Methylation Modelling and Epigenetic Analysis of Sunflower (Helianthus annuus L.) Seedlings Exposed to Cadmium Heavy Metal Stress

Ekrem Bölükbaşı

doi:10.18016/ksutarimdoga.vi.883985

Research Article

Methylation Modelling and Epigenetic Analysis of Sunflower (Helianthus annuus L.) Seedlings Exposed to Cadmium Heavy Metal Stress

Year 2022, Volume: 25 Issue: 3, 467 - 475, 30.06.2022

Ekrem Bölükbaşı

https://doi.org/10.18016/ksutarimdoga.vi.883985

Cited By: 4

Abstract

Environmental pollution, especially heavy metal pollution, is an important environmental problem all over the world. Heavy metals that accumulate in high concentrations in soil and water ecosystems are known to damage most functional biomolecules such as DNA, RNA and protein in living organisms and cause genotoxicity. For example, cadmium heavy metal is one of the heavy metals that negatively affect plant growth and development. The aim of this study is to determine the methylcytosine level in the sunflower plant genome and the changes in the methylation pattern under cadmium stress. The purpose of this study is to determine the methylcytosine level in the sunflower plant genome and the changes in the methylation pattern under cadmium stress. Sunflower seeds were grown with different concentrations of cadmium heavy metal solution (20 to 1280 ppm) for 3 weeks. According to the data obtained in the study, as the cadmium concentration increased, the growth and development of sunflower seedlings decreased. After detecting DNA band variations by RAPD analysis, methylcytosine levels in the sample genome were determined by CRED-RA technique. As a result of RAPD analysis, the highest GTS rate was 87.83% at 20 ppm cadmium concentration and the lowest rate was 81.75% at 320 ppm. Four different methylation patterns (Type I-IV) were determined according to the CRED-RA analysis. As a result of the study, significant changes in the DNA methylation pattern were observed by CRED-RA analysis in the sunflower genome exposed to cadmium heavy metal stress.

Keywords

Methylation, CRED-RA, Heavy Metal, Cadmium, Sunflower

Supporting Institution

Amasya University Scientific Research Unit

Project Number

FMB-BAP 20-0480

Thanks

The author gratefully acknowledge the financial support of this work by Amasya University Scientific Research Unit (FMB-BAP 20-0480). And also, the author acknowledges to Prof. Dr. Emine Sumer ARAS at Ankara University, Science Faculty, and Department of Biology for her valuable support.

References

Atienzar FA, Venier P, Jha AN, Depledge MH, 2002. Evaluation of the random amplified polymorphic DNA (RAPD) assay for the detection of DNA damage and mutations. Mutation Research, 521: 151-163.
Blackmana BK, Scascitellic M, Kanec NC, Lutona HH, Rasmussena DA, Byed RA, Lentze DL, Rieseberga LH, 2011. Sunflower domestication alleles support single domestication center in eastern North America. PNAS, 108(34): 14360-14365.
Bolukbasi E, Aras ES, 2016. Determination of DNA Methylation Levels with CRED-RA Technique in the Genome of Sunflower Seedlings (Helianthus annuus L.) Subjected to Zinc Stress. International Journal of Environment, Agriculture and Biotechnology, 1(3): 438-444.
Boyko A, Kovalchuk I, 2008. Epigenetic control of plant stress response. Environ Mol. Mutagen, 49(1): 61-72.
Cai Q, Guy CL, Moore GA, 1996. Detection of cytosine methylation and mapping of a gene influencing cytosine methylation in the genome of Citrus. Genome, 39: 235-242.
Chinnusamy V, Zhu JK, 2009. Epigenetic regulation of stress responses in plants. Current opinion in plant biology, 12: 133-139.
Conte C, Mutti I, Puglisi P, Ferrarini A, Regina GRG, Maestri E, Marmiroli N, 1998. DNA fingerprinting analysis by a PCR based method for monitoring the genotoxic effects of heavy metals pollution. Chemosphere, 37: 2739-2749.
Davis PH, 1985. Flora of Turkey and the East Aegean Island. V.5, Endinburg University Press, Edinburg. Grigg G, Clark S, 1994. Genes and genomes: Sequencing 5-methylcytosine residues in genomic DNA,. Bioessays, 16: 431-436.
Gupta M, Sarin NB, 2009. Heavy metal induced DNA changes in DNA analysis and identification of sequence characterized amplified region marker. J. Environ. Sci, 21: 686-690.
Hart JJ, Welch RM, Norvell WA, Sullivan LA, Kochian LV, 1998. Characterization of Cd binding, uptake and translocation in intact seedlings of bread and durum wheat cultivars. Plant Physiol, 116: 1413-1420.
Hu H, 2005. Heavy metal poisoning. In: Kasper DL et al (eds) Harrison’s principles of internal medicine, 16th edn. McGraw-Hill, New York, 2577-2580.
Kachenko A, Singh B, 2004. Heavy metals contamination of home grown vegetables near smelters in NSW. SuperSoil: 3rd Australian New Zealand Soils Conference, 5-9 December. University of Sydney, Australia.
Karan R, DeLeon T, Biradar H, Subudhi PK, 2012. Salt stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PloS one, 7: e40203.
Khurana N, Chatterjee C, 2001. Influence of variable zinc on yield, oil content, and physiology of sunflower. Commun Soil Sci. Plant Anal, 32: 3023-3030.
Kosnett MJ, 2007. Heavy metal intoxication and chelators. In: katzung BG(ed) Basic and clinical pharmacology. 10th edn. McGraw-Hill, New York, 945-957.
Kumar N, Soni H, Kumar RN, Bhatt I, 2009. Hyperaccumulation and mobility of heavy metals in vegetable crops in India. The Journal of Agricultural and Environment, 10: 29-38.
Lefort F, Lally M, Thompson D, Douglas G, 1998. Morphological traits, microsatellite fingerprinting and genetic relatedness of a stand of elite oaks (Q. robur L.) at Tullynally, Ireland. Silvae Genetica, 47: 257-261.
Leljak-Levanic D, Bauer N, Mihaljevic S, Jelaska S, 2004. Changes in DNA methylation during somatic embryogenesis in Cucurbita pepo L. Plant cell reports, 23: 120-127.
Lentz DL, Pohl MD, Alvarado JL, Tarighat S, Bye R, 2008. Sunflower (Helianthus annuus L.) as a pre-Columbian domesticate in Mexico. PNAS, 105: 6232-6237.
Liu W, Li P, Qi X, Zhou Q, Zheng L, Sun T, Yang Y, 2005. DNA changes in barley Hordeum vulgare seedlings induced by cadmium pollution using RAPD analysis. Chemosphere, 61: 158-167.
Liu W, Yang YS, Li PJ, Zhou QX, Xie LJ, Han YP, 2009. Risk assessment of cadmium contaminated soil on plant DNA damage using RAPD and physiological indices. Journal of Hazardous Material, 161: 878-883.
Liu W, Yang YS, Zhou QX, Xie LJ, Li PJ, Sun TH, 2007. Impact assessment of cadmium contamination on rice (Oryza sativa L.) seedlings at molecular and population levels using multiple biomarkers. Chemosphere, 67: 1155-1163.
Martin C, Zhang Y, 2007. Mechanisms of epigenetic inheritance. Current Opinion in Cell Biology, (19)3: 266–272.
Meyerowitz EM, Somerville CR, 1994. Arabidopsis, Cold Spring Harbor Press, New York, 1300 pp.
Mirouze M, Paszkowski J, 2011. Epigenetic contribution to stress adaptation in plants. Current opinion in plant biology, 14: 267-274.
Pan Y, Wang W, Zhao X, Zhu L, Fu B, Li Z, 2011. DNA methylation alterations of rice in response to cold stress. Plant Omics J, 4: 364-369.
Pontvianne F, Blevins T, Pikaard CS, 2010. Arabidopsis Histone Lysine Methyltransferases. Adv. Bot. Res, 53(1): 1-22.
Rein T, DePamphilis ML, Zorbas H, 1998. Identifying 5-methylcytosine and related modifications in DNA genomes. Nucleic acids research, 26: 2255-2264.
Savva D, 2000. The use of arbitrarily primed PCR (AP-PCR) fingerprinting to detect exposure to genotoxic chemicals. Ecotoxicology, 9: 341-353.
Schutzendubel A, Schawnz P, Teichman T, Gross K, 2001. Cd-induced changes in antioxidative systems, hydrogen peroxide content and differentiation in Scots Pine roots. Plant Physiol, 127: 887-898.
Suzuki MM, Bird A, 2008. DNA methylation landscapes: provocative insights from epigenomics. Nature Reviews Genetics, 9: 465-476.
Tani E, Polidoros A, Nianiou-Obeidat I, Tsaftaris A, 2005. DNA methylation patterns are differently affected by planting density in maize inbreds and their hybrids. Maydica, 50: 19-24.
Theodorakis CW, Bickham JW, Lamb T, 2001. Integration of genotoxicity and population genetic analyses in kangaroo rats (Dipodomys merriami) exposed to radionuclide contamination at the Nevada test site, USA. Environmental Toxicology and Chemistry, 20: 317-326.
Toppi L, Gabrielli R, 1999. Response to Cd in higher plants. Environ. Exp. Botany, 41: 105-130.
Wang WS, Pan YJ, Zhao XQ, Dwivedi D, Zhu LH, Ali J, Fu BY, Li ZK, 2011. Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). Journal of experimental botany, 62: 1951-1960.
Yarsan E, Bilgili A, Turel I, 2000. Heavy metal levels in mussels (Unio stevenianus Krynicki) obtained from Van Lake. Turk J. Vet. Animal Science, 24: 93-96.
Yıldız M, Terzi H, Urusak B, 2011. Bitkilerde krom toksisitesi ve hücresel cevaplar. Erciyes Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 27(2): 163-176.

Kadmiyum Ağır Metal Stresine Maruz Kalmış Ayçiçeği (Helianthus annuus L.) Fidelerinin Metilasyon Modellemesi ve Epigenetik Analizi

Year 2022, Volume: 25 Issue: 3, 467 - 475, 30.06.2022

Ekrem Bölükbaşı

https://doi.org/10.18016/ksutarimdoga.vi.883985

Cited By: 4

Abstract

Çevre kirliliği, özellikle ağır metal kirliliği, tüm dünyada önemli bir çevre sorunudur. Toprak ve su ekosistemlerinde yüksek konsantrasyonlarda biriken ağır metallerin canlı organizmalardaki DNA, RNA ve protein gibi çoğu fonksiyonel biyomoleküle zarar verdiği ve genotoksisiteye neden olduğu bilinmektedir. Örneğin kadmiyum ağır metal, bitki büyümesini ve gelişmesini olumsuz etkileyen ağır metallerden biridir. Bu çalışmanın amacı, ayçiçeği bitki genomundaki metilsitozin düzeyini ve kadmiyum stresi altında metilasyon modelindeki değişiklikleri belirlemektir. Bu çalışmanın amacı, ayçiçeği bitki genomundaki metilsitozin düzeyini ve kadmiyum stresi altında metilasyon modelindeki değişiklikleri belirlemektir. Ayçiçeği tohumları, 3 hafta boyunca farklı konsantrasyonlarda kadmiyum ağır metal çözeltisi (20 ile 1280 ppm) ile büyütüldü. Çalışmada elde edilen verilere göre kadmiyum konsantrasyonu arttıkça ayçiçeği fidelerinin büyüme ve gelişmesi azalmıştır. RAPD analizi ile DNA bandı varyasyonları tespit edildikten sonra, numune genomundaki metilsitozin seviyeleri CRED-RA tekniği ile belirlendi. RAPD analizi sonucunda, en yüksek GTS oranı 20 ppm kadmiyum konsantrasyonunda % 87.83 ve en düşük oran 320 ppm'de % 81.75 olmuştur. CRED-RA analizine göre dört farklı metilasyon modeli (Tip I-IV) belirlendi. Çalışma sonucunda kadmiyum ağır metal stresine maruz kalan ayçiçeği genomunda CRED-RA analizi ile DNA metilasyon modelinde önemli değişiklikler gözlemlendi.

Keywords

Metilasyon, CRED-RA, Ağır Metal, Kadmiyum, Ayçiçeği

Project Number

FMB-BAP 20-0480

References

Atienzar FA, Venier P, Jha AN, Depledge MH, 2002. Evaluation of the random amplified polymorphic DNA (RAPD) assay for the detection of DNA damage and mutations. Mutation Research, 521: 151-163.
Blackmana BK, Scascitellic M, Kanec NC, Lutona HH, Rasmussena DA, Byed RA, Lentze DL, Rieseberga LH, 2011. Sunflower domestication alleles support single domestication center in eastern North America. PNAS, 108(34): 14360-14365.
Bolukbasi E, Aras ES, 2016. Determination of DNA Methylation Levels with CRED-RA Technique in the Genome of Sunflower Seedlings (Helianthus annuus L.) Subjected to Zinc Stress. International Journal of Environment, Agriculture and Biotechnology, 1(3): 438-444.
Boyko A, Kovalchuk I, 2008. Epigenetic control of plant stress response. Environ Mol. Mutagen, 49(1): 61-72.
Cai Q, Guy CL, Moore GA, 1996. Detection of cytosine methylation and mapping of a gene influencing cytosine methylation in the genome of Citrus. Genome, 39: 235-242.
Chinnusamy V, Zhu JK, 2009. Epigenetic regulation of stress responses in plants. Current opinion in plant biology, 12: 133-139.
Conte C, Mutti I, Puglisi P, Ferrarini A, Regina GRG, Maestri E, Marmiroli N, 1998. DNA fingerprinting analysis by a PCR based method for monitoring the genotoxic effects of heavy metals pollution. Chemosphere, 37: 2739-2749.
Davis PH, 1985. Flora of Turkey and the East Aegean Island. V.5, Endinburg University Press, Edinburg. Grigg G, Clark S, 1994. Genes and genomes: Sequencing 5-methylcytosine residues in genomic DNA,. Bioessays, 16: 431-436.
Gupta M, Sarin NB, 2009. Heavy metal induced DNA changes in DNA analysis and identification of sequence characterized amplified region marker. J. Environ. Sci, 21: 686-690.
Hart JJ, Welch RM, Norvell WA, Sullivan LA, Kochian LV, 1998. Characterization of Cd binding, uptake and translocation in intact seedlings of bread and durum wheat cultivars. Plant Physiol, 116: 1413-1420.
Hu H, 2005. Heavy metal poisoning. In: Kasper DL et al (eds) Harrison’s principles of internal medicine, 16th edn. McGraw-Hill, New York, 2577-2580.
Kachenko A, Singh B, 2004. Heavy metals contamination of home grown vegetables near smelters in NSW. SuperSoil: 3rd Australian New Zealand Soils Conference, 5-9 December. University of Sydney, Australia.
Karan R, DeLeon T, Biradar H, Subudhi PK, 2012. Salt stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PloS one, 7: e40203.
Khurana N, Chatterjee C, 2001. Influence of variable zinc on yield, oil content, and physiology of sunflower. Commun Soil Sci. Plant Anal, 32: 3023-3030.
Kosnett MJ, 2007. Heavy metal intoxication and chelators. In: katzung BG(ed) Basic and clinical pharmacology. 10th edn. McGraw-Hill, New York, 945-957.
Kumar N, Soni H, Kumar RN, Bhatt I, 2009. Hyperaccumulation and mobility of heavy metals in vegetable crops in India. The Journal of Agricultural and Environment, 10: 29-38.
Lefort F, Lally M, Thompson D, Douglas G, 1998. Morphological traits, microsatellite fingerprinting and genetic relatedness of a stand of elite oaks (Q. robur L.) at Tullynally, Ireland. Silvae Genetica, 47: 257-261.
Leljak-Levanic D, Bauer N, Mihaljevic S, Jelaska S, 2004. Changes in DNA methylation during somatic embryogenesis in Cucurbita pepo L. Plant cell reports, 23: 120-127.
Lentz DL, Pohl MD, Alvarado JL, Tarighat S, Bye R, 2008. Sunflower (Helianthus annuus L.) as a pre-Columbian domesticate in Mexico. PNAS, 105: 6232-6237.
Liu W, Li P, Qi X, Zhou Q, Zheng L, Sun T, Yang Y, 2005. DNA changes in barley Hordeum vulgare seedlings induced by cadmium pollution using RAPD analysis. Chemosphere, 61: 158-167.
Liu W, Yang YS, Li PJ, Zhou QX, Xie LJ, Han YP, 2009. Risk assessment of cadmium contaminated soil on plant DNA damage using RAPD and physiological indices. Journal of Hazardous Material, 161: 878-883.
Liu W, Yang YS, Zhou QX, Xie LJ, Li PJ, Sun TH, 2007. Impact assessment of cadmium contamination on rice (Oryza sativa L.) seedlings at molecular and population levels using multiple biomarkers. Chemosphere, 67: 1155-1163.
Martin C, Zhang Y, 2007. Mechanisms of epigenetic inheritance. Current Opinion in Cell Biology, (19)3: 266–272.
Meyerowitz EM, Somerville CR, 1994. Arabidopsis, Cold Spring Harbor Press, New York, 1300 pp.
Mirouze M, Paszkowski J, 2011. Epigenetic contribution to stress adaptation in plants. Current opinion in plant biology, 14: 267-274.
Pan Y, Wang W, Zhao X, Zhu L, Fu B, Li Z, 2011. DNA methylation alterations of rice in response to cold stress. Plant Omics J, 4: 364-369.
Pontvianne F, Blevins T, Pikaard CS, 2010. Arabidopsis Histone Lysine Methyltransferases. Adv. Bot. Res, 53(1): 1-22.
Rein T, DePamphilis ML, Zorbas H, 1998. Identifying 5-methylcytosine and related modifications in DNA genomes. Nucleic acids research, 26: 2255-2264.
Savva D, 2000. The use of arbitrarily primed PCR (AP-PCR) fingerprinting to detect exposure to genotoxic chemicals. Ecotoxicology, 9: 341-353.
Schutzendubel A, Schawnz P, Teichman T, Gross K, 2001. Cd-induced changes in antioxidative systems, hydrogen peroxide content and differentiation in Scots Pine roots. Plant Physiol, 127: 887-898.
Suzuki MM, Bird A, 2008. DNA methylation landscapes: provocative insights from epigenomics. Nature Reviews Genetics, 9: 465-476.
Tani E, Polidoros A, Nianiou-Obeidat I, Tsaftaris A, 2005. DNA methylation patterns are differently affected by planting density in maize inbreds and their hybrids. Maydica, 50: 19-24.
Theodorakis CW, Bickham JW, Lamb T, 2001. Integration of genotoxicity and population genetic analyses in kangaroo rats (Dipodomys merriami) exposed to radionuclide contamination at the Nevada test site, USA. Environmental Toxicology and Chemistry, 20: 317-326.
Toppi L, Gabrielli R, 1999. Response to Cd in higher plants. Environ. Exp. Botany, 41: 105-130.
Wang WS, Pan YJ, Zhao XQ, Dwivedi D, Zhu LH, Ali J, Fu BY, Li ZK, 2011. Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). Journal of experimental botany, 62: 1951-1960.
Yarsan E, Bilgili A, Turel I, 2000. Heavy metal levels in mussels (Unio stevenianus Krynicki) obtained from Van Lake. Turk J. Vet. Animal Science, 24: 93-96.
Yıldız M, Terzi H, Urusak B, 2011. Bitkilerde krom toksisitesi ve hücresel cevaplar. Erciyes Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 27(2): 163-176.

There are 37 citations in total.

Details

Primary Language	English
Subjects	Structural Biology
Journal Section	RESEARCH ARTICLE
Authors	Ekrem Bölükbaşı 0000-0003-3828-1226
Project Number	FMB-BAP 20-0480
Publication Date	June 30, 2022
Submission Date	February 20, 2021
Acceptance Date	September 7, 2021
Published in Issue	Year 2022Volume: 25 Issue: 3

Cite

APA	Bölükbaşı, E. (2022). Methylation Modelling and Epigenetic Analysis of Sunflower (Helianthus annuus L.) Seedlings Exposed to Cadmium Heavy Metal Stress. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 25(3), 467-475. https://doi.org/10.18016/ksutarimdoga.vi.883985