Research Overview

A number of epigenetic regulatory layers are superimposed on the genome. In plants, small RNA regulators play a major role in the establishment and maintenance of epigenetic marks. We are interested in understanding the mechanism of small RNA biogenesis, their functions and their role in establishment of epigenetics using a number of model systems.

Link to our lab webpage

Dr.  P. V.  Shivaprasad

Associate Professor, Associate Dean of Faculty

National Centre for Biological Sciences (NCBS)

Tata Institute of Fundamental Research (TIFR), Bangalore, India

E-mail: shivaprasad at ncbs dot res dot in


Office: +91-80-2366-6511



M.Sc. Applied Botany, Mangalore University, India.

Ph.D. Biotechnology, Madurai Kamaraj University, India. Thesis advisor: Prof. K. Veluthambi.

Postdoctoral Research (EMBO and SNF), Viral suppressors of gene silencing, Prof. Thomas Hohn's lab, University of Basel, Switzerland.

Postdoctoral Research (BBSRC grant), Gene silencing in tomato, Prof. Sir. David Baulcombe's lab, University of Cambridge, United Kingdom.


Recent Publications
Recent Publications (last 5 years)

1.   Kannan Pachamuthu, Vivek Hari Sundar, Anushree N.,Rahul R Singh, Soumita Das, Harshith CY, Avik Pal, and Padubidri V Shivaprasad. (2022). Nitrate-dependent regulation of miR444-OsMADS27 signaling cascade controls root development in rice. J. Exp. Bot. In Press.

2.  Vivek Hari Sundar, and P.V. Shivaprasad (2022). Investigation of transposon DNA methylation and copy number in plants using Southern hybridization. Bio-Protoc. In Press.

3.  Swetha Chenna, Anushree N, Awadhesh Pandit, Varsha Tirumalai, and P. V. Shivaprasad (2022). Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs. BMC Genomics 23:53.

4.  Vikram Jha, Anushree N., Debjani Basu, Kannan Pachamuthu, Swetha Chenna, Ashwin Nair, P.V. Shivaprasad. (2021). Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions. New Phytol. 232:1674-1691.

5.   Lakshmanan V, T N Sujith, Bansal D, Padubidri V. Shivaprasad, Palakodeti D, Krishna S. (2021). Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs). RNA. rna.077701.120.

6.  Kannan Pachamuthu, Chenna Swetha, Debjani Basu, Soumita Das, Indira Singh, Vivek Hari Sunder, T.N. Sujith, and P.V. Shivaprasad (2021). Rice-specific Argonaute 17 controls reproductive growth and yield-associated phenotypes. Plant Mol Biol.  05:99-114

7.     Vinoth Kumar and P.V. Shivaprasad (2020).  Plant-insect-virus tritrophic interaction: Insights into the functions of geminiviral virion-strand genes. Proceedings of Royal Soc. B. 287:20201846.

8.  Ashwin Nair, Kiran Chatterjee, Vikram Jha, Ranabir Das, P.V. Shivaprasad (2020). Stability of Begomoviral pathogenicity determinant βC1 is modulated by mutually antagonistic SUMOylation and SIM interactions. BMC Biology. 18:110.

9.    Walavalkar K, Saravanan B, Singh AK, Jayani RS, Nair A, Farooq U, Islam Z, Soota D, Mann R, Shivaprasad PV, Freedman ML, Sabarinathan R, Haiman CA, Notani D. (2020). A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer. Nat Commun.  11:3598.

10.  Varsha Tirumalai, Melvin Prasad, P.V. Shivaprasad (2020). RNA blot analysis to quantify plant miRNAs. J. Vis Exp. 161.

11.  Anushree N, Ashwin Nair, Vivek Hari Sundar, Varsha Tirumalai, and P. V. Shivaprasad. (2020). A conserved sequence signature is essential for robust plant miRNA biogenesis. Nucleic Acids Res. 48:3103-3118.

12. Prathibha Sanjenbam, Radhika Budhidati, Radhika Venkatesan, P.V. Shivaprasad, Deepa Agashe (2020). Phenotypic Diversity Of Methylobacterium Associated With Rice Landraces In Northeast India. PLOS One. 15(2):e0228550

13. Soumita Das, Chenna Swetha, K. Pachamuthu, Ashwin Nair, and P. V. Shivaprasad (2020).  Oryza sativa Argonaute 18 is a regulator of male sterility and developmental phase transition. Plant Reprod 33:59-73.

14. Varsha Tirumalai, Chenna Swetha, Ashwin Nair, and P. V. Shivaprasad (2019). A cluster of miRNAs regulate MYB repressors to promote anthocyanin and flavonol accumulation in grapes.  J. Exp Bot. 70:4775-4792.

15. Daniel  GR  Yim, S. Krishna, V.  Lakshmanan, J.L. V. Tirumalai, Koh, J. E. Park, J.  E.  Park, J.K. Cheong, J.L. Low, M.J. Lim, J.M. Nah, I. Tan, Huili Guo, S.K. Sze, A. Gulyani, P.V. Shivaprasad, S. Raghavan, D. Palakodeti, R. Dasgupta (2019). Dynamic  expression  of  tRNA-derived  small  RNAs  define cellular  states. EMBO Rep. 20:e47789

16.  Chenna Swetha and P.V. Shivaprasad (2019). Extraction and purification of laccases from rice. Bio-Protocol. 10.21769/ 3208

17.  Padubidri V. Shivaprasad (2019). New clues into the mechanisms of rice domestication. J. Biosci. 44(2). 28.

18.  Chenna Swetha, Debjani Basu, Kannan Pachamuthu, Varsha Tirumalai, Ashwin Nair, Melvin Prasad, and P. V. Shivaprasad (2018). Major domestication-related phenotypes in indica rice are associated with loss of miRNA-mediated cascade silencing of laccases. Plant Cell 30:2649–2662.

19. P.V. Shivaprasad (2018). New insights into the mechanisms of crop domestication. Cambridge Scholars Publishers, UK.

20. Soumita Das, Akshay Hegde, P.V. Shivaprasad (2018). Molecular characterization of Synedrella yellow vein virus, a new Begomovirus from South India. Arch Virol. 163:2551-2554

21. Anushree N and P.V. Shivaprasad (2018).  Regulation of plant miRNA biogenesis.  Proc Indian Natn Sci Acad.  84:439-453.

22. Prasad Melvin, K. Bankapalli, Patrick D’Silva, P. V. Shivaprasad (2017). Methylglyoxal detoxification by a DJ-1 family protein provides dual abiotic and biotic stress tolerance in transgenic plants. Plant Mol. Biol. 94:381-397.

23. Soumita Das, Rahul Singh, P.V. Shivaprasad (2017). Artificial induction and maintenance of epigenetic variations in plants. Plant Gene Silencing: Phenomena and Applications. CABI publishers, UK.


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