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 roles in establishment of epigenetics.
Link to our lab webpage
CONTACT
Dr.  P. V.  Shivaprasad
Associate Professor, Associate Dean of Research
National Centre for Biological Sciences (NCBS)
Tata Institute of Fundamental Research (TIFR), Bangalore, India
E-mail: shivaprasad at ncbs dot res dot in
Telephone:
Office: +91-80-2366-6511
 
Biography
M.Sc. Applied Botany, Mangalore University, India.
Ph.D. Biotechnology, Madurai Kamaraj University, India. Thesis advisor: Prof. K. Veluthambi.
Postdoctoral Research (EMBO), Prof. Thomas Hohn's lab, University of Basel, Switzerland.
Postdoctoral Research, Prof. Sir. David Baulcombe's lab, University of Cambridge, UK.
 
Recent Publications
Recent Publications (last 5 years)
 

  1. Vivek Hari-Sundar Gandhivel, Paula Sotelo-Parrilla, Steffi Raju, Shaileshanand Jha, Anjitha Gireesh, Chitthavalli Y. Harshith, Fabian Gut, Kutti R. Vinothkumar, Frédéric Berger, A. Arockia Jeyaprakash, P. V. Shivaprasad (2025). An Oryza-specific histone H4 variant predisposes H4 lysine 5 acetylation to modulate salt stress responses. Nature Plants 11, 790-807

  2. Prasad M, Shetty P, Pal Avik, Rigó G, Kant K, Zsigmond L, Nagy I, Shivaprasad PV, Szabados L. (2025). Transcriptional and epigenomic changes in response to PEG-triggered osmotic stress in rapeseed (Brassica napus L.). J Exp Bot. eraf123

  3. Avik Kumar Pal, Vivek Hari-Sundar Gandhivel, Amruta B. Nambiar and P.V. Shivaprasad (2024). Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler. Nat Communications 15, 7807

  4. Chitthavalli Y. Harshith, Avik Pal, Monoswi Chakraborty, Ashwin Nair, Steffi Raju, Padubidri V. Shivaprasad (2024). Wound-induced small-peptide-mediated signaling cascade, regulated by OsPSKR, dictates balance between growth and defense in rice. Cell reports. 43(7): 114515

  5. Vivek Hari Sundar, Chenna Swetha, Debjanu Basu, Kanna Pachamuthu, Steffi Raju, Tania Chakraborty, Rebecca A. Mosher and P. V. Shivaprasad (2023). Plant Polymerase IV sensitizes chromatin through histone modification to preclude spread of silencing into protein-coding domains. Genome Research. 023. 33: 715-728 

  6. Ashwin Nair, Harshith CY, Anushree N and P.V. Shivaprasad (2023). Begomoviral βC1 orchestrates organellar genomic instability to augment viral infection by hijacking host RecA. The Plant Journal. 114: 934-950 

  7. Vivek Hari Sundar G, Madhu A, Archana A, Shivaprasad PV. Plant histone variants at the nexus of chromatin readouts, stress and development (2023). Biochim Biophys Acta Gen Subj. 868(2)

  8. Ashwin Nair and P.V. Shivaprasad (2023). "Novel regulators in mitochondrial genome integrity". Journal of Biosciences. 48, 39

  9. Prasad Melvin, Priyanka Kataria, Sunayana Ningaraju, Kondalarao Bankapalli, Radhika Reddy, Chenna Swetha, Gautam Susarla, Radhika Venkatesan, Patrick D’Silva and P. V. Shivaprasad (2022). Methylglyoxalase DJ-1D from Arabidopsis is a robust macromolecule deglycase. New Phytol.  236: 1061-1074

  10. Tripathi Abhinandan, Singh Rajneesh, Verma Ashwani, Singh Akanksha, Mishra Parneeta, Dwivedi Varun, Narayan Shiv, Vivek Hari Sundar, Shirke Pramod, Shivaprasad P.V., Roy Sribash (2023). "Indian Himalayan natural Arabidopsis thaliana accessions with abolished miR158 levels exhibit robust miR173-initiated trans-acting cascade silencing", is accepted for publication in The Plant Journal.114:855-874

  11. Deepa Jaganathan, Raja Rajakani, Dadakhalandar Doddamani, Divya Saravanan, Shalini Pulipati, Vivek Hari Sundar G, Gothandapani Sellamuthu, Shilpha Jayabalan, Kumkum Kumari, Pavithra Parthasarathy, Punitha S., Sivaprakash Ramalingam, Padubidri V. Shivaprasad & Gayatri Venkataraman (2023). A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance. Scientific Reports. 13, 2195

  12. Pratibha Sanjenbam, P.V. Shivaprasad, and Deepa Agashe (2022). Impact of phyllosphere Methylobacterium on host rice landraces. Microbiology Spectrum. 10:4

  13. Varsha Tirumalai, Swetha Chenna, Anushree N., Vivek Hari Sundar, Sujith, T.N., P.V. Shivaprasad (2022). Cultivar-specific miRNA targeting in grapes. Planta. 256:17

  14. Vivek Hari Sundar, and P.V. Shivaprasad (2022). Investigation of transposon DNA methylation and copy number in plants using Southern hybridization. Bio-Protoc. 12:e4432

  15. 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. 73:3511-3530

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.  105:99-114

  21. 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

  22. 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.

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

  24. 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

  25. 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

  26. 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.

  27. 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

  28. 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

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

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

  31. 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.

  32. Soumita Das, Akshay Hegde, P.V. Shivaprasad (2018). Molecular characterization of Synedrella yellow vein virus, a new Begomovirus from South India. Arch Virol. 163:2551-255

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