Plant RNAi Biology


Research Interests

microRNA, RNAi, suppressors of RNAi, salt stress, heat stress, virus infection

Description of Research

The Group is involved in understanding the RNAi mechanisms operative in rice plants in response to increasing soil salinity, high temperature 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 new approaches are required to address the emerging challenges for sustainable agriculture.

microRNAs (miRNAs) have been recognized as important regulatory factors in plant development and disease expression. We have adopted a two-pronged strategy of using bioinformatic predictions along with the traditional molecular biology and biochemical approaches to understand the miRNA regulatory networks operative in rice during abiotic (salt and temperature) and biotic (viruses) stresses. We have deep sequenced and analyzed the small RNAs in response to salt stress, viral infection and developmental cues from different local rice varieties. Work has been initiated to analyze the spatial and temporal accumulation of miRNAs to understand the fine- tuning of target gene expression in plant development. Few novel sequences have been identified and validated. This information is being used to tap the natural variation existent in the Indian rice cultivars and generate a small RNA database for rice (ARMOUR) in the Indian context. The translation of this knowledge by raising miRNA over-expressing rice plants is in progress. 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. To gain an insight into the mechanism of miRNA (dis)-regulation studies are being done using viral suppressors of RNAi. This work involves understanding the role of suppressors in local and systemic silencing of miRNAs and identification of host interacting factors to gain an understanding of the suppressor mediated action. Suppressor overexpressing transgenic lines have been generated to follow the effects on miRNA expression profiles.

The Group has recently investigated the miRNAs that were co-modulated in response to salinity and high temperature stress (HTS) in rice, to integrate stress responses with light regulated development. We have identified the miRNAs that differentially alter expression of HSFs and HSPs in response to thermopriming and HTS (Kushwaha et al., Life 2021). They also studied the influence of the abiotic environment on host–virus interactions in plants (Rahman et al., PCR 2021), using tobacco plants expressing Flock House Virus-encoded B2 protein.

Recent Publications

Sarkar, S.D.,Yadav, S., Singh, A., Gautam, V., Sarkar, A.K., Nandi A.K., Karmakar, P., Majee M., Sanan Mishra, N. 2017. Expression dynamics of miRNAs and their targets during seed germination conditions reveals miR390-tasiR-ARF module as regulator of seed germination. Sci Rep 8, 1233 PubMed link

Tripathi, A., Goswami, K., Tiwari, M., Mukherjee, S.K., Sanan-Mishra, N. 2017. Identification and comparative analysis of novel microRNAs from tomato varieties showing contrasting response to ToLCV infections. Physiol Mol Biol Plants 24, 185-202 PubMed link

Tripathi, A., Chacon, O., Singla-Pareek, S.L., Sopory, S.K., Sanan-Mishra, N. 2017. Mapping the microRNA expression profiles in glyoxalase over-expressing salinity tolerant rice. Curr Genomics 19, 21-35 PubMed link

Shafrin, F., Ferdous, A.S., Sarkar, S.K., Ahmed, R., Amin, A., Hossain, K., Sarker, M., Rencoret, J., Gutiérrez, A., Del Rio, J.C., Sanan-Mishra, N., Khan, H. 2016. Modification of monolignol biosynthetic pathway in jute: different gene, different consequence. Sci Rep 7, 39984 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, 892-99 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