The research in our laboratory is primarily focused on regulatory non-coding RNAs in eukaryotes. Recent advances in transcriptome-wide techniques including RNA sequencing (RNA-seq) have revealed the pervasive nature of eukaryotic transcriptomes, and concurrently, have led to the discovery of a plethora of transcripts with little or no protein-coding capacities. Growing evidence clearly indicates that such a genome's repertoire of non-coding RNAs plays key regulatory and functional roles in maintaining cellular fitness.
Non-coding RNAs fall into two categories based on their functions: structural non-coding RNAs and regulatory non-coding RNAs. Structural non-coding RNAs include transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs). Constantly expressed and incorporated into macromolecular ribonucleoprotein (RNP) complexes involved in the flow of genetic information (e.g., ribosomes, spliceosomes), these structural non-coding RNAs participate in the faithful build-up of cellular transcriptome and proteome. On the other hand, regulatory non-coding RNAs are often differentially expressed with defined spatio-temporal patterns and regulate the expression of genome accordingly, thereby shaping and fine-tuning the transcriptome and proteome in a tissue-specific or developmental-stage-specific manner.
The last decade has witnessed the emergence of small non-coding RNAs with big regulatory roles. Small non-coding RNAs are in sizes of 18-30 nucleotides and elicit profound changes in the genome and transcriptome of the host cell by targeting both chromatins and transcripts. Represented by microRNAs, endogenous small-interfering RNAs (endo-siRNAs), and Piwi-interacting RNAs (piRNAs), these tiny molecules are involved in the regulation of biological processes as diverse as developmental timing, cell differentiation, cell proliferation, cell death, metabolic control, transposon silencing and antiviral defence. We investigate various aspects of small RNA biogenesis, targeting, and functions in animals and plants, employing molecular genetics and biochemistry as well as bioinformatic approaches. Selected research topics currently ongoing in our laboratory are as below:
- Mechanism of microRNA biogenesis
- Function of microRNAs
- Epigenomics and transcriptomics study related to regulatory non-coding RNAs
- Application of RNAi
A novel class of regulatory non-coding RNAs whose significance is recently emerging is long noncoding RNAs (lncRNAs), which are defined as non-protein-coding transcripts of sizes of >200 nucleotides transcribed from intergenic regions. LncRNAs seem to regulate nearby protein-coding genes through a variety of mechanisms, with one emergent theme being their association with chromatin-modifying machineries. Recent genome-wide studies in mammals identified over a thousand highly conserved lncRNAs and led to preliminary hypotheses about their involvement in a variety of cellular aspects from stem cell pluripotency to cell cycle regulation. However, their study in plants remains comparatively in its infancy although in-depth analyses of the transcriptional outputs of the model plant genomes have suggested the existence of numerous putative lncRNAs. We investigate the biological significance of lncRNAs in plants.