Neeti Sanan-Mishra

Group leader, Plant RNAi Biology
International Centre for Genetic Engineering and Biotechnology
Aruna Asaf Ali Marg
110 067 New Delhi, India
E-mail: [email protected] 
Tel: +91-11-26741358, ext. 280


Jawaharlal Nehru University, New Delhi, India, PhD, 1997
Jawaharlal Nehru University, New Delhi, India, MSc, 1992
University of Delhi, India, BSc, 1990

Career History

Since 2016 – Group Leader, Plant RNAi Biology,International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
2006-2015, Staff Research Scientist, Plant Molecular Biology, ICGEB, New Delhi, India
2000-2005, Research Associate, ICGEB, New Delhi, India
1998-1999, Research Scientist, University of Delhi, South Campus, New Delhi, India

Scientific Activity

The Group is involved in understanding the RNAi mechanisms operative in plants in response to increasing abiotic stress factors (salt, high temperature, drought) and virus infection. The endeavour is to use this knowledge for crop improvement and protection through employing RNAi based technology. This assumes importance in the era of global climate change, as crop productivity is being affected by rise in temperature, accompanied by increase in soil salinity, decline in fresh water and high incidence of virus infection. Thus new approaches are required to address the emerging challenges for sustainable agriculture.

The microRNAs (miRs) play an important regulatory role in plant development and adaptation towards stresses. Thus, it is proposed to identify the miRs that may play a key role under multiple environmental stresses to deregulate the metabolic circuits related to grain yield. This will not only contribute to basic knowledge but also provide new insights into the mechanisms regulating grain yield. Thus research activities have been directed towards:

i) Genome-wide profiling of the miR expression with the aim to tap the natural variation existent in Indian rice cultivars. The knowledge gained was used to create a miRNA:mRNA database for rice called ARMOUR, that is available as a free web resource. This comprehensive database covers 689 known and 1664 predicted novel miRs along with their predicted target transcripts. The understanding of miR interactome in regulation of functional cellular machinery is supported by the information on the GO annotation and the associated biological pathways.

To decipher the detailed miR-dependent regulatory circuits operative in response to salt stress we performed comparative and integrated data-mining using natural rice varieties and transgenic lines with contrasting behaviors in response to salt-stress (JIB 2017, 14(1), 1613; Curr Genomics 2017, 19(1): 21-35). The information obtained from sRNAseq, RNAseq and degradome datasets was integrated to identify the salt-deregulated miRs, their targets and the associated metabolic pathways. The study was extended to map the expression profiles of miRs in the roots of salt tolerant Pokkali (PK) when grown in the presence and absence of salt. The salt-induced changes in expression profiles of miRs were much controlled in the PK roots as compared to larger variations seen in the PB roots. (Biomoecules 2020, 10:498). The results indicate that in PK, the miR expression levels are genetically programmed to enable the plants to withstand the salt-induced variations.

The study was extended to profile the drought and salt stress deregulated miRs in 11 elite sorghum genotypes (Gene Exp Patterns 2016, 20(2), 88-98) and 2 soybean genotypes (Plant Env Interactions 2020, 20(2), 88-98). This revealed the genetically determined dynamic modulation of miR164:NAC module which plays an important role in determining the adaptive response of plants to stress. The data has provided insights into potential role of conserved miRs in regulating the stress response in different crops.

ii) Functional analysis of specific miRs by generating over-expressing or knockout lines to follow their effect on plant stress responses. The translation of the knowledge genearted is in progress by raising miRNA over-expressing rice plants. This will be useful to gain fundamental knowledge of plant responses to the environment leading to a range of applications for improving plant adaptation and sustaining yields.

iii) To understand the functional role of miRs in managing plant responses to diverse stresses, the viral encoded suppressors of RNAi (VSR) can be employed as an excellent tool. The identification and evaluation of VSR has become an integral part of virus characterization. We have utilized the in-planta reversal of GFP silencing assay developed in the lab to identify VSRs from diverse viruses including in Southern rice black-streaked dwarf virus (SRBSDV), Rice tungro virus (RTBV ans RTSV), Chikungunya virus (CHIKV) etc. The same assay was used to define the parameters for assaying the strength of VSRs by measuring the relative levels of RNA silencing reversion and analyzing the time period for which they were able to sustain the reversion (AUPP 2020, 10:498). This study will be useful in under-standing the molecular mechanism of host-virus interactions to evolve effective antiviral strategies.

The host–virus interactions in plants are greatly influenced by the abiotic environment. To understand the involvement of RNA silencing in regulating the response of virus infected plants to abiotic stresses, functional VSR activity of non-plant virus encoded Flock house virus B2 protein (FHVB2) was utilized. FHVB2 is functionally similar to Cucumber mosaic virus 2b protein and can act as a RSS in plants. Tobacco plants over-expressing FHVB2 could tolerate high concentrations of salt and showed enhanced accumulation of proline (Phytoparasitica 2020). This preliminary evidence for cross talk between the abiotic and biotic stresses is being further validated to understanding the mechanistic pathways.

Teaching Activity

ICGEB PhD Course on “Molecular Biology of Plant Stress”
ICGEB PhD Course on “Research Methodology (Biosafety)”

Selected publications

Sanan-Mishra N., Jailani A.A.K, Mandal B. and Mukherjee S.K. (2021) Secondary siRNAs in plants: biosynthesis, various functions and applications in virology. Frontiers in Plant Science. In Press

Sinha K.V., Jailani A.K., Mandal B., Mukherjee S.K. and Sanan-MishraN. (2021) Overexpression of an insect virus encoded silencing suppressor does not enhance plants’ susceptibility to its natural virus. Virus Disease. In Press

Kumar S. and Sanan-Mishra N.(2021) A rapid method for stably transforming rice seeds. In: Rice genome engineering, molecular biology and gene editing. Eds Bandyopadhyay A, and Thilmony, R. Methods in Molecular Biology. Humana, New York, vol 2238. Chp 4 pp 63-68

More P., Agarwal P., Anand A., Sanan-Mishra N. and Agarwal P.K. (2021) Artificial miRNA mediated resistance in tobacco against Jatropha leaf curl Gujarat virus by targeting RNA silencing suppressors. Scientific Reports. 11: 890

Singh J.K.D, Jalaluddin N.S.M., Sanan-Mishra N. and Harikrishna J.A. (2021) Challenges to the adoption of modern crop biotechnology: insights from Indian and Malaysian GM regulatory frameworks. Malaysian Applied Biology Journal (MABJ). 49(5): 1–9

Sinha K.V., Das S.S. and Sanan-Mishra N. (2020) Overexpression of a RNA silencing suppressor, B2 protein encoded by Flock House virus, in tobacco plants results in tolerance to salt stress. Phytoparasitica. 1-18

Hernandez Y., Goswami K. and Sanan-Mishra N. (2020) Stress induced dynamic adjustment of conserved miR164:NAC module. Plant Environment Interactions. 1(2): 134-151

Goswami K., Mittal D., Gautam B., Sopory S.K. and Sanan-Mishra N. (2020) Mapping the salt stress-induced changes in the root miRNome in Pokkali rice. Biomolecules. 10(4): 498

Sundaresan G., Das S.S., Tripathi A., Mukherjee S.K. and Sanan-Mishra N.(2020) Evaluating the strength of RNA silencing suppressor proteins encoded by two geminiviruses using assay based on reversal of GFP silencing. Australasian Plant Pathology. 49(2): 95-106

A.K. Kushawaha, A. Khan, S.K. Sopory and N. Sanan-Mishra (2019) Light regulated osa-miR169e is implicated during priming under high temperature stress in rice.American Journal of Plant Sciences. 10(9): 1662-1674

J.K.D. Singh, N.S.M. Jalaluddina, N. Sanan-Mishra and J.A. Harikrishna (2019) Genetic modification in Malaysia and India: Current regulatory framework and the special case of exogenous RNAi in agriculture. Plant Cell Reports. 38(12):1449-1463

N. Sanan-Mishra (2019) Electric signaling and long distance communication in plants. In: Sensory Biology of Plants. Eds S.K. Sopory Springer. pp 509-535

S. Goel, K. Goswami, V.K. Pandey, M. Pandey and N. Sanan-Mishra(2019) Identification of microRNA-target modules from rice variety Pusa Basmati-1 (PB-1) under high temperature and salt stress. Functional and Integrative Genomics. 19(6): 867-888

K. Goswami, A. Tripathi, B. Gautam and N. Sanan-Mishra (2019) Impact of Next Generation Sequencing in elucidating the role of microRNA related to multiple abiotic stresses, In: Plant Abiotic Stress: Molecular Biology and Biotechnological Advances. Eds A. Roychoudhury and D.K. Tripathi. JohnWiley & Sons Ltd. Chp 20. pp 389-426

Kumar R., Kumar S., Sanan-Mishra N. 2018. miRNAs: the game changer in producing salinity stress tolerant crops. In: Salinity responses and tolerance in plants Vol. II. Eds: V. Kumar, S.H. Wani, P. Suprasanna and L.S. Tran, Springer Cham. PubMed Link

Sanan-Mishra N., Tripathi A., Goswami K., Shukla R.N., Vasudevan M., Goswami H. 2018. ARMOUR – a rice miRNA : mRNA interaction resource. Frontiers Plant Sci. 9, 602. Pubmed Link

Gautam B., Goswami K., Sanan-Mishra N., Wadhwa G., Singh S. 2018. The Role of Bioinformatics in Epigenetics. In: Wadhwa G., Shanmughavel P., Singh A., Bellare J. (eds) Current trends in Bioinformatics: An Insight. Springer, Singapore. Pubmed Link

Sahu A.K., Verma R.K., Gaur R.K., Sanan-Mishra N. 2018. Complexity and recombination analysis of novel begomovirus associated with Spinach yellow vein disease in India. Plant Gene. 13, 42-49. PubMed Link

Singh A.K., Furtado A., Brozynska M., Sanan-Mishra N., Henry R.J. 2018. Phylogeney and molecular evolution of miR820 and miR396 microRNA families in Oryza AA genomes. Tropical Plant Biol. 11, 1-16. PubMed Link

Tripathi A., Goswami K., Tiwari M., Mukherjee S.K., Sanan-Mishra N. 2018. Identification and comparative analysis of novel microRNAs from tomato varieties showing contrasting response to ToLCV infections. Physiol Mol Biol Plants. 24, 185-202. PubMe Link

Das S.S., Yadav S., Singh A., Gautam V., Sarkar A.K., Nandi A.K., Karmakar P., Majee M., Sanan-Mishra N. 2018. Dynamic expression of miRNAs and their targets in seed germination conditions reveals miR390-tasiR-ARF module as regulator of seed germination. Scientific Reports. 8,1233. PubMed Link

Tripathi A., Chacon O., Singla-Pareek S.L., Sopory S.K., Sanan-Mishra N. 2018. Mapping the microRNA expression profiles in glyoxalase over-expressing salinity tolerant rice. Current Genomics. 19, 21-35. PubMed Link

Khan A., Goswami K., Sopory S.K., Sanan-Mishra N. 2017. Mirador on the potential role of miRNAs in synergy of light and heat networks. Indian J Plant Physiol. 22, 587–607. PubMed Link

Hernandez Y., Sanan-Mishra N. 2017. miRNA mediated regulation of NAC Transcription factors in plant development. Plant Gene. 11B, 190-198. PubMed Link

Goswami K., Tripathi A., Sanan-Mishra N. 2017. Comparative miRomics of salt-tolerant and salt-sensitive rice. Journal of Integrative Bioinformatics. 14, 1-18. PubMed Link

Sanan-Mishra N., Chakraborty S., Gupta D., Mukherjee S.K. 2017. RNAi suppressors: Biology and Mechanisms. In Plant Epigenetics, RNA Technologies Eds N Rajewsky, S. Jurga, J. Barciszewski, Springer Nature. 199-230. PubMed Link

Sharma N., Mittal D., Sanan-Mishra N. 2017. Micro-Regulators of Hormones and Stress. In “Mechanism of Plant Hormone Signaling under Stress. Volume 2.” Ed G. K. Pandey, John Wiley & Sons, Inc., Hoboken, NJ, USA pp 319-351. PubMed Link

Sinha V., Anand A., Mukherjee S.K., Sanan-Mishra N. 2017. RNAi based strategies for enhancing plant resistance to virus infection. In: Advances in Biotechnology. Eds: A. Datta, M. Fakruddin, H.M.N. Iqbal and J. Abraham. Open Access eBooks: Chapter 4. PubMed Link

Djami-Tchatchou A.T., Sanan-Mishra N., Ntushelo K., Dubery I.A. 2017. Functional roles of microRNAs in agronomically important plants – potential as targets for crop improvement and protection. Frontiers Plant Sci. 8, 378.  PubMed Link

Shafrin F., Ferdous A.S., Sarkar S.K., Ahmed R., Al-Amin, Zaman A., Hossain K., Sarker M., Rencoret J., Gutiérrez A., del Rio J.C., Sanan-Mishra N., Khan H. 2017. Modification of monolignol biosynthetic pathway in jute: different gene, different consequence. Sci Reports. 7, 39984. PubMed Link

Mathur K., Anand A., Dubey S.K., Sanan-Mishra N., Bhatnagar R., Sunil S. 2016. Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity. Scientific Reports. 6, 38065. PubMed Link

El Sanousi R.S., Hamza N.B., Abdelmula A.A., Mohammed I.A., Seif M.G., Sanan-Mishra N. 2016. Differential expression of miRNAs in Sorghum bicolor under drought and salt stress.  American J Plant Sci. 7, 870-878.PubMed Link

Hamzaa N.B., Sharma N., Tripathi A., Sanan-Mishra N. 2016. MicroRNA expression profiles in response to drought stress in Sorghum bicolor. Gene Expression Patterns. 20, 88-98. PubMed Link

Mittal D., Sharma N., Sharma V., Sopory S.K., Sanan-Mishra N. 2016. Role of microRNAs in rice plant under salt-stress. Annals Applied Biol 168, 2-18. PubMed Link

Saraf S., Sanan-Mishra N., Gursanscky N.R., Carroll B.J., Gupta D., Mukherjee S.K. 2015. 3’ and 5’ microRNA-end post-biogenesis modifications in plant transcriptomes: evidences from small RNA next generation sequencing data analysis. Biochem Biophys Res Commun 467, 892-899. PubMed link

Shafrin F., Das S.S., Sanan-Mishra N., Khan H. 2015. Artificial miRNA- mediated down-regulation of two monolignoid biosynthetic genes (C3H and F5H) cause reduction in lignin content in jute. Plant Mol Biol 89, 511-552. PubMed link

Tripathi A., Goswami K., Sanan-Mishra N. 2015. Role of bioinformatics in establishing miRs as modulators of abiotic stress responses: the new revolution. Front Physiol 6, 286. PubMed link

Das S.S., Karmakar P., Nandi A.K., Sanan-Mishra N. 2015. Small RNA mediated regulation of seed germination. Front Plant Sci 6, 828. PubMed link

Kumar V., Karjee S., Rehman J., Taneja J., Sundaresan G., Sanan-Mishra N., S.K. Mukherjee. 2015. Mungbean yellow mosaic Indian virus encoded AC2 protein suppresses RNA silencing by inhibiting Arabidopsis RDR6 and AGO1 activities. Virology. 486, 158–172. PubMed link

Ngoc T.T., Sanan-Mishra N. (2015) Effect of antibiotics on callus regeneration during transformation of IR 64 rice. Biotechnology Reports. 7, 143-149. PubMed Link

Sharma N., Panchal S., Sanan-Mishra N. (2015) Protocol for artificial microRNA mediated over-expression of miR820 in indica rice. American J Plant Sci. 6, 1951.PubMed Link

Sharma N., Tripathi A., Sanan-Mishra N. (2015) Profiling the expression domains of a rice-specific microRNA under stress. Frontiers Plant Sci. 6, 333.PubMed Link

El Sanousi R.S., Abdelmula A.A., Mohammed I.A., Sanan-Mishra N., Hamza N.B. (2015) Evaluation of Performance and Variability of Six Sorghum Genotypes under Salinity Stress. International J Res Studies Biosci. 3, 23-27. PubMed Link

Das S.S., Sanan-Mishra N. (2015) A direct method for genetically transforming rice seeds with suppressors of RNAi. Plant Cell Tissue and Organ Culture: (J Plant Biotechnol). 120, 277-289. PubMed Link

Rahman J., Sanan-Mishra N., Mukherjee S.K. (2014) RNAi-hairpin mediated gene silencing and suppression of the silencing with Geminivrial MYMIV-AC2 protein. Plant Biotechnol Reports 8, 337-347

Das S.S., Sanan-Mishra N. (2014) Comparative analysis of RNAi Suppression Activity of proteins from two disparate viruses. American J Plant Sci 5, 1789-1798. PubMed Link

Kumar, V., Anand, A., Mukherjee, S.K., Sanan-Mishra, N. 2013. Engineering Viral Suppressors of RNA Silencing: requirement and applications. In “Genetically Engineered Crops in Developing Countries.” Eds A. Kumar, G. Lobenstein and D.V.R. Reddy, Studium Press Texas, USA.

Ngoc, T.T., Ta, H.A., Nang, V.D., Sanan-Mishra, N. 2013. Isolation and molecular analysis of SRBSDV isolates infecting rice in Vietnam. Asian J Agri Food Sci. 1, 5, 258-263. PubMed Link

Anand, A., Mukherjee, S.K., Sanan-Mishra, N. 2013. Tools for pathogenicity: virus encoded RNA silencing suppressors. In “Recent Microbial pathogens and strategies for combating them: science, technology and education” Microbiology Book Series, number 4. Ed A. Mendez-Vilas, Formatex Research Center, Spain 751-763. PubMed Link

Sanan-Mishra, N., Karjee, S., Mukherjee, S.K. 2013. RNAi technology. In “Biotechnology in Medicine and Agriculture: Principles and Practices”, Eds Kumar A., Pareek A., Gupta SM., I.K. International Publishing House, India pp 316-337