National Institute of Plant Genome Research
Digital India   Azadi Ka Amrit Mahotsav     
 
    Dr. Shiv Meena
    Scientist, RNA Biology Lab (102)
    Postdoctoral fellow: Umeå, Plant Science, Center, Umeå, Sweden
    PhD: Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
    Tel: Phone: 91-11-26741612/14/17 Extn. 104
    Direct: 91-1126735221
    Email: shiv@nipgr.ac.in

 Professional & Academic Background:
Staff Scientist III (2023- Present) : National Institute of Plant Genome Research, New Delhi
Post-Doctoral Fellow (2021-2023) : Umeå Plant Science, Center, Umeå, Sweden
Post-Doctoral Fellow (2020-2021) : Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
Ph.D (2014-2020) : Leibniz Institute of Plant Biochemistry, Halle (Saale),Germany/Martin-Luther-University Halle-Wittenberg, Germany
 Awards and Fellowships:
Carl Tryggers Foundation Postdoctoral Fellowship (2021), UPSC, Umeå, Sweden
Graduiertenkolleg (Deutsche Forschungsgemeinschaft [GRK-1591], German Research Foundation) 2019
Erasmus Mundus Doctoral Scholarship (2014) European Union (Germany)
National Institute of Immunology, New Delhi, India, Fellowship (2010)
Qualified Graduate Aptitude Test in Engineering [GATE] (2010)
Junior Research Fellowship [JRF-NET, 2009], Council of Scientific and Industrial Research, India
 Research Interests:
Functional characterization of the widespread noncoding transcription in plants

One of the most important sets of discoveries in the past two decades is the illumination of the 'dark matter' of the genome. The advent of novel sequencing technologies could result in showing that most eukaryotic genomes undergo pervasive transcription, comprising more than ~95% of the transcriptome as noncoding RNA. These noncoding RNA transcripts can be of various types such as housekeeping small RNAs, t-RNA, r-RNA, snoRNA, small regulatory RNAs, and long noncoding RNAs (lncRNAs), among others. A substantial portion of this noncoding transcriptome is made up of lncRNAs, the non-protein coding RNA molecules that are longer than 200 nucleotides in length and can be transcribed by RNA Pol II from genomic regions categorized as promoters, introns, intergenic DNA, or the antisense DNA strand. lncRNAs have emerged as key regulators in various fundamental biological processes, including growth, development, disease, and stress responses in both animals and plants. lncRNAs can regulate expression of target gene directly or indirectly through a variety of mechanisms, e.g., via target mimicry of miRNAs, R-loop formation, transcriptional collisions, RNA silencing, etc. A growing number of evidence(s) indicates that the functional and mechanistic exploration of lncRNAs will not only unlock the mysteries of the 'dark matter' of the genome but also pave the way for novel findings and noncoding RNA-based applications in agriculture and biotechnology.

Although high-throughput sequencing studies have enabled the identification of tens of thousands of lncRNAs, only a tiny fraction of lncRNAs have been experimentally characterized in plants. Notably, in comparison to the relative progress made in animal systems, our understanding of the roles of lncRNAs, or noncoding transcription in general, their molecular modes of actions, and general RNA mediated regulatory mechanisms involving lncRNAs (if any), in plants is just beginning.

Some of the primary research directions in our RNA biology group at NIPGR, New Delhi include investigations into i) the identification and functional characterization of novel regulatory lncRNAs, ii) study of biologically important noncoding RNA mediated genome-wide transcriptional behaviors, and iii) investigations into whether lncRNAs adapt general regulatory mechanisms, for example, antisense lncRNAs as a class iv) application, adaptation and advancement of novel genomics tools in plants.

We employ diverse molecular genetic, RNA biology, biochemical, biophysical, and high-throughput sequencing approaches in our experiments. Our studies emphasize on development, abiotic and biotic stress conditions. We particularly focus on using transient cold (frost), heat, and drought as model stresses in Arabidopsis thaliana, chickpea, and tomato. In the long run, we ultimately aim to generate molecular understandings of noncoding transcription and lncRNA roles in plants that can be exploited in applied agriculture and in the development of climate-resilient crops.

Study of sense-antisense transcription, antisense lncRNAs, and overlapping protein-coding factors

Up to 40-70% of total annotated genes in plants are estimated to produce antisense lncRNAs. Some of the few available examples of functionally characterized antisense lncRNAs in plants include COOLAIR, asDOG1, asHSFB2A, SVALKA, NATsUGT73C6 among others. To contribute towards the understanding of 'sense-antisense'phenomenon, we focus on the following themes in the group-

  • Characterization of the roles of antisense lncRNAs that overlap with protein-coding genes, and the associated molecular mechanism(s) of action.

  • Investigation into the local and global transcriptional dynamics of widespread sense-antisense transcription, and the regulatory processes that govern optimal non-coding and coding transcriptional output during developmental and stress responses in plants.
Adaptation and advancement of novel genomics tools in plants (e.g., plaNET-Seq, Ribo-Seq)
Climate change challenges: unlocking lncRNAs and noncoding transcription centric solutions for sustainable agriculture

Due to the climate change, the future weather seasons are suspected to be extreme and unpredictable including high frequency severe spring and winter frosts, unpredicted drought and other abiotic stresses and thereby posing a major challenge to crops and sustainable agriculture. lncRNAs are shown to be crucial for both development and stress responses and potentially hold the key for plant's ability to withstand against harsh weather conditions.By understanding and harnessing the regulatory roles of lncRNAs, we aim to develop crop varieties with improved tolerance to abiotic stress conditions such as frost and drought.

 Group Members
 Tota Mondal Ph.D student

Tota grew up in Bankura, West Bengal, India. She earned her bachelor's degree in Botany from the University of Burdwan and completed her master's in Botany from Visva-Bharati University, supported by SVMCM fellowship. After her M.Sc., she joined our RNA Biology Group as a project associate at NIPGR (New Delhi), where she got familiarized with antisense long non-coding RNAs and their role in plants. Fascinated by lncRNAs, she started her PhD journey in the same laboratory at NIPGR, in August 2024. Her PhD work focuses on exploring the molecular mechanism(s) by which lncRNAs regulate gene expression under transient abiotic stresses. She also aims to contribute to the development of stress-resilient Chickpea varieties by advancing high-end transcriptomics tools such as cropNET-seq.
Gourav Maharia Ph.D student

Gourav was born and raised in Hanumangarh, Rajasthan. He earned his bachelor's degree from Banaras Hindu University, Varanasi in Agriculture. He then completed his master's in biotechnology from Jawaharlal Nehru University, New Delhi with master thesis work in the group of Dr. Manoj Kumar Sharma. In August 2024, he joined our group as a PhD scholar at National Institute of Plant Genome Research (NIPGR). His work focuses on noncoding RNA-encoded small peptides during abiotic stresses in Chickpea. Gourav will employs cutting-edge technologies such as Ribo-seq, mass spectrometry, and in-silico approaches to unravel the in-planta roles of small peptides.
Sanya Bajaj Project assosciate-1

Sanya hails from Bhiwani, Haryana, India. She completed her bachelor's degree from Choudhary Bansilal University in Bhiwani and earned her master's degree from Guru Jambheshwar University of Science and Technology in Hisar. Her master thesis in our group at the National Institute of Plant Genome Research (NIPGR) focused over the analysis of the role of chromatin remodelers in plant's development. She decided to continue as a Project Associate in our lab. Sanya is motivated to further explore the molecular mechanisms by which rapid chromatin remodeling can contribute to transient noncoding transcription waves in-plants, such as Arabidopsis and Chickpea.
Manobika Das Visiting student

Manobika was raised in Bankura, India. She completed her B.Sc. degree in Botany from Bankura Christian College. She then enrolled at Visva-Bharati University to pursue an M.Sc. in Botany, with a focus on Plant Physiology and Biochemistry. She has a special interest in understanding the role of miRNA-mediated regulation of plant development. In April 2023, Manobika joined Jawaharlal Nehru University as a PhD student in Prof. Ananda Sarkar's lab. She joined our group as a collaborative student to study the role of selected miRNA in vegetative phase change.
Nitya Tiwari Master student

Nitya is the native of Uttar Pradesh, India.She developed a strong interest in science during her schooling. She pursued her higher education (B.Sc. & M.Sc.) in Biotechnology from Banasthali Vidyapith, Rajasthan. She is a motivated master's student and wants to utilize molecular genetics and RNA biology approaches to explore sense-antisense enigma in plants. Nitya's master thesis work in our group at NIPGR explores the cis and trans regulatory aspects of select sense-antisense transcriptional units in Arabidopsis.
Akshita Nayak Master student

Akshita comes from Madhya Pradesh, India She pursued her B.Sc. in Biology and M.Sc. in Biotechnology from the Dr. Hari Singh Gour, Central University.She likes to solve complex abstract puzzles and very much interested in studying lncRNAs in plants. She is enthusiastic to learn how antisense lncRNA functions at molecular level during long stress conditions. Akshita joined the RNA Biology Lab in January 2025 for her master thesis to characterize role a lncRNA during drought stress in Arabidopsis.
 Collaborations
 Are you insterested to become a member of our plant RNA Biology lab at NIPGR

We are continuously looking for 'genuinely motivated' colleagues with diverse backgrounds who wish to gain experience(s) and/or willing to contribute in any of the above research directions. You can join us as postdoctoral fellow, PhD student or M.Sc./MTech/B.Sc./B. Tech thesis/dissertation trainee(s).

Postdoctoral fellows:

Experienced researchers can contact the group leader directly with very well-structured plans synchronized with a putative time frame along with potential funding options. Prospective postdoc applicants may choose any of the above research theme(s) or can propose their own innovative idea(s) with overlapping/complementary research interests. Interested postdoc candidate(s) may please contact PI by sending a detailed motivation letter and CV explaining their suitability to the group, previous expertise, vision and future goals along with details of 1-3 references.

PhD students/project associates:

PhD admissions takes place via NIPGR, New Delhi PhD program each year which requires the candidates to have qualified CSIR-UGC NET exam/DBT-JRF /DST INSPIRE fellowship etc. Project associate positions are advertised directly on the institute's website.

Bachelor/Master/Thesis/Dissertation/Summer/Trainee:

Please contact the group leader directly by describing your motivation 2-3 months well before the desired start date.

International researchers:

If you ever had intentions to visit India, our laboratory is interested in hosting international researchers for both short term and long-term stays. Depending on the various funding opportunities applicable to individual applicants, the options can be mutually explored. Several programs such as DFG (German Research Foundation, Deutsche Forschungsgemeinschaft) postdoc fellowship, Erasmus traineeship, TWAS- DBT Ph.D. Scholarship for candidates from developing countries etc. allow hosting of international researchers in the group. Candidates are advised to contact the group leader directly to jointly figure out the possibilities.

 Publications
Shiv Kumar Meena, Marti Quevedo, Sarah Muniz Nardeli, Clément Verez, Susheel Sagar Bhat, Vasiliki Zacharaki, Peter Kindgren, Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis, The Plant Cell, 2024;, koae160,
Vasiliki Zacharaki, Shiv Kumar Meena, Peter Kindgren, The non-coding RNA SVALKA locus produces a cis- natural antisense transcript that negatively regulates the expression of CBF1 and biomass production at normal temperatures, Plant Communications, 2023, 100551
Meena, S.K., Heidecker, M., Engelmann, S., Jaber, A., de Vries, T., Triller, S., Baumann-Kaschig, K., Abel, S., Behrens, S.-E. and Gago-Zachert, S. (2022), Altered expression levels of long noncoding natural antisense transcripts overlapping the UGT73C6 gene affect rosette size in Arabidopsis thaliana. Plant J
Meena, S. K., Wagner, C., Caggegi, L., Baumann-Kaschig, K. and Ried, M. K. (2021). A user- friendly protocol for the cultivation and successful crossing of Lotus japonicus. Bio-protocol
Srivastava A*, Meena SK*, Alam M, Nayeem SM, Deep S, Sau AK (2013) Structural and functional insights into the regulation of Helicobacter pylori arginase activity by an evolutionary non-conserved motif. Biochemistry 2013 52(3), 508-519. (*-Co first author)