Plant Molecular Biology

, Volume 95, Issue 1–2, pp 63–88 | Cite as

Comparative analysis of Histone modifications and DNA methylation at OsBZ8 locus under salinity stress in IR64 and Nonabokra rice varieties

  • Amit Paul
  • Pratiti Dasgupta
  • Dipan Roy
  • Shubho Chaudhuri


Rice being an important cereal crop is highly sensitive to salinity stress causing growth retardation and loss in productivity. However, certain rice genotypes like Nonabokra and Pokkali show a high level of tolerance towards salinity stress compared to IR64 variety. This differential response of tolerant varieties towards salinity stress may be a cumulative effect of genetic and epigenetic factors. In this study, we have compared the salinity-induced changes in chromatin modifications at the OsBZ8 locus in salt-tolerant Nonabokra and salt-sensitive IR64 rice varieties. Expression analysis indicates that the OsBZ8 gene is highly induced in Nonabokra plants even in the absence of salt stress, whereas in IR64, the expression significantly increases only during salt stress. Sequence analysis and nucleosomal arrangement within the region −2000 to +1000 of OsBZ8 gene show no difference between the two rice varieties. However, there was a considerable difference in histone modifications and DNA methylation at the locus between these varieties. In Nonabokra, the upstream region was hyperacetylated at H3K9 and H3K27, and this acetylation did not change during salt stress. However, in IR64, histone acetylation was observed only during salt stress. Moreover, the upstream region of OsBZ8 gene has highly dynamic nucleosome arrangement in Nonabokra, compared to IR64. Furthermore, loss of DNA methylation was observed at OsBZ8 locus in Nonabokra control plants along with low H3K27me3 and high H3K4me3. Control IR64 plants show high DNA methylation and enriched H3K27me3. Collectively these results indicate a significant difference in chromatin modifications between the rice varieties that regulates differential expression of OsBZ8 gene during salt stress.


Salinity stress IR64 Nonabokra Histone modification DNA methylation Chop-PCR 



Basic leucine zipper8




Abscisic acid response element


Dehydration-responsive element


Histone acetyltransferase


Transcription start site


TATA-box binding protein



The authors sincerely thank Dr Ronita Nag Chaudhuri for critically reviewing the manuscript. The authors also thank Prof. A. N. Lahiri Majumder and Prof. Dibyendu Narayan Sengupta for their valuable scientific advice during this study. This work was supported by DBT, Government of India, Grant No. BT/AB/05/02/2007. The authors sincerely acknowledge the Bose Institute for the institutional fund support. Contents of this manuscript are solely the responsibility of the authors and do not necessarily represent the official views of the funding agencies.

Author contributions

SC designed the research. AP and SC designed and performed the experiments shown in Figs. 1, 2, 3, 4, 5, 6, 7, 8 and 11. AP, DR and SC standardised and performed the experiments shown in Figs. 2, 3, 4, 5, 11. AP, PD and SC performed the experiments shown in Figs. 9 and 10. SC, AP and PD analysed the data and SC wrote the manuscript. All the authors reviewed the results and approved the final version of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest with the contents of this article.

Supplementary material

11103_2017_636_MOESM1_ESM.pdf (1.8 mb)
Supplementary material 1 (PDF 1893 KB)


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Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Amit Paul
    • 1
  • Pratiti Dasgupta
    • 1
  • Dipan Roy
    • 1
  • Shubho Chaudhuri
    • 1
  1. 1.Division of Plant BiologyBose InstituteKolkataIndia

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