Biopolym. Cell. 2014; 30(3):197-202.
Structure and Function of Biopolymers
Chromatin enrichment of histone marks H4Ac
and H3K9me3 in TP53 gene domain in breast cells
1Santos G. C. Jr, 2Goes A. C. S., 1de Moura Gallo C. V.
- Departament of Genetics, Institute of Bilogy, University of State of Rio de Janeiro (UERJ)
Rua Sao Francisco Xavier, 524, sala 525-6, Maracana, Rio de Janeiro, CEP, 20.550-013, Brazil - Department of Science and Biology, Institute of Bilogy, University of State of Rio de Janeiro (UERJ)
Rua Sao Francisco Xavier, 524, sala 525-6, Maracana, Rio de Janeiro, CEP, 20.550-013, Brazi
Abstract
In non-cancerous breast cell lines HB2 and MCF10A the TP53 gene is localized inside a relatively small ~ 50 kb loop domain delimited by two S/MARs. Aim. To analyze the chromatin markers H4Ac and H3K9me3 of these two S/MARs and of the TP53 gene P1 promoter in different breast cells lines. Methods. We used chromatin immunoprecipitation (ChIP) to characterize the chromatin status of these S/MARs elements in breast non-cancerous cell lines HB2 and MCF10A and cancerous MCF-7, MDA-MB-231, BT-474 and T47D cell lines, by chromatin enrichment of H4Ac and H3K9me3 epigenetic markers, hallmarks of open and closed chromatin, respectively. Results. We found that these chromatin epigenetic markers are differentially distributed in S/MARs for all analyzed breast cell lines. Conclusions. We found no correlation between S/MARs and chromatin epige- netic status, suggesting that nuclear matrix fixation and chromatin status can be independent. High enrichment of H3K9me3 in the TP53 gene P1 promoter region in MCF-7, could explain lower levels of the TP53 expression, described earlier by our group.
Keywords: TP53, loop domain, MAR, breast cancer, chromatin markers, ChIP assay
Full text: (PDF, in English)
References
[1]
Choe MK, Hong CP, Park J, Seo SH, Roh TY. Functional elements demarcated by histone modifications in breast cancer cells. Biochem Biophys Res Commun. 2012;418(3):475-82.
[2]
Budhavarapu VN, Chavez M, Tyler JK. How is epigenetic information maintained through DNA replication? Epigenetics Chromatin. 2013;6(1):32.
[3]
Terweij M, van Leeuwen F. Histone exchange: sculpting the epigenome. Front Life Sci. 2013; 7(1–2):63–79.
[4]
Luo XG, Guo S, Guo Y, Zhang CL. Histone modification and breast cancer. Breast cancer – focusing tumor microenvironment, stem cells and metastasis. Eds M Gunduz, E Gunduz. 2011; Ch. 15:321–342.
[5]
Chicoine LG, Schulman IG, Richman R, Cook RG, Allis CD. Nonrandom utilization of acetylation sites in histones isolated from Tetrahymena. Evidence for functionally distinct H4 acetylation sites. J Biol Chem. 1986;261(3):1071-6.
[6]
O'Neill LP, Turner BM. Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner. EMBO J. 1995;14(16):3946-57.
[7]
Thorne AW, Kmiciek D, Mitchelson K, Sautiere P, Crane-Robinson C. Patterns of histone acetylation. Eur J Biochem. 1990;193(3):701-13.
[8]
Leroy G, Dimaggio PA, Chan EY, Zee BM, Blanco MA, Bryant B, Flaniken IZ, Liu S, Kang Y, Trojer P, Garcia BA. A quantitative atlas of histone modification signatures from human cancer cells. Epigenetics Chromatin. 2013;6(1):20.
[9]
Bell O, Tiwari VK, Thom? NH, Sch?beler D. Determinants and dynamics of genome accessibility. Nat Rev Genet. 2011;12(8):554-64.
[10]
Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 2012;22(2):246-58.
[11]
Baylin SB, Jones PA. A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer. 2011;11(10):726-34.
[12]
Vassetzky YS, Hair A, Razin SV. Rearrangement of chromatin domains in cancer and development. J Cell Biochem Suppl. 2000;Suppl 35:54-60.
[13]
Razin SV, Iarovaia OV, Vassetzky YS. A requiem to the nuclear matrix: from a controversial concept to 3D organization of the nucleus. Chromosoma. 2014;123(3):217-24. http://dx.doi.org10.1007/s00412-014-0459-8
[14]
Eivazova ER, Gavrilov A, Pirozhkova I, Petrov A, Iarovaia OV, Razin SV, Lipinski M, Vassetzky YS. Interaction in vivo between the two matrix attachment regions flanking a single chromatin loop. J Mol Biol. 2009;386(4):929-37.
[15]
Razin SV, Vassetzky YS, Hancock R. Nuclear matrix attachment regions and topoisomerase II binding and reaction sites in the vicinity of a chicken DNA replication origin. Biochem Biophys Res Commun. 1991;177(1):265-70.
[17]
Wilson RH, Coverley D. Relationship between DNA replication and the nuclear matrix. Genes Cells. 2013;18(1):17-31.
[18]
Rivera-Mulia JC, Hernandez-Mu?oz R, Martnnez F, Aranda-Anzaldo A. DNA moves sequentially towards the nuclear matrix during DNA replication in vivo. BMC Cell Biol. 2011;12:3.
[19]
Bode J, Maass K. Chromatin domain surrounding the human interferon-beta gene as defined by scaffold-attached regions. Biochemistry. 1988;27(13):4706-11.
[20]
Forrester WC, Fern?ndez LA, Grosschedl R. Nuclear matrix attachment regions antagonize methylation-dependent repression of long-range enhancer-promoter interactions. Genes Dev. 1999;13(22):3003-14.
[21]
Fernandez LA, Winkler M, Grosschedl R. Matrix attachment region-dependent function of the immunoglobulin mu enhancer involves histone acetylation at a distance without changes in enhancer occupancy. Mol Cell Biol. 2001;21(1):196–208.
[22]
Martens JH, Verlaan M, Kalkhoven E, Dorsman JC, Zantema A. Scaffold/matrix attachment region elements interact with a p300-scaffold attachment factor A complex and are bound by acetylated nucleosomes. Mol Cell Biol. 2002;22(8):2598-606.
[23]
Keaton MA, Taylor CM, Layer RM, Dutta A. Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes. PLoS One. 2011;6(3):e17912.
[24]
Kisseljova NP, Dmitriev P, Katargin A, Kim E, Ezerina D, Markozashvili D, Malysheva D, Planche E, Lemmers RJ, van der Maarel SM, Laoudj-Chenivesse D, Lipinski M, Vassetzky YS. DNA polymorphism and epigenetic marks modulate the affinity of a scaffold/matrix attachment region to the nuclear matrix. Eur J Hum Genet. 2014 Jan 22.
[25]
Hendzel MJ, Sun JM, Chen HY, Rattner JB, Davie JR. Histone acetyltransferase is associated with the nuclear matrix. J Biol Chem. 1994;269(36):22894-901.
[26]
Davie JR. Nuclear matrix, dynamic histone acetylation and transcriptionally active chromatin. Mol Biol Rep. 1997;24(3):197-207.
[27]
Goes AC, Cappellen D, Santos GC Jr, Pirozhkova I, Lipinski M, Vassetzky Y, de Moura-Gallo CV. Loop domain organization of the p53 locus in normal and breast cancer cells correlates with the transcriptional status of the TP53 and the neighboring genes. J Cell Biochem. 2011;112(8):2072–81.
[28]
Trevilla-Garc?a C, Aranda-Anzaldo A. Cell-type-specific organization of nuclear DNA into structural looped domains. J Cell Biochem. 2011;112(2):531-40.
[29]
Dijkwel PA, Hamlin JL. Matrix attachment regions are positioned near replication initiation sites, genes, and an interamplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells. Mol Cell Biol. 1988;8(12):5398-409.
[30]
Boulikas T. Chromatin domains and prediction of MAR sequences. Int Rev Cytol. 1995;162A:279-388.
[32]
Khoury MP, Marcel V, Fernandes K, Diot A, Lane DP, Bourdon JC. Detecting and quantifying p53 isoforms at mRNA level in cell lines and tissues. Methods Mol Biol. 2013;962:1-14.
[33]
Wang B, Niu D, Lam TH, Xiao Z, Ren EC. Mapping the p53 transcriptome universe using p53 natural polymorphs. Cell Death Differ. 2014;21(4):521-32.
[34]
Razin SV, Petrov A, Hair A, Vassetzky YS. Chromatin domains and territories: flexibly rigid. Crit Rev Eukaryot Gene Expr. 2004;14(1-2):79-88.
[35]
Espinoza CA, Ren B. Mapping higher order structure of chromatin domains. Nat Genet. 2011;43(7):615-6.
[37]
Zuleger N, Robson MI, Schirmer EC. The nuclear envelope as a chromatin organizer. Nucleus. 2011;2(5):339-49.
[38]
Gargiulo G, Minucci S. Epigenomic profiling of cancer cells. Int J Biochem Cell Biol. 2009;41(1):127-35.
[39]
Dalvai M, Bystricky K. The role of histone modifications and variants in regulating gene expression in breast cancer. J Mammary Gland Biol Neoplasia. 2010;15(1):19-33.
[40]
Majocchi S, Aritonovska E, Mermod N. Epigenetic regulatory elements associate with specific histone modifications to prevent silencing of telomeric genes. Nucleic Acids Res. 2014;42(1):193-204.
