جۆری توێژینه‌وه‌: Original Article

نوسه‌ر

Kalar-sulaimaniyah main road

پوخته‌

Transposable elements and other sequences of repetitive DNA including microsatellite are usually subject to both DNA methylation and transcriptional silencing. However, anti-silencing mechanisms which lead to promote transcription in such regions are not well investigated. A recent genetic screening in Arabidopsis thaliana identified an anti-silencing factor, named Bromodomain and ATPase domain-containing protein 1 (BRAT1). This protein is involved in DNA demethylation through a valuable association between histone acetylation and transcriptional anti-silencing at methylated genomic loci. This involvement can be conserved in eukaryotes. Although protein acts as an anti-silencing factor, there is no previous study identifies its contribution in gene regulation under unfavorable conditions. This study was analyzed several molecular patterns of the respective gene including protein-protein interactions, Nuclear Localization Signals (NLS), Cis regulatory elements (CREs) and intron-mediated enhancement (IMEter) using recent bioinformatic data bases. Results showed protein-protein interactions between the respective gene product and other proteins are involved against abiotic stresses, the protein of this gene is localized in nucleus. Results were also observed several CREs of non-coding regions representing their roles as stresses-responsive factors, according to IMEter analysis, this response is expected to valuably present in Intron 1, suggesting experimental studies on mutant lines that contain insertions in their non-coding regions specifically intron 1of the underlying gene.

وشه‌ بنچینه‌ییه‌كان

1. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences. 2009;106(23):9362-7.
2. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012:1222794.
3. Hill RE, Lettice LA. Alterations to the remote control of Shh gene expression cause congenital abnormalities. Philosophical Transactions of the Royal Society B: Biological Sciences. 2013;368(1620):20120357.
4. Naville M, Ishibashi M, Ferg M, Bengani H, Rinkwitz S, Krecsmarik M, et al. Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome. Nature communications. 2015;6:6904.
5. Köhler S, Vasilevsky N, Engelstad M, Foster E, McMurry J, Aymé S, et al. The human phenotype ontology in 2017. 2017.
6. Wright CF, Fitzgerald TW, Jones WD, Clayton S, McRae JF, Van Kogelenberg M, et al. Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data. The Lancet. 2015;385(9975):1305-14.
7. McRae JF, Clayton S, Fitzgerald TW, Kaplanis J, Prigmore E, Rajan D, et al. Prevalence and architecture of de novo mutations in developmental disorders. Nature. 2017;542(7642):433.
8. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536(7616):285.
9. Koren A, Handsaker RE, Kamitaki N, Karlić R, Ghosh S, Polak P, et al. Genetic variation in human DNA replication timing. Cell. 2014;159(5):1015-26.
10. Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, Jonasdottir A, et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature. 2010;467(7319):1099.
11. Gao T, He B, Liu S, Zhu H, Tan K, Qian J. EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. Bioinformatics. 2016;32(23):3543-51.
12. Shooshtari P, Huang H, Cotsapas C. Integrative genetic and epigenetic analysis uncovers regulatory mechanisms of autoimmune disease. The American Journal of Human Genetics. 2017;101(1):75-86.
13. Zhang C-J, Hou X-M, Tan L-M, Shao C-R, Huang H-W, Li Y-Q, et al. The Arabidopsis acetylated histone-binding protein BRAT1 forms a complex with BRP1 and prevents transcriptional silencing. Nature communications. 2016;7:11715.
14. Rose AB, Elfersi T, Parra G, Korf I. Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression. The Plant Cell. 2008;20(3):543-51.
15. Bao W, He F, Gao J, Meng F, Zou H, Luo B. Alpha-1-antitrypsin: a novel predictor for long-term recovery of chronic disorder of consciousness. Expert review of molecular diagnostics. 2018;18(3):307-13.
16. Kaundal R, Saini R, Zhao PX. Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis thaliana. Plant physiology. 2010:pp. 110.156851.
17. Higo K, Ugawa Y, Iwamoto M, Korenaga T. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic acids research. 1999;27(1):297-300.
18. Grzybkowska D, Morończyk J, Wójcikowska B, Gaj MD. Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis. Plant Growth Regulation. 2018;85(2):243-56.
19. Lu X, Zhang X, Duan H, Lian C, Liu C, Yin W, et al. Three stress‐responsive NAC transcription factors from Populus euphratica differentially regulate salt and drought tolerance in transgenic plants. Physiologia plantarum. 2018;162(1):73-97.
20. Efroni I, Han S-K, Kim HJ, Wu M-F, Steiner E, Birnbaum KD, et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Developmental cell. 2013;24(4):438-45.
21. Han S-K, Sang Y, Rodrigues A, Wu M-F, Rodriguez PL, Wagner D. The SWI2/SNF2 chromatin remodeling ATPase BRAHMA represses abscisic acid responses in the absence of the stress stimulus in Arabidopsis. The Plant Cell. 2012:tpc. 112.105114.
22. Wu M-F, Sang Y, Bezhani S, Yamaguchi N, Han S-K, Li Z, et al. SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors. Proceedings of the National Academy of Sciences. 2012;109(9):3576-81.
23. Wang J, Tadeo X, Hou H, Tu PG, Thompson J, Yates JR, et al. Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries. Genes & development. 2013;27(17):1886-902.
24. Cui H, Qiu J, Zhou Y, Bhandari DD, Zhao C, Bautor J, et al. Antagonism of transcription factor MYC2 by EDS1/PAD4 complexes bolsters salicylic acid defense in Arabidopsis effector-triggered immunity. Molecular Plant. 2018.
25. Gaponenko A, Shulga O, Mishutkina Y, Tsarkova E, Timoshenko A, Spechenkova N. Perspectives of Use of Transcription Factors for Improving Resistance of Wheat Productive Varieties to Abiotic Stresses by Transgenic Technologies. Russian Journal of Genetics. 2018;54(1):27-35.
26. Reis RR, da Cunha BADB, Martins PK, Martins MTB, Alekcevetch JC, Chalfun-Júnior A, et al. Induced over-expression of AtDREB2A CA improves drought tolerance in sugarcane. Plant science. 2014;221:59-68.
27. Cecchini NM, Monteoliva MI, Alvarez ME. Proline dehydrogenase contributes to pathogen defense in Arabidopsis. Plant Physiology. 2011;155(4):1947-59.
28. Borges AA, Jiménez-Arias D, Expósito-Rodríguez M, Sandalio LM, Pérez JA. Priming crops against biotic and abiotic stresses: MSB as a tool for studying mechanisms. Frontiers in plant science. 2014;5:642.
29. Yamaguchi-Shinozaki K, Shinozaki K. The plant hormone abscisic acid mediates the drought-induced expression but not the seed-specific expression of rd22, a gene responsive to dehydration stress in Arabidopsis thaliana. Molecular and General Genetics MGG. 1993;238(1-2):17-25.
30. Grandperret V, NICOLAS‐FRANCÈS V, Wendehenne D, Bourque S. Type‐II histone deacetylases: elusive plant nuclear signal transducers. Plant, cell & environment. 2014;37(6):1259-69.
31. Chen ZJ, Tian L. Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression. 2007;1769(5-6):295-307.
32. Bakhoum SF, Ngo B, Laughney AM, Cavallo J-A, Murphy CJ, Ly P, et al. Chromosomal instability drives metastasis through a cytosolic DNA response. Nature. 2018.
33. Etchegaray J-P, Chavez L, Huang Y, Ross KN, Choi J, Martinez-Pastor B, et al. The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine. Nature cell biology. 2015;17(5):545.
34. Gallegos JE, Rose AB. Intron-mediated enhancement is not limited to introns. bioRxiv. 2018:269852.
35. Wittkopp PJ, Kalay G. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nature Reviews Genetics. 2012;13(1):59.
36. Zhao B, Cao JF, Hu GJ, Chen ZW, Wang LY, Shangguan XX, et al. Core cis‐element variation confers subgenome‐biased expression of a transcription factor that functions in cotton fiber elongation. New Phytologist. 2018;218(3):1061-75.
37. Wang H, Caruso LV, Downie AB, Perry SE. The embryo MADS domain protein AGAMOUS-Like 15 directly regulates expression of a gene encoding an enzyme involved in gibberellin metabolism. The Plant Cell. 2004;16(5):1206-19.
38. Short PJ, McRae JF, Gallone G, Sifrim A, Won H, Geschwind DH, et al. De novo mutations in regulatory elements in neurodevelopmental disorders. Nature. 2018;555(7698):611.
39. Zhou D-X. Regulatory mechanism of plant gene transcription by GT-elements and GT-factors. Trends in plant science. 1999;4(6):210-4.
40. Park HC, Kim ML, Kang YH, Jeon JM, Yoo JH, Kim MC, et al. Pathogen-and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor. Plant physiology. 2004;135(4):2150-61.
41. Li T, Sun J, Li C, Lu Z, Xia J. Cloning and expression analysis of the FvNCED3 gene and its promoter from ash (Fraxinus velutina). Journal of Forestry Research.1-12.
42. Wenkel S, Turck F, Singer K, Gissot L, Le Gourrierec J, Samach A, et al. CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. The Plant Cell. 2006;18(11):2971-84.
43. Srivastava R, Rai KM, Srivastava R. Plant Biosynthetic Engineering Through Transcription Regulation: An Insight into Molecular Mechanisms During Environmental Stress. Biosynthetic Technology and Environmental Challenges: Springer; 2018. p. 51-72.
44. Yadav V, Mallappa C, Gangappa SN, Bhatia S, Chattopadhyay S. A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light–mediated photomorphogenic growth. The Plant Cell. 2005;17(7):1953-66.
45. Dunn MA, White AJ, Vural S, Hughes MA. Identification of promoter elements in a low-temperature-responsive gene (blt4. 9) from barley (Hordeum vulgare L.). Plant molecular biology. 1998;38(4):551-64.
46. Zhang C, Jia H, Wu W, Wang X, Fang J, Wang C. Functional conservation analysis and expression modes of grape anthocyanin synthesis genes responsive to low temperature stress. Gene. 2015;574(1):168-77.
47. Simpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K, Yamaguchi‐Shinozaki K. Two different novel cis‐acting elements of erd1, a clpA homologous Arabidopsis gene function in induction by dehydration stress and dark‐induced senescence. The Plant Journal. 2003;33(2):259-70.
48. Solano R, Nieto C, Avila J, Canas L, Diaz I, Paz‐Ares J. Dual DNA binding specificity of a petal epidermis‐specific MYB transcription factor (MYB. Ph3) from Petunia hybrida. The EMBO Journal. 1995;14(8):1773-84.
49. Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. The Plant Cell. 2003;15(1):63-78.
50. Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki K. An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. The Plant Cell. 1993;5(11):1529-39.
51. Busk PK, Pagès M. Regulation of abscisic acid-induced transcription. Plant molecular biology. 1998;37(3):425-35.
52. Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, et al. OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought‐, high‐salt‐and cold‐responsive gene expression. The Plant Journal. 2003;33(4):751-63.
53. Tran L-SP, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K, et al. Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. The Plant Cell. 2004;16(9):2481-98.