We study RNA modifications, RNA splicing, long non-coding RNAs and regulation of gene expression during germline development in animals.
During development, cells constantly face a decision between cell division and differentiation. Regulation of gene expression is key to this decision-making process. RNA is at the centre of many gene regulatory processes. We try to understand how different RNA-mediated mechanisms regulate gene expression during germ cell proliferation and differentiation.
There are more than 150 distinct chemical modifications found on RNA. RNA modifications control the processing, stability, expression and function of diverse types of RNAs.
RNA modifications
For the majority of RNA modifications, we don’t know their biological role in multicellular organisms. We use a combination of genetic and biochemical tools to study the function of RNA-modifying enzymes and RNA modifications during animal development.
RNA splicing
RNA splicing is generally known to remove intronic sequences and ligate exons to preserve accurate expression of both coding and non-coding genes. In addition, many organisms change the 5′ end of their mRNAs using SL trans-splicing. We study how RNA modifications and splicing factors regulate both cis- and trans-splicing mechanisms during germline development.
Metabolic regulation of gene expression
Dietary metabolites are required for a large number of cellular processes. Among these, vitamin B12 is essential for the cellular regeneration of S-adenosyl methionine (SAM). All methyltransferase enzymes use SAM during methylation reactions. We are studying how changing SAM levels in an organism affects gene expression and cellular methylations.
In the lab, we use a wide range of techniques
- liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMs) to quantify RNA modifications
- Oxford Nanopore Direct RNA Sequencing to detect modified RNAs
- Genetics and CRISPR/Cas9 genome editing to generate mutants and transgenes
- In vivo and in vitro assays to analyse RNA splicing. modification and gene expression
- Confocal microscopy for co-localisation and gene expression
We use the nematode Caenorhabditis elegans as a discovery organism. The germline development of C. elegans provides an ideal model system to study the role of RNA modifications and RNA modifying enzymes, RNA splicing and gene expression during cell proliferation and differentiation. In addition to C. elegans, we use bacteria and yeast for various techniques.