacharomyces57 and acetylizes the lysine 5 and 12 of histone 4 (H4) in vitro, amino-acids which were known to be found acetylated, in the newly synthesized Η410. The enzyme HAT1 constitutes a multifactor complex whose subunits includes 14 proteins HAT2 and CAF1, connected with the redevelopment and the aggregation of the components of the chromatin, respectively82,55. Despite the particular significance attached to HAT1, the transformation of HAT2 has no problems in the incorporation of H4 to the chromatin 82, which clearly indicates that its action can be replaced by other enzymes when the HAT1 is absent or inactive.
Many of the proteins with HAT activity can acetylized free histones when used in vitro, while others such as the nuclear ones cannot acetylized their physiologic substrate in case only they are in the whole complex with other factors. Another family of acetylates is MYST containing proteins MOZ, Ybf/Sas3, Sas2 and Tip60 22. The Esa1 of Sacharomyces, the MOF of Drosofilla and the human HBO1 and MORF 76 constitute newer members of family MYST.
The strong relation between transcriptional activation and acetylation of the histones was clarified when the larger subunit of the complex factors connected with TVR (TVR Associated factors-TAFs), Taf1-taf250, was shown to allocate the enzyme activity in the acetylation of histones 73. The complex TFIID can bind to the DNA via the TVR factor recognizing specific sequences, although TFIID without TVR can transcript in vitro.
The acetylotransferases are involved in the transcriptional regulation not only via the acetylation of histones but also by transcriptional factors 25.
Histone Deacetylases-HDACS
The acetylation of histones is a reversal procedure, as the acetyl group can be removed from special enzymes, apoacetylase histones- (HDACS), which their prescence discovered shortly afterwards the presence of acetylases 102. The deacetylases are categorized in families and the enzymes of human class I, II and III are homologue to the ones of the sacharomyces Rpd3, Hda2 and Sir2, respectively 103. Deacetylase histones are divided in units in which some of them function and regulate the enzyme activation. Apoacetylases together with histone acetylases contribute to the acetylation of certain histones as well as the regulation and the differentiation of different megafactors responsible for their modification. The interaction between megafactors regulates the amount of quantity and the availability of the enzyme 4,63
4
Histone Methyltranferases-HMTs
The methylation of histones is performed by specific enzymes, the methylase histones, HMTs. Recently other enzymes have been discovered that methylate the histones in specific residues and contribute to the transcription mechanism.
The methylation of the histone does not change the total charge of protein and it appears as a stable modification, whereas certain enzymes which remove methylgroup have been discovered, but concurrently present special action 99,28,111. The enzymes contributing to the methylation of histones can be divided to two groups, these which methylate the lysine residues18,100 and those methylated the arginine residues, such as the family of PRMT. The amino-acid arginin can undergo only one- or di-methylation. The enzymes for the methylation of arginin residues are separated in two categories: Type I, which leads to a single and asymmetrical di-methylation and Type II, which involves in a single and symmetrtical di-methylation. There are five enzymes which involved in the methylation reaction of arginin and present high degree of maintainance of catalytic region18, named prmt1-5. The histone methylation is involved in the up- or down-regulation of transcription. Moreover, the number of methylated groups on a residue is related to different attributes. 66
The Methylation of the histone aminoacid lysine
The histone lysine that undergo methylation are the Lysine 4, 9, 27 and 36 and 79 on histone 3 and lysine 20 on histone 4. The enzymes that are involved in this, the specific transformation bring characteristic region SET. The enzymes that methylated lysine of the histones can be categorized in four large families: the SET1, which includes enzymes that methylate the K4 of H3, the SET2, which includes the enzymes that methylate the K36 of H3, the RIZ and the family SUV39, which consisting of enzymes that can methylate the K9 and K27 of H3 18 The methylation the K79 of H3 is an exception since the enzyme that is responsible for the modification, DOT1, does not brings the characteristic SET region 36. The methylation of K79 is related to the activity of the transcription and is participating in preventing the spread Heterochromatosis. The first methylated lysine which was discovered in mammals and brings upon itself an active methylated of K9 of H3 is Suv39h1, the same of Su (var) the 3-9 Drosofila 52 In certain cases, there is a later expressive modification of factors from enzymes that modifies the chromatin during methylation of arginin or acetylase have been found and their function appears in biological reactions, such as translation 25,38 But the only known enzymes from the methylated lysine family with characteristic domain SET, are the histones. Recently other enzymes that methylate the K4 of H3, including the MLL, the ALL, hSET1 and hSMYD3 these 72,75,117,48 have been excluded from humans. These proteins are usually part of micromolecular structures, which include more the one enzyme activity that modifiy the chromatin. In contrast with heterochromatin situation which was mentioned, the potential role of the modification of the histone in the consseration of the active translational chromatins has not been defined. If the modifications of the histone press for some
5
reaction to the controversial of the translational, the methylation works as inactivation means for the gonads, because contrary to the acetylation, the methylation of the lysine is stable. In addition, significant levels of methylation of H3-K4 have been observed in the genes of region of b-globulin and in the NF-4 during the cell diffentiation, before the translation, showing that this specific modification is involved in the resolution and the conservation of one strong active chromatin 49,48 . The cause of myelodysplasian patients is unknown. Radiation, chemotherapy with agents such as benzide and other organic compounds cause great damage to the majority of patients who have undergone such treatments. Myelodysplastic syndromes (MDS) are clonal haematologic disorders characterized clinically and morphologically by ineffective haematopoiesis43. The natural history of these syndromes may range from a chronic course spanning many years to a rapid course of leukaemic progression50. Myelodysplastic syndromes are viewed by most haematologists as encompassing stages of neoplastic haematopoiesis associated with cytopenias. Neoplastic transformation of haematopoetic cells can occur at various levels of stem cell development107. Finding the exact level of myeloid neoplastic transformation is difficult, as blood cells can continue to mature beyond the level of the stem cell that has sustained the neoplastic injury58. In myelodysplastic transformation to acute myelocytic leukaemia (AML), the neoplastic event occurs at the level of a committed myeloid stem cells in most patients31-94. Tumourogenesis is a multistep process of accumulated genetic alterations that can eventually lead to overt cancer after passing through premalignant phase that may be identified morphologically as dysplasia109. In myelodysplasia, malignant transformation at the level of a myeloid stem cell can result in chromosomal abnormalities that act as signatures of disease and can be identified in precursor cells giving rise to granulocytes, monocytes, red cells and platelets1,15. For the development of the leukaemic clone, further genetic events are required for the rapid expansion of leukaemic blasts5.Myelodysplasia generally affects older adults, with a median age at the onset in the seventh decade, although many cases in children have been reported1.The cause of myelodysplasia is unknown in majority of patients, but mostly by exposure to radiation, chemotherapeutic agents, benzene or other organic compounds91,44. In the past few years transcriptional inactivation of tumour suppressor genes by promoter CpG island hypermethylation has been a subject of intense interest as a causal factor in haematologic malignancies32. One of the most frequently and best studied epigenetic events in MDS is the silencing of the cyclin-dependent kinase inhibitor gene p15INKB, which controls the progression of cells from G1 to S phase16. Hypermethylation of the p15INKB promoter region occurs in approximately 50 per cent of MDS cases66. It has been reported to be acquired during disease progression106,88 and associated with leukaemic transformation104 and poor prognosis. AML shows promoter hypermethylation of p15 and E-cadherin genes32,71. Hypermethylation of hMLH1 gene had been found to be associated with acute myeloid leukaemia64. Early loss of cell cycle control (by p16/ p15 hypermethylation, deregulation of transcription factors), (disruption of cell adherence/cell-cell interaction by E-cadherin hypermethylation) can contribute to uncontrolled proliferation and cellular immortalization14. Furthermore, the methylation of patients with ERM (36 cases with AML), showed that ERM was often hypermethylated (47%), such as the MYOD1, Pitx2, Gpr37 and SDC4. It is significant that the concentration of methylation of each island CpG, related to the ER concentration showing the presence
6
of phenotype of methylation in AML71 . Also it has been found that patients having in chromosome 11 methylase, are the ones with-de-novo AML. Most of the times, the increase of methyltransferases DNMT1, DNMT3a, is related to hypermethylation p15 which occurs AML88. However, the exact relationship between hypermethylation instigator of the genes, and the involvement in the development of MDS which appears in children, remains unexplained with the exception maybe of the CDNKN2B. The development to AML occurs often in patients with RAEB (28%) and RAEBt (45%) but lesss in RA (10%) and RARS (8%) the chromosomal abnormalities (chromosome 7) and the larger increase of blastocytes constitute important indicators of leykemia metamorphosis. The hypermethylation of CDNKN2B hypokinase seems to be important for the development of MDS. The P1ÏNK4b gets out of during the in vitro reaction of blastocytosis and megakaryocytosis differentiation of physiologic of CD34 of haematopoietic cell factors66. Lack of CDNKN2B mutations are low (23%) in immature MDS, however the percentage of its methylation in the diagnosis is prognostic of development of illness and its existence also accompanies the development of disease92. Also the hypermethylation of CDNKN2B occurs in RAEB, RAEBt and particularly in disease with a percentage larger than 10% in blastocytes. Methylated cases of CDNKN2B are 58%, in chronic CMML and 60% – 70% in the Mds-AML. Thus, the CDNKN2B seems to play an important role in the progress and development of high risk MDS.
Category
Μethylated genes
No. of cases
Percentage 1 p15
25
61.0 2 P16
15
36.6 3. MGMT
2
4.9 4. E-cadherin
16
39 5. P15 +p16
8
19.5 6. P15+MGMT
1
2.4 7. P15,MGMT
10
24.4 8. P15,E-cadh
1
2.4 9. P16,MGMT
6
14.6 10. P16,E-cadh
1
2.4 11. P16,MGMT,E-cadh
1
2.4 12. P15 .MGMT,E-cadh
1
2.4 13 Methylation absent
8
19.5 Table I. Precentage of methylated genes in patients with myelidysplastic syndromes
FAB subtypes Number Genes methylated No. of cases Percentage RA 17 P15 P16 7 4 41.2 23.5
7
MGMT E-cadherin – 3 – 17.6 RAEB 9 P15 P16 MGMT E-cadherin 7 5 – 4 77.8 55.6 – 44.4 RARS 4 P15 P16 MGMT E-cadherin 2 1 – 2 50 25 – 50 RAEB-t 6 P15 P16 MGMT E-cadherin 5 2 – 3 83.3 33.3 – 50 MDS/AML 5 P15 P16 MGMT E-cadherin 4 3 2 4 89.0 60.0 40.0 80.0 Table II. Differential of mathylation genes in Myelodysplastic syndrome subtypes.
In addition, has been found that transcription of an anti-apoptotic factor of the NFKappaB is triggered in the high risk MDS and AML. Under the triggering of one of the suppressors methyltransferases and the apocetylated histones , the triggering of the NFKappaB is also suppressed in the malignant myeloblasts in vitro and in vivo 33
For the time being two different categories of drugs are under study. The suppressor of the apocetylated histone HDACi, and the suppressor of the methyl-transferase of the DNA. 115
A recent study from the laboratory of Schubeler has addressed the distribution and the silencing potential of promoter DNA methylation throughout the human genome.
They measured the DNA methylation, RNA polymerase occupancy, and histone modifications at 16,000 promoters in different primary human cells; CpG-poor promoters were hypermethylated in somatic cells which, however, did not preclude their transcriptional activity30. In contrast, strong CpG promoters were mostly unmethylated even when transcriptionally inactive. Promoters with only weak CpG island were distinct in being preferential targets for de novo methylation and somatic cells7. Interestingly, most tissue-specific genes were methylated in somatic cells, implicating additional functional selection. Notably in this study, inactive unmethylated CpG island promoters showed higher levels of demethylation of lysine 4 of histone H3 62,36,96, suggesting that this particular chromatin mark may protect promoters from DNA methylation. In the last years, a large and growing number of genes has been studied for methylation changes in hematopoietic neoplasias. Investigations have focused on genes involved in cell cycle regulation, tumour suppressor genes, and other genes involved in growth, differentiation, and cell adhesion. A remarkable lineage specificity of some genes inactivated by
8
methylation needs further investigation. For example, the p15 or INK4B gene4,88,104, but not the closely related p16 or INK4A gene, is frequently hypermethylated in myeloid neoplasias and acute lymphoid leukemia. In contrast, p16 is frequently methylated in solid tumors and Non-Hodgkin’s lymphoma . Promoter methylation was demonstrated in the leukemia model of acute promyelocytic leukemia expressing the chimeric transcription factor PML-RARα, which was found 5’ mCpG 3’ to mediate silencing by DNA methylation of a RARα target gene via recruitment of DNA methyltransferase 3a12. In vitro treatment with retinoic acid induced demethylation of the promoter, resulting in gene re-expression and cellular differentiation . Thus, a link between genetic changes in leukemia (fusion protein formation) and epigenetic modification (hypermethylation) were first demonstrated in this model. Interestingly, the AML-specific fusion protein AML1–ETO34, which results from the translocation (8;21) has also very recently been demonstrated to act as an epigenetic modifier. Specifically, AML1–ETO protein counteracts retinoic acid by participating in a protein complex with RARα at RA regulatory reagents of the RAR beta 2 promoter. AML1–ETO34,71 was demonstrated to recruit HDAC, DNMT, and DNA methyl-CpG binding activities, thus, promoting a closed chromatin conformation. Interestingly, both the demethylating agent 5-azacytidine79 and AML1–ETO knocked down by siRNA reverted these epigenetic alterations and reintroduced RA differentiation responses in myeloid blasts . Very revently, the same group could also demonsrtare a direct functional interaction between AML1-ETO and miR-223, which allso could reverted by demethylating agents and induced cell differentiation.
CONCLUDING REMARKS
Both DNA methylation and histone deacetylation are reversible modifications,and inhibitors of each procces exist.Epigenetic modification ,has led to novel therapeutic approaches in recent years.The area of cancer epigenetics for the better target therapy is open.
Finally improvements in antisense and gene therapy procedures may also allow correction of the molecular defects in MDS.
REFERENCES
1.Abruzzese E,Buss D,Rainer R,Rao PN,Pettenati MJ.Studi of clonality in myelodysplastic syndromes;detection of trisomy 8 in bone marrow cell smears by fluorescene in situ hybridization.Leuk Res 1996;20:551-7.
2.Agalioti, T., Chen, G., and Thanos, D. (2002). Deciphering the transcriptional histone acetylation code for a human gene. Cell 111, 381-392.
3.Agalioti, T., Lomvardas, S., Parekh, B., Yie, J., Maniatis, T., and Thanos, D. (2000).Ordered recruitment of chromatin modifying and general transcription factors to theIFN-beta promoter. Cell 103, 667-678.
4.Aggerholm A,Holm MS,Guldberg P,Ol;essen LH,Hokland P.Promoter hypermethylation of p 15INK4B,HIC1,CDH1,and ER is frequent in myelodyspastic syndrome and predicts poor prognosis in early-stage patients.Eur J Haematol 2006;
76:23-32.
5.Anderson RL,Bagby
9
GC Jr,Richert-Boe K,Magenis RE,Koler RD.Therapy-related preleukemic syndrome.Cancer 1981;47:1867-71.
6.Andrea Kuedgen.Michael Lubbert.Current status of epigenetic treatment in myelodysplastic syndromes Ann Hematol. 2008 Aug;87(8):601-11
7. Andrian Bird DNA methylation patterns and epigenetic memory Genes Dev. 2002 Jan 1;16(1):6-21
8.Ahmad, K., and Henikoff, S. (2002). The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 9, 1191-1200.
9.Allis, C. D., Chicoine, L. G., Richman, R., and Schulman, I. G. (1985). Depositionrelated histone acetylation in micronuclei of conjugating Tetrahymena. Proc Natl Acad Sci U S A 82, 8048-8052.
10.Allis, C. D., Chicoine, L. G., Richman, R., and Schulman, I. G. (1985). Depositionrelated histone acetylation in micronuclei of conjugating Tetrahymena. Proc Natl Acad Sci U S A 82, 8048-8052.
11.Bader-Meunier B,Mielot F,Tchernia G,Buisine J,Delsol G,Duchyane E.Myelodysplastic syndromes in chilhood:report of 49 patients from a French multicenter study.Br J Haematol 1996;92:344-50.
12. Bannister, A. J., Zegerman, P., Partridge, J. F., Miska, E. A., Thomas, J. O., Allshire, R. C., and Kouzarides, T. (2001). Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120-124.
13.Baylin SB(2002).Mechanisms ubderlying epigenetically mediated gene silencing in ancer.Semin Cancer Biol ;12:331-337
14. Baylin SB, Herman JG. DNA hypermethylation in tumorigenesis:epigenetics joins genetics. Trends Genet 2000;16 : 168-74
15.Bernell P,Jacobsonn B,Nordgren A,Hast R.Clonal cell lineage involvement in myelodysplastic syndromes studied by fluorescene in situ hybridization and morphology. Leukemia 1996;10:662-8
16. Bell A.C. and Felsenfeld, G.2000. Methylation of a CTCF dependent boundary controls imprinted expression of the Igf2 gene Nature 405: 482-485
17. Bell A.C., West, A.G., and Felsenfeld, G. 1999. The protein CTCF is required for the enhancer blocking activity of a vertabrate insulators. Cell 98: 387-396
18. Bernstein, B. E., Humphrey, E. L., Erlich, R. L., Schneider, R., Bouman, P., Liu, J. S., Kouzarides, T., and Schreiber, S. L. (2002). Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A 99, 8695-8700.
19. Brownell, J. E., and Allis, C. D. (1996). Special HATs for special occasions: linking histone acetylation to chromatin assembly and gene activation. Curr Opin Genet Dev6, 176-184.
20.Brownell, J. E., Zhou, J., Ranalli, T., Kobayashi, R., Edmondson, D. G., Roth, S. Y., and Allis, C. D. (1996). Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84, 843-851.
21.Brownell, J. E., and Allis, C. D. (1995). An activity gel assay detects a single, catalytically active histone acetyltransferase subunit in Tetrahymena macronuclei. Proc Natl Acad Sci U S A 92, 6364-6368.
22.Borrow, J., Stanton, V. P., Jr., Andresen, J. M., Becher, R., Behm, F. G., Chaganti, R.
S., Civin, C. I., Disteche, C., Dube, I., Frischauf, A. M., et al. (1996). The translocation t(8;16)(p11;p13) of acute myeloid leukaemia fuses a putative acetyltransferase to the CREB-binding protein. Nat Genet 14, 33-41.
23. Candau, R., Moore, P. A., Wang, L., Barlev, N., Ying, C. Y., Rosen, C. A., and Berger, S. L. (1996). Identification of human proteins functionally conserved with the yeast putative adaptors ADA2 and GCN5. Mol Cell Biol 16, 593-602.
24. Candau, R., Zhou, J. X., Allis, C. D., and Berger, S. L. (1997). Histone acetyltransferase activity and interaction with ADA2 are critical for GCN5 function in vivo. Embo J 16, 555-565.
25.Chen, H., Tini, M., and Evans, R. M. (2001). HATs on and beyond chromatin. Curr Opin Cell Biol 13, 218-224.
26.Claus R, Lubbert M(2003).Epigenetic targets in hematopoietic malignancies.Oncogene ;22:6489-6496
27.Cosma, M.P. , Tanaka, T. and Nasmyth , K. 1999. Ordrered requitment of transcription and chromatin remodeling factors to a cell cycle and developmentally regulated promoter. Cell: 299-311
28.Cuthbert, G. L., Daujat, S., Snowden, A. W., Erdjument-Bromage, H., Hagiwara, T., Yamada, M., Schneider, R., Gregory, P. D., Tempst, P., Bannister, A. J., and Kouzarides, T. (2004). Histone deimination antagonizes arginine methylation. Cell 118, 545-553.
29.Dhalluin, C., Carlson, J. E., Zeng, L., He, C., Aggarwal, A. K., and Zhou, M. M. (1999). Structure and ligand of a histone acetyltransferase bromodomain. Nature 399, 491-496.
10
30.Di Croce L, Raker VA, Corsaro M, Fazi F, Fanelli M, Faretta M, Fuks F, Lo Coco F, Kouzarides T, Nervi C, Minucci S, Pelicci PG (2002) Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science 295:1079–1082
31.Escudier SM,Albitar M,Robertson LE,Andreeff M,Pierce S,Kantarjian HM. Acute lymphoblastic leukemia following preleukemic syndromes in adults. Leukemia 1996:10:473-7
32.Esteller M.Profiling aberrant DNA methylation in hematologic neoplasmas:a view from the tip of the iceberg.Clin Immunol 2003; 109:80-8.
33.Fabre C,Grosjean J,Tailler M,Boehrer S,Ades L,Perfettini JL,de Botton S,Fenaux P, Kroemer G.A novel effect of DNS methyltransferase and histone deacetylase inhibitors: NFkappaB inhibition in malignant myeloblasts.Cell cycle.2008 Jul;7(14):2139-45.Epub 2008 May 9.
34.Fazi F,Racanicchi S,Zardo G,Starnes LM,Mancini M,Travaglini L,Diverio D,Ammatuna E,Cimino G,Lo-Coco F,Grignani F,Nervi C(2007). Epigenetic silencing of the myelopoiesis regulator micro RNA-223 by the AML1/ETO oncoprotein.Cancer Cell :12:457-466
35.Fazi F, Zardo G, Gelmetti V, Travaglini L, Ciolfi A, Di Croce L, Rosa A, Bozzoni I, Grignani F, Lo-Coco F, Pelicci PG, Nervi C (2007) Heterochromatic gene repression of the retinoic acid pathway in acute myeloid leukemia. Blood 109:4432–4440
36.Feng, Q., Wang, H., Ng, H. H., Erdjument-Bromage, H., Tempst, P., Struhl, K., and Zhang, Y. (2002). Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol 12, 1052-1058.
37.Fischle, W., Tseng, B. S., Dormann, H. L., Ueberheide, B. M., Garcia, B. A., Shabanowitz, J., Hunt, D. F., Funabiki, H., and Allis, C. D. (2005). Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature.
38. Freiman, R. N., and Tjian, R. (2003). Regulating the regulators: lysine modifications make their mark. Cell 112, 11-17.
39.Georgakopoulos, T., and Thireos, G. (1992). Two distinct yeast transcriptional activators require the function of the GCN5 protein to promote normal levels of transcription. Embo J 11, 4145-4152.
40.Giles, R. H., Peters, D. J., and Breuning, M. H. (1998). Conjunction dysfunction: CBP/p300 in human disease. Trends Genet 14, 178-183.
41.Gilbert C, Kristjuhan A, Winkler G, Svejstrup JQ (2004) Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation. Mol Cell 14: 457-464
42.Giordano, A., and Avantaggiati, M. L. (1999). p300 and CBP: partners for life and death. J Cell Physiol 181, 218-230.
43.Golde DW,Cline MJ.Human preleukemia:identification of a maturation defect in vitro.N Engl J Med 1973;288:1083-6.
44.Golomb HM,Alimena G,Rowley JD,Vardiman JW,Testa JR,Sovik C.Correlation of occupation and karyotype in adults with acute nonlymphocytic leukemia.Blood 1982;60:404-11
45. Grant, P. A., Schieltz, D., Pray-Grant, M. G., Steger, D. J., Reese, J. C., Yates, J. R., 3rd, and Workman, J. L. (1998). A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell 94, 45-53.
46.Grant, P. A., Sterner, D. E., Duggan, L. J., Workman, J. L., and Berger, S. L. (1998). The SAGA unfolds: convergence of transcription regulators in chromatin-modifying complexes. Trends Cell Biol 8, 193-197.
47.Gurdon ,J.B.1999.Genetic reprogramming following nuclear transplantation in Amphibia.Semin.Cell Dev.Biol.10:239-243
48.Hamamoto, R., Furukawa, Y., Morita, M., Iimura, Y., Silva, F. P., Li, M., Yagyu, R., and Nakamura, Y. (2004). SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells. Nat Cell Biol 6, 731-740.
49.Hatzis, P., and Talianidis, I. (2002). Dynamics of enhancer-promoter communication during differentiation-induced gene activation. Mol Cell 10, 1467-1477.
50.Heaney ML,Golde DW.Myelodysplasia .N Engl J Med 2006;340:1649-60.
51.Henikoff, S., and Ahmad, K. (2005). Assembly Of Variant Histones Into Chromatin. Annu Rev Cell Dev Biol 21, 133-153.
52.Jenuwein, T. (2001). Re-SET-ting heterochromatin by histone methyltransferases. Trends Cell Biol 11, 266-273.
53. Jenuwein, T., and Allis, C. D. (2001). Translating the histone code. Science 293, 1074-1080.
54.Jones PA,Baylin SB(2007).The epigenomics of cancer.Cell ;128:683-692
55.Kaufman, P. D., Kobayashi, R., Kessler, N., and Stillman, B. (1995). The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication. Cell 81, 1105-1114.
11
56.Kim, J. H., Lane, W. S., and Reinberg, D. (2002). Human Elongator facilitates RNA polymerase II transcription through chromatin. Proc Natl Acad Sci U S A 99, 1241- 1246.
57.Kleff, S., Andrulis, E. D., Anderson, C. W., and Sternglanz, R. (1995). Identification of a gene encoding a yeast histone H4 acetyltransferase. J Biol Chem 270, 24674- 24677.
58.Koeffler HD,Golde DW.Human preleukemia.Ann Intern Med 1980;93:347-53.
59.Korzus, E., Torchia, J., Rose, D. W., Xu, L., Kurokawa, R., McInerney, E. M., Mullen, T. M., Glass, C. K., and Rosenfeld, M. G. (1998). Transcription factorspecific requirements for coactivators and their acetyltransferase functions. Science 279, 703-707.
60.Korzus, E., Torchia, J., Rose, D. W., Xu, L., Kurokawa, R., McInerney, E. M., Mullen, T. M., Glass, C. K., and Rosenfeld, M. G. (1998). Transcription factorspecific requirements for coactivators and their acetyltransferase functions. Science 279, 703-707.
61.Kuo, M. H., Brownell, J. E., Sobel, R. E., Ranalli, T. A., Cook, R. G., Edmondson, D. G., Roth, S. Y., and Allis, C. D. (1996). Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines. Nature 383, 269-272.
62.Lachner, M., O’Carroll, D., Rea, S., Mechtler, K., and Jenuwein, T. (2001). Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116-120.
63.Legube, G., and Trouche, D. (2003). Regulating histone acetyltransferases and deacetylases. EMBO Rep 4, 944-947.
64.Lenz G,Hunter G, Hiddeman W, Dreyling M. Promoter methylation and expression of DNA repair genes hMLH1 and MGMT in acute myeloyd leykaimia. Ann Hematol 2004; 83: 628-33
65.Loyola, A., and Almouzni, G. (2004). Bromodomains in living cells participate in deciphering the histone code. Trends Cell Biol 14, 279-281.
66.Lubbert M.Gene silencing of the p15/INK4B cell-cycle inhibitor by hypermethylation:an early or later epigenetic alteration in myelodysplastic syndromes? Leukemia 2003;17 :1762-4
67.Margueron, R., Trojer, P., and Reinberg, D. (2005). The key to development: interpreting the histone code? Curr Opin Genet Dev 15, 163-176.
68.Marmorstein, R. (2001). Protein modules that manipulate histone tails for chromatin regulation. Nat Rev Mol Cell Biol 2, 422-432.
69.Martinez-Balbas, M. A., Bannister, A. J., Martin, K., Haus-Seuffert, P., Meisterernst, M., and Kouzarides, T. (1998). The acetyltransferase activity of CBP stimulates transcription. Embo J 17, 2886-2893.
70.McKittrick, E., Gafken, P. R., Ahmad, K., and Henikoff, S. (2004). Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc Natl Acad Sci U S A 101, 1525-1530.
71.Μelki JR,Vincent PC,Clark SJ.Concurrent DNA hypermethylation of multiple genes in AML.Cacner Res 1999; 59:3730-40
72.Milne, T. A., Briggs, S. D., Brock, H. W., Martin, M. E., Gibbs, D., Allis, C. D., and Hess, J. L. (2002). MLL targets SET domain methyltransferase activity to Hox gene promoters. Mol Cell 10, 1107-1117.
73.Mizzen, C. A., Yang, X. J., Kokubo, T., Brownell, J. E., Bannister, A. J., Owen- Hughes, T., Workman, J., Wang, L., Berger, S. L., Kouzarides, T., et al. (1996). The TAF(II)250 subunit of TFIID has histone acetyltransferase activity. Cell 87, 1261- 1270.
74.Mutskov, V., Gerber, D., Angelov, D., Ausio, J., Workman, J., and Dimitrov, S.
(1998). Persistent interactions of core histone tails with nucleosomal DNA following acetylation and transcription factor binding. Mol Cell Biol 18, 6293-6304.
75.Nakamura, T., Mori, T., Tada, S., Krajewski, W., Rozovskaia, T., Wassell, R., Dubois, G., Mazo, A., Croce, C. M., and Canaani, E. (2002). ALL-1 is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation. Mol Cell 10, 1119-1128.
76.Neuwald, A. F., and Landsman, D. (1997). GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Trends Biochem Sci 22, 154-155.
77.Ng, H. H., Robert, F., Young, R. A., and Struhl, K. (2003). Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11, 709-719.
78.Nishioka, K., Chuikov, S., Sarma, K., Erdjument-Bromage, H., Allis, C. D., Tempst, P., and Reinberg, D. (2002). Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev 16, 479-489.
79.Ο’ Dwyer K,Maslak P.Azacitidine and the beginnings of therapeutic epigenetic modulation.Expert Opin Pharmacother.2008 Aug;9(11):1981-6
12
80.Ogryzko, V. V., Kotani, T., Zhang, X., Schiltz, R. L., Howard, T., Yang, X. J., Howard, B. H., Qin, J., and Nakatani, Y. (1998). Histone-like TAFs within the PCAF histone acetylase complex. Cell 94, 35-44.
81.Otero, G., Fellows, J., Li, Y., de Bizemont, T., Dirac, A. M., Gustafsson, C. M., Erdjument-Bromage, H., Tempst, P., and Svejstrup, J. Q. (1999). Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol Cell 3, 109-118.
82.Parthun, M. R., Widom, J., and Gottschling, D. E. (1996). The major cytoplasmic histone acetyltransferase in yeast: links to chromatin replication and histone metabolism. Cell 87, 85-94.
83.P.R. Solomon, A.K.Munirajan, Nobuo Tsutsida, Kottampati Muthukumarasamy Andiappan Rathinavel, G.S. Selvan and G.Shanmugam. Promoter hypermethylation analysis in myelodisplastic syndromes:Diagnostic & prognostic implication Indian J Med Res. 2008 Jan;127(1):52-7.
84.Pray-Grant, M. G., Daniel, J. A., Schieltz, D., Yates, J. R., 3rd, and Grant, P. A. (2005). Chd1 chromodomain links histone H3 methylation with SAGA- and SLIKdependent acetylation. Nature 433, 434-438.
85.Pokholok, D. K., Hannett, N. M., and Young, R. A. (2002). Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol Cell 9, 799-809.
86.Polach, K. J., Lowary, P. T., and Widom, J. (2000). Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes. J Mol Biol 298, 211-223.
87.Puri, P. L., Sartorelli, V., Yang, X. J., Hamamori, Y., Ogryzko, V. V., Howard, B. H., Kedes, L., Wang, J. Y., Graessmann, A., Nakatani, Y., and Levrero, M. (1997). Differential roles of p300 and PCAF acetyltransferases in muscle differentiation. Mol Cell 1, 35-45.
88.Quesnel B,Guillerm G,Vereecque R,Wattel E,Preudhomme C.Bauters F,et al.Methylation of the p15(INKB) gene in myelodysplastic syndromes is frequent and acquired during disease progression.Blood 1998;91:2985-90.
89.Rea, S., Eisenhaber, F., O’Carroll, D., Strahl, B. D., Sun, Z. W., Schmid, M., Opravil, S., Mechtler, K., Ponting, C. P., Allis, C. D., and Jenuwein, T. (2000). Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593- 599.
90.Rideout,I.W.,Eggan,K., and Jaenisch,R.2001.Nuclear cloning and epigenetic reprogramming of the genome.Science 293:1093-1098
91.Rowley JD,Golomb HM,Vardiman JW.Nonrandom chromosome abnormalities in acute leukemia and dysmyelopoietic syndromes in patients with previoysly treated malignant disease.Blood 1981;58:759-67.
92.Russo,V.E.A .,Martiensen,R.A.,and Riggs,A.D.1996.Epigenetic mechanisms of gene regulation.Gold Spring Harbor Laboratory Press,Cold Spring Harbor,NY
93.Ruiz-Carrillo, A., Wangh, L. J., and Allfrey, V. G. (1975). Processing of newly synthesized histone molecules. Science 190, 117-128.
94.Saitoh K,Miura I,Takahashi N,Miura AB.Dluorescene in situ hybridization of progenitor cells obtained by fluorescene-activated cell sorting for the detection of cells affected by chromosome abnormality trisomy 8 in patients with myelodysplastic syndromes.Blood 1998;92:1886-92.
95.Saleh, A., Schieltz, D., Ting, N., McMahon, S. B., Litchfield, D. W., Yates, J. R., 3rd, Lees-Miller, S. P., Cole, M. D., and Brandl, C. J. (1998). Tra1p is a component of the yeast Ada.Spt transcriptional regulatory complexes. J Biol Chem 273, 26559-26565.
96.Santos-Rosa, H., Schneider, R., Bannister, A. J., Sherriff, J., Bernstein, B. E., Emre, N. C., Schreiber, S. L., Mellor, J., and Kouzarides, T. (2002). Active genes are trimethylated at K4 of histone H3. Nature 419, 407-411.
97.Schiltz, R. L., Mizzen, C. A., Vassilev, A., Cook, R. G., Allis, C. D., and Nakatani, Y. (1999). Overlapping but distinct patterns of histone acetylation by the human coactivators p300 and PCAF within nucleosomal substrates. J Biol Chem 274, 1189- 1192.
98.Schneider, R., Bannister, A. J., Myers, F. A., Thorne, A. W., Crane-Robinson, C., and Kouzarides, T. (2004). Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat Cell Biol 6, 73-77.
99.Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J. R., Cole, P. A., Casero, R. A., and Shi, Y. (2004). Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941-953.
100.Sims, R. J., 3rd, Nishioka, K., and Reinberg, D. (2003). Histone lysine methylation: a signature for chromatin function. Trends Genet 19, 629-639.
101.Smith, E. R., Belote, J. M., Schiltz, R. L., Yang, X. J., Moore, P. A., Berger, S. L.,
102.Taunton, J., Hassig, C. A., and Schreiber, S. L. (1996). A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272, 408-411.
13
103.Thiagalingam, S., Cheng, K. H., Lee, H. J., Mineva, N., Thiagalingam, A., and Ponte, J. F. (2003). Histone deacetylases: unique players in shaping the epigenetic histone code. Ann N Y Acad Sci 983, 84-100.
104.Tien HF,Tang JH,Liu MC,Lee FY,Wang CH.Methylation of the p15(INKB) gene in myelodysplastic syndrome:it can be detected early at diagnosis or during disease progression and is highly associated with leukaemic tranformation.Br J Haematol 2001;112:148-54.
105.Turner, B. M. (2000). Histone acetylation and an epigenetic code. Bioessays 22, 836- 845.
106.Uchida T,Kinoshita T,Nagai H,Nakahara Y,Saito H,Hotta T,et al.Hypermethylation of the p15INKB gene in myelodysplastic syndromes.Blood 1997; 90 :1403-9.
107.Varmus HE,Lowell CA.Cancer genes and hematopoiesis. Blood 1994;83 : 5-9.
108. Vassilev, A., Yamauchi, J., Kotani, T., Prives, C., Avantaggiati, M. L., Qin, J., and Nakatani, Y. (1998). The 400 kDa subunit of the PCAF histone acetylase complex belongs to the ATM superfamily. Mol Cell 2, 869-875.
109.Vogelstein B,Fearon ER,Hamilton SR,erm SE,Preisinger AC,Leppert M.Genetic alterations during colorectal-tumor development.N.Eng J Med 1988;319:525-32.
110. Wakayama ,T and Yanagimachi,R. 2001.Mouse cloning with nucleus donor cellsof different age and type.Mol.Reprod.Dev.58:376-383
111.Wang, Y., Wysocka, J., Sayegh, J., Lee, Y. H., Perlin, J. R., Leonelli, L., Sonbuchner, L. S., McDonald, C. H., Cook, R. G., Dou, Y., et al. (2004). Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306, 279-283.
112.Wang, H., Cao, R., Xia, L., Erdjument-Bromage, H., Borchers, C., Tempst, P., and Zhang, Y. (2001). Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase. Mol Cell 8, 1207-1217.
113.Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schόbeler D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457–466
114.Wittschieben, B. O., Otero, G., de Bizemont, T., Fellows, J., Erdjument-Bromage, H., Ohba, R., Li, Y., Allis, C. D., Tempst, P., and Svejstrup, J. Q. (1999). A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme. Mol Cell 4, 123-128.
115.Wolffe AP (2001).Transcriptional regulation in the contex of chromatin structure.Essays Biochem ;37:45-47
116.Wolffe, A. P., and Hayes, J. J. (1999). Chromatin disruption and modification. Nucleic Acids Res 27, 711-720
117.Wysocka, J., Myers, M. P., Laherty, C. D., Eisenman, R. N., and Herr, W. (2003). Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. Genes Dev 17, 896-911.
118.Wysocka, J., Swigut, T., Milne, T. A., Dou, Y., Zhang, X., Burlingame, A. L., Roeder, R. G., Brivanlou, A. H., and Allis, C. D. (2005). WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121, 859-872.
119.Yang, X. J., Ogryzko, V. V., Nishikawa, J., Howard, B. H., and Nakatani, Y. (1996). A p300/CBP-associated factor that competes with the adenoviral oncoprotein E1A. Nature 382, 319-324.
120. Grewal,S.I.,and Elgin S.C. (2002). Heterochromatin:new possibilities for the inheritance of structure. Curr Opin Genet Dev 12, 178-187
121.St.Allachiotis.Principles of Genetics.
Publishing Ellinika Grammata,2005 526-527.
122 .Αmr H.Sawalha,Ryan Webb,et al.
Common Variants within MECP2 Confer Risk of Systemic Lupus Erythematosus.
www.plosone.org March 2008/Volume 3/Issue 3/e1717.
123 Gorelik G, Richardson B. Αberrant T cell ERK pathway signaling and chromatin structure in lupus.Autoimmun Rev. 2008 Aug 21.
124 Tsay GJ, Zouali M.
Τoxicogenomics — a novel opportunity to probe lupus susceptibility and pathogenesis.
Int Immunopharmacol. 2008 Oct;8(10):1330-7. Epub 2008 Apr 10.
125 Tao J, Yang M, Chen Z, Huang Y, Zhao Q, Xu J, Ren H, Zhao H, Chen Z, Ren Q, Yang R. 125 .
Decreased DNA methyltransferase 3A and 3B mRNA expression in peripheral blood mononuclear cells and increased plasma SAH concentration in adult patients with idiopathic thrombocytopenic purpura.
J Clin Immunol. 2008 Sep;28(5):432-9. Epub 2008 Aug
14
