The PIRNA Pathway in the Drosophila Germline - an RNA based Genome Immune System
Small RNA pathways – referred to as RNA interference (RNAi) pathways – govern a diverse array of cellular processes. Among those are control of gene expression, suppression of viral replication, formation of heterochromatin and protection of the genome against selfish genetic elements such as transposons. Our group focuses on the piRNA pathway, an evolutionarily conserved RNAi pathway acting in the animal germline. It is the key genome surveillance system that suppresses the activity of transposons. Recent work has provided a conceptual framework for this pathway: According to this, the genome stores transposon sequences in defined heterochromatic loci called piRNA clusters. These provide the RNA substrates for the biogenesis of piRNAs. An intricate amplification cycle steers piRNA production predominantly to those cluster regions that are complementary to transposons being active at a given time. Finally, piRNAs guide a protein complex centered on Piwi-proteins to complementary transposon RNAs in the cell, leading to their silencing.We systematically dissect the piRNA pathway regarding its molecular architecture as well as its biological functions in Drosophila. For our studies we combine fly genetics, proteomics and genomics approaches.
Contact:
Jennifer Rohit
Head & Coordinator
Email: jenniferr@cbmb.org.in
Asymmetric cell division in Drosophila and mouse stem cells
Stem cells have the unique ability to divide asymmetrically and generate both self-renewing and differentiating daughter cells. In the Knoblich lab, we use Drosophila and mouse genetics to identify the molecular mechanisms that control asymmetric cell division and allow cells to create daughter cells of such dramatically different properties.In Drosophila, asymmetric cell divisions are established via the segregation of cell fate determinants into only one of the two daughter cells and identifying the mechanism of this polarized segregation has been a key focus of the lab. Defects in asymmetric cell division can lead to the formation of transplantable tumors in flies and understanding the mechanism of stem cell derived tumor formation is a more recent goal. For this, we use in vivo transgenic RNAi to analyze stem cell self renewal on a genome-wide level and apply in-utero electroporation to study homologs of the identified genes in vertebrate neural stem cells.
Contact:
Mahesh Chandran
Professor & Head
Email: chandran_m@cbmb.org.in
Design and function of molecular machines
What keeps cells and organisms alive are specific functions performed by highly organized macromolecular assemblies. Thomas Marlovits' research group wants to understand the architectural design of these 'biological nanomachines'. The team explores such structures under normal and disease-related conditions. In order to elucidate the molecular mechanisms, the research group uses high-resolution three-dimensional electron microscopy to directly visualize molecular machines in action. As a joint IMP-IMBA group leader Thomas Marlovits works for both IMBA and the partner institute IMP.
Contact:
Vikram Govindan
Principle Professor
Email: govindan_v@cbmb.org.in
RNA metabolism in mammalian cells
The Martinez group focuses in themes of RNA metabolism. Our strategy is novel in that we use siRNAs as substrates to discover enzymes that phosphorylate and ligate RNA molecules. With this approach we have identified Clp1, a component of the tRNA splicing and mRNA 3' end formation machineries as the first human RNA-kinase. We have recently uncovered a second nucleic-acid kinase, which localizes at the nucleolus. On the other hand, RNA-ligases remain mysterious in human cells. Searching for the elusive human tRNA ligase, we have purified an activity that ligates siRNAs displaying similar termini as 5' and 3' tRNA exons. Another challenging project is to reveal the enzyme that re-ligates Xbp1 mRNA, in a non-canonical splicing event, during the Unfolded Protein Response. For this, we have performed a genome-wide RNAi screen in Drosophila cells. We would like to understand the mechanism of action of these enzymes and identify their cellular substrates. With these new players in hand we will re-visit, with a distinctive angle, processes such as tRNA splicing, mRNA 3' end formation and ribosomal RNA processing, and further explore connections between them. To study the biology of RNA-kinases and RNA-ligases, we combine: chromatography and genome-wide RNAi screens at the discovery phase; in vitro and in silico experiments to understand molecular mechanisms; deep sequencing to identify RNA substrates, and in vivo studies to analyze the phenotype of knock-out and knock-in mice.
Contact:
Kannan Malarvizhi
Senior Professor
Email: kannan_mal@cbmb.org.in
Small RNA-directed DNA elimination in Tetrahymena
Transposable elements are molecular parasites that are able to move from one genome position to another. Cells in our body have a mechanism to silence these potentially harmful elements: locking transposable element into a closed form chromatin, called heterochromatin. Chemically, both transposable elements and the other parts of the genome are just stretches of DNA. So, how can cells distinguish junk from precious DNA? Evidence suggests that small RNAs, ~20-30 nucleotides in length, act as security guards to identify transposable elements. However, many remains unknown about how these small RNAs are produced, how they patrol the genome, and how they induce heterochromatin. Our group studies how short RNAs lock transposable elements into heterochromatin using the tiny-hairy protozoan Tetrahymena as a model. Moreover, Tetrahymena is able to eliminate heterochromatinized transposable elements from the genome. We are trying to understand how this special ability has been evolved.
Contact:
Francis Kennedy
Head & Coordinator
Email: francisk@cbmb.org.in
Bones, immunity and cancer
The basic approach of the Penninger group is to genetically manipulate and change genes in mice and to determine the effects of these mutations on the development of the whole organism and in diseases. His group has also developed new models in flies to model diseases at the whole genome level and compare such models with human SNP maps. From these studies, the team is trying to establish basic principles of physiology and basic mechanisms of disease pathogenesis. In particular, the Penninger laboratory focuses on heart and lung diseases, cancer, and bone diseases.
Contact:
Geetha Dinesh
Head of the Department
Email: geetha_dinesh@cbmb.org.in
Epigenetic regulation by the Polycomb and Trithorax group proteins
How do different cell types remember their identities over many cell generations? Part of the answer lies in the Polycomb and Trithorax groups of proteins. The Polycomb (PcG) and Trithorax (TrxG) groups of proteins work antagonistically on the same target genes, to maintain repressed (PcG) or active (TrxG) transcription states. We use a combination of quantitative live imaging, mathematical modelling, computational approaches and molecular and developmental biology to understand the interaction of the Polycomb and Trithorax proteins with their chromatin targets. We aim to unravel this fascinating epigenetic gene regulatory system in terms of the design, function and dynamic behaviour of its components. Our goal is to understand how a system whose components are in constant flux can ensure both stability and flexibility of gene expression states.
Contact:
Ramakrishnan Haridass
Senior Professor
Email: r_haridass@cbmb.org.in
Mechanisms underlying cell migration
It moves, it's alive! In the micro-cosmos of our body tissues movement is likewise vital to life- and can also contribute to death! Organ development, wound repair and immune defense all rely on the movement of single cells or cell groups. And in metastasis, renegade cells that escape from primary tumours find their way, by migration, to propagate in multiple sites elsewhere. Discovering how cells move is therefore important for understanding normal and pathological processes, with perspectives of bringing unwanted events under control. We already know that cell movement relies on the turnover of the protein filament systems comprising the so-called "cytoskeleton". Our research is directed towards understanding the structural basis of cytoskeleton turnover and the underlying molecular mechanisms. To this end we are combining molecular biology techniques with live cell imaging technologies and electron microscopy, including electron tomography for 3D imaging of cytoskeleton networks.
Contact:
Arun Gunasheelan
Head & Coordinator
Email: a_gunasheelan@cbmb.org.in