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.