Bio

I am working in field of plant epigenetics to decipher the role of epigenetic components in transposable elements (TEs) silencing, seed dormancy and abiotic stress tolerance in plants. I am also trying to associate the role of RNA helicases (STRS1 & STRS2) in epigenetic control of plant responses to abiotic stresses.

I studied the regulation of the low copy long TEs, located in euchromatin region, class II transposon Tag1 (two copy in Ler ecotype) and class I copia-like retroelement Evelknievel (EK, single copy in Ler ecotype) and ATCOPIA18A (single copy in Ler/ Col ecotype). The expression analysis revealed that all three transposons are inactive in WT Ler and available methylome databases elucidated that Tag1 and EK are heavily methylated at all cytosine contexts in WT Ler. I observed strong transcriptional activation of Tag1 and EK in cmt3 and kyp2 mutants but not in ddm1 or RNA-directed DNA methylation pathway (RdDM) mutants, which was associated with a significant reduction in gene body non-CG methylation. This study demonstrated CMT3-KYP/SUVH4 as the major pathway, controlling silencing of the low copy long TEs located in euchromatin region via inducing non-CG methylation (CHG) independently of DDM1 and RdDM pathways. In conclusion, our data pointed to the existence of at least three distinct pathways that cooperate to maintain silencing of almost all kinds of TEs in the Arabidopsis genome, namely, (1) DDM1-MET1/CMT2/CMT3, (2) RdDM and the (3) CMT3-KYP (Khan et al 2016, BBA-Gene Regulatory Mechanism, 1859: 1289-1298 #Joint first author). Soon we are going submit one more paper from this data Narendra et al 2017, title “CHROMOMETHYLASE3 and KRYPTONITE/SUVH4 mediated silencing of the exonic retroelement Evelknievel is essential for reconstitution of CMT1 mRNA."

I am also working on epigenetic regulation of abiotic stress tolerance in plants. For this, I have screened many epigenetic/ gene silencing mutants (chromatin remodeling mutants (ddm1 and drd1); RdDM pathway related mutants or small RNA biogenesis mutants (nrpd2, rdr2, dcl3, ago4 etc); Histone-modifying enzymes kyp, lhp1 and hda6; DNA methyltransferases (met1, drm1/drm2 and cmt3) under various abiotic stresses like salt, osmotic, ABA and heat stress. I tested the stress response in different developmental stage seeds as well as in mature plants. Out of all these mutants, I found 4 promising mutants kyp, lhp1, cmt3 and hda6 in response to salt, osmotic, ABA and heat stress, which are playing differential regulatory role at different developmental stage as well as in different stresses.

Apart from this, I am also trying to associate the role of RNA helicase STRS2 in epigenetic control of plant responses to abiotic stresses. In a previous study the Barak Lab revealed that STRS2 is involved in response to abiotic stress as a negative regulator and localized in the nucleolus and chomocenters, and exhibits mis-localization in some RdDM pathway-related mutants (drd1, dcl3 and rdr2). This suggests that STRS2 is involved in epigenetic gene silencing (Khan et al. 2014, doi:10.1111/tpj.12533; Barak et al 2014, Plant Signaling & Behavior 9(12): e977729). Therefore, I tried to identify STRS2-interacting factors from the RdDM pathway using the co-immunoprecipitation ChromoTek GFP_A trap kit on our 35S:GFP-STRS2 lines with 35S:GFP lines as a control. The co-IP blots were probed with antibodies against various epigenetic factors and RdDM components. STRS2 showed interaction with epigenetic factor and play role as early component of the RdDM pathway. Overall, the results from this study will add another key factor to the RdDM pathway.

Partially, I was also involved in project investigating the S1-type endonucleases role in chromatin decondensation via double strand DNA breaks into superhelical DNA in dedifferentiated cell. I observed the higher expression of the S1-type endonuclease 2 (ENDO2) in dedifferentiating protoplasts concomitantly with chromatin decondensation. Interestingly, the endo2 mutant did not display delayed chromatin decondensation upon protoplasting as compared to WT. I also carried out subcellular localization which revealed that ENDO2 is essentially localized to endoplasmic reticulum in non-stress cells, but moving to the nucleus in senescing/dying cells and where it is associated with fragmented nuclei (Yemima et al 2017, PLoS ONE 12(1): e0170067).

During PhD, I carried out research in the area of Plant Molecular Biology and Biotechnology with primary aim to understand the molecular mechanisms of salinity tolerance (SOS signal transduction pathway) and drought tolerance in plants. For this, I have cloned and characterized the many salt tolerant genes (Like SOS1, NHX1 and unknown/ novel genes) from an extreme halophytes Salicornia brachiata by overexpression in the heterologous system. First time, I have overexpressed the extremophile S. brachiata SbSOS1 gene in tobacco, which conferred high degree of salt tolerance, enhanced morphological growth and various biochemical traits. I have also studied the role of SbSOS1 Na+/H+ antiporter in ion homeostasis and in partitioning of Na+ between different plant organs through long-distance Na+ transport (Yadav et al 2012, BMC Plant Biology, 12: 188). Apart from known genes studies, I also have functionally characterized the few salt-inducible unknown/ novel genes (SbSI-1 (Yadav et al 2012, Molecular Biology Reports, 39:1943-1948); SbSI-2 (Yadav et al 2012, Plos One, 9(7): e101926), SbSLSP (Singh et al 2012, Frontiers in Plant Science, 7: 737, #Joint first author); SbSI-3, SbSI-4 etc) from S. brachiata. This work received internationally recognition as my interview related to this research work published in American prestigious science magazine "Scientific American" from Nature publication under title ‘Saltwater Solution’. My ultimate goal is to explore the molecular mechanisms of abiotic stress tolerance and genetic engineering of crop plants for enhanced stress tolerance.  

Research Areas:
Systems Biology

Publications

  1. Narendra Singh Yadav, Janardan Khadka and Gideon Grafi (2018). Arabidopsis mutants may represent recombinant introgression lines. BMC research notes11(1), 227. https://doi.org/10.1186/s13104-018-3326-5
  2. Yemima Givaty-Rapp, Narendra Singh Yadav, Asif Khan and Gideon Grafi (2016). S1-type Endonuclease 2 in Dedifferentiating Arabidopsis Protoplasts: translocation to the nucleus in senescing protoplasts is associated with de-glycosylation. PLoS ONE 12(1): e0170067; doi:10.1371/journal. pone.0170067 
  3. Pal S, Zhao J, Khan A, Narendra Singh Yadav, Batushansky A, Barak S, Rewald B, Fait A, Lazarovitch N and  Rachmilevitch S (2016). Paclobutrazol induces tolerance in tomato to deficit irrigation through diversified effect on plant morphology, physiology and metabolism.  SCIENTIFIC REPORTS, 6: 39321; doi:10.1038/srep39321 
  4. Asif Khan#,, Narendra Singh Yadav#, Yaakov Morgenstern, Assaf Zemach, Gideon Grafi (2016). Activation of Tag1 transposable elements in Arabidopsis dedifferentiating cells and their regulation by CHROMOMETHYLASE 3-mediated CHG methylation. Biochimica et Biophysica Acta (BBA)- Gene Regulatory Mechanisms, 1859(10): 1289-1298; http://dx.doi.org/10.1016/j.bb... (#Joint first author)
  5. Dinkar Singh#,, Narendra Singh Yadav#, Vivekanand Tivari, Pradeep K. Agarwal, Bhavanath Jha (2016). A SNARE-Like Superfamily Protein SbSLSP from the Halophyte Salicornia brachiata Confers Salt and Drought Tolerance by Maintaining Membrane Stability, K+/Na+ Ratio, and Antioxidant Machinery. Frontiers in Plant Science, 7: 737; doi: 10.3389/fpls.2016.00737  (#Joint first author)
  6. Simon Barak, Narendra Singh Yadav, Asif Khan (2014). DEAD-box RNA helicases and epigenetic control of abiotic stress-responsive gene expression. Plant Signaling & Behavior, 9(12): e977729; http://dx.doi.org/10.4161/1559...
  7. Narendra Singh Yadav, Vijay Kumar Singh, Dinkar Singh, Bhavanath Jha (2013). A novel gene SbSI-2 encoding nuclear protein from a halophyte confers abiotic stress tolerance in E. coli and tobacco. Plos One, 9(7): e101926; doi:10.1371/journal.pone.0101926
  8. Narendra Singh Yadav, Pushp Sheel Shukla, Anupama Jha, Pradeep K. Agarwal, Bhavanath Jha (2012). The SbSOS1 gene from the extreme halophyte Salicornia brachiata enhances Na+ loading in xylem and confers salt tolerance in transgenic tobacco. BMC Plant Biology, 12: 188; doi:10.1186/1471-2229-12-188 
  9. Narendra Singh Yadav, Deo Rashmi, Dinkar Singh, Pradeep K. Agarwal and Bhavanath Jha (2012). A novel salt-inducible gene SbSI-1 from Salicornia brachiata confers salt and desiccation tolerance in E. coli. Molecular Biology Reports, 39: 1943-1948; doi:10.1007/s11033-011-0941-9 
  10. Anupama Jha, Mukul Joshi, Narendra Singh Yadav, Pradeep K Agarwal, Bhavanath Jha (2011). Cloning and characterization of the Salicornia brachiata Na+/H+ antiporter gene SbNHX1 and its expression by abiotic stress. Molecular Biology Reports, 38: 1965-1973; doi:10.1007/s11033-010-0318-5
  11. Amrita Ghosh, Amit Mandoli, D Krishna Kumar, Narendra Singh Yadav, Tamal Ghosh, Bhavanath Jha, Jim A Thomas, Amitava Das (2009). DNA binding and cleavage properties of a newly synthesised Ru(II)-polypyridyl complex. Dalton Transactions, 14 (42): 9312-9321; doi: 10.1039/b906756f
  12. Pradeep K. Agarwal, Narendra Singh Yadav, Bhavanath Jha (2013) Role of Na+/H+ Antiporters in Na+ Homeostasis in Halophytic Plants, In: Climate Change and Plant Abiotic Stress Tolerance (Eds N. Tuteja and S. S. Gill), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. pp. 685-704. doi: 10.1002/9783527675265.ch25  


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